This interactive report provides an overview of miR-eCLIP +siRNA results, accessible at the different tabs. For each table and plot, the button can be clicked to get more information. The menus in the top right corner of each plot can be used to modify the plots (zoom, hide samples, and save a copy of the plot). This report is optimized for viewing on a desktop and plots have been tested on several browsers but in some cases they may not render correctly, please use an alternate browser if plots do not load.

If you are interested in performing your own miR-eCLIP +siRNA experiment please contact us.

Experiment Summary

This report summarizes a miR-eCLIP +siRNA experiment performed with a standard siRNA (APP-01-Unmod), a Dharmacon-modified siRNA (APP-05), and an untransfected control. The samples were processed using Eclipsebio's proprietary miR-eCLIP +siRNA technology to identify off target siRNA binding. Full methods details are available upon a request.

Quality Control Metrics

The following table shows important quality control metrics for each sample. Two libraries are made for each sample, one containing immunoprecipitated (IP) RNA and the other containing input RNA. For each sample ("Sample"), two rows are included that list the metrics for each library. The identity of the library is included in the "IP or Input" column.

The following columns describe the processing of the libraries:

  1.  Initial reads: the number of sequenced reads for each library.
  2.  % Pass trim: reads first underwent adapter trimming to remove both adapters and sequences shorter than 18 nucleotides. The percentage of sequenced reads that passed this trimming step is listed in this column.
  3.  % Repetitive elements: trimmed reads are aligned to Eclipsebio's custom database of repetitive elements. This database includes rRNAs, tRNAs, snoRNAs, and other features. The percentage of trimmed reads that were filtered is listed in the column.
  4.  % Uniquely aligned to the genome: the remaining reads from the repetitive element filtering were aligned to the genome, and the percent of those reads that map uniquely to the genome is listed in this column.
  5.  % PCR duplicates: PCR duplicates were defined as uniquely mapped reads that map to the same read coordinates and have an identical unique molecular identifier (UMI). The percentage of mapped reads that were identified as PCR duplicates is included in this column.
  6.  Final nonchimeric reads: this column lists the number of uniquely mapped, deduplicated, nonchimeric reads that were used for this analysis.
  7.  AGO2 clusters: AGO2 clusters are found using the peak calling tool CLIPper. The clusters are identified from nonchimeric reads in the IP samples and are not input normalized.
  8.  AGO2 peaks: A peak is defined as a cluster with a log2(fold enrichment over the matched input) > 3 and p-value < 0.001.
  9.  Final chimeric reads: The number of chimeric reads that mapped to the genome after trimming the miRNA component of the chimeric read.
  10.  % Chimeras: percentage of chimeric reads that mapped to the genome out of the total number of reads that mapped to the genome (chimeric + nonchimeric)
  11.  Chimeric clusters: chimeric clusters are found using the peak calling tool CLIPper. The clusters are identified from genome mappinf component of chimeric reads in the IP samples and are not input normalized.
Sample IP or Input Initial reads % Pass trim % Repetitive elements % Uniquely aligned to genome % PCR duplicates Final nonchimeric reads AGO2 clusters AGO2 peaks Final chimeric reads % Chimeras Chimeric clusters
APP-01-Unmod_Input_rep1 Input 65,519,521 98.88% 56.54% 64.38% 13.32% 15,711,065
APP-01-Unmod_Input_rep2 Input 58,473,690 98.16% 53.63% 64.21% 12.21% 15,003,949
APP-05_Input_rep1 Input 66,248,677 96.72% 55.16% 66.79% 12.52% 16,786,399
APP-05_Input_rep2 Input 69,135,647 97.19% 58.32% 65.48% 12.91% 15,972,357
Untransfected_Input_rep1 Input 70,911,737 96.55% 56.61% 62.94% 12.93% 16,279,528
Untransfected_Input_rep2 Input 72,531,030 96.54% 57.53% 64.22% 13.69% 16,484,935
APP-05_IP_rep2 IP 90,365,901 78.50% 61.24% 46.68% 15.03% 10,904,904 324,370 7,511 169,216 1.53% 2,915
APP-01-Unmod_IP_rep1 IP 75,065,701 75.63% 53.92% 47.35% 14.12% 10,636,624 343,680 8,196 176,037 1.63% 3,297
APP-01-Unmod_IP_rep2 IP 95,063,987 75.30% 51.28% 50.05% 17.41% 14,416,246 343,680 10,556 244,433 1.67% 4,228
Untransfected_IP_rep1 IP 91,929,733 74.56% 58.08% 46.22% 13.94% 11,430,425 331,791 8,371 137,009 1.18% 2,378
Untransfected_IP_rep2 IP 130,837,039 79.88% 63.68% 45.51% 17.89% 14,185,128 331,791 7,394 259,065 1.79% 4,588
APP-05_IP_rep1 IP 105,519,575 79.85% 62.32% 45.31% 16.77% 11,972,134 324,370 6,913 184,483 1.52% 3,274

This tab summarizes the identified AGO2 peaks from the nonchimeric reads.

AGO2 Peak Counts

AGO2 clusters are found using the peak calling tool CLIPper. The clusters identified in the IP sample are then normalized against a paired input sample. An AGO2 peak is defined as a cluster with log2(fold change) ≥ 3 and p-value ≤ 0.001. The bar plot below shows the number of significantly enriched AGO2 peaks detected in each sample, as well as the number of significantly enriched reproducible AGO2 peaks for each set of replicates. Hover over each bars to see the number of peaks in each set. All plots in this report are interactive, meaning you can zoom in/out, pan to a certain location, and select elements from the legend to remove. Plots can also be downloaded as a separate file. Hover over the top right corner of the plot to see the interactive options.

AGO2 Gene Counts

The bar plot below shows the number of genes containing at least one significantly enriched AGO2 peak per sample, as well as the number of genes containing at least one significantly enriched reproducible AGO2 peak for each set of replicates. Hover over the bars to see the number of genes in each peak set. All plots in this report are interactive, meaning you can zoom in/out, pan to a certain location, and select elements from the legend to remove. Plots can also be downloaded as a separate file. Hover over the top right corner of the plot to see the interactive options.

AGO2 Peak Feature Distribution

The following bar plot depicts the feature distribution of significantly enriched AGO2 peaks in each sample, as well as reproducible AGO2 peaks for each set of replicates. Peaks are annotated according to the following hierarchy: CDS, 5'UTR or 3'UTR, miRNA, intron, and other. Hover over the bars to see the number of peaks and percentage of peaks per feature in each peak set. All plots in this report are interactive, meaning you can zoom in/out, pan to a certain location, and select elements from the legend to remove. Plots can also be downloaded as a separate file. Hover over the top right corner of the plot to see the interactive options.

AGO2 Peak Width Distribution

This boxplot shows the AGO2 peak width distribution of significantly enriched peaks in each sample, as well as reproducible AGO2 peaks for each set of replicates. Hover over the boxplot to see the minimum, lower fence, q1, median, q3, upper fence, and maximum peak widths for each peak set. All plots in this report are interactive, meaning you can zoom in/out, pan to a certain location, and select elements from the legend to remove. Plots can also be downloaded as a separate file. Hover over the top right corner of the plot to see the interactive options.

AGO2 Metagene

The metagene plot shows the average number of AGO2 peaks along the 5'UTR, CDS, and 3'UTR for peaks called in each sample, as well as reproducible AGO2 peaks for each set of samples. In order to create the metagene, peaks were downsampled to match the peak set with the smallest number in order to account for differences in the number of significant peaks. Gene lengths were normalized, and the average number of peaks along each normalized condition was calculated and plotted for each peak set. Hoever over the line to see the average number of peaks at that position. All plots in this report are interactive, meaning you can zoom in/out, pan to a certain location, and select elements from the legend to remove. Plots can also be downloaded as a separate file. Hover over the top right corner of the plot to see the interactive options.

AGO2 Motifs

This plot shows the top five most significant motifs found by HOMER de novo motif analysis, as well as the feature distribution for AGO2 peaks containing each motif. The top portion of the plot shows each motif as a dot, where the percentage of peaks containing that motif is plotted against the -log10(p-value) for that motif. The bottom portion of the plot is a bar plot showing the feature distribution for all peaks (left side) compared to the feature distribution of peaks containing the selected motif (right side). Click on one of the motifs in the scatterplot, and the bar plot will populate with the feature distribution for peaks containing the selected motif. Click off of that point to unselect that motif. The drop down menu in the bottom left corner can be used to navigate between different sets of peaks. For this plot, only motifs called from reproducible peaks are shown (if applicable). All plots in this report are interactive, meaning you can zoom in/out, pan to a certain location, and select elements from the legend to remove. Plots can also be downloaded as a separate file. Hover over the top right corner of the plot to see the interactive options.

AGO2 Gene Enrichment

This wordcloud shows significantly enriched GO terms and KEGG pathways identified using the tool clusterProfiler. This analysis looks for enriched functional types or pathways in the set of genes that contain at least one AGO2 peak. The GO terms are split into the following three categories: Biological Process, Cell Component, and Molecular Function. The drop down menu in the bottom left corner can be used to navigate between different sets of peaks. For this plot, only motifs called from reproducible peaks are shown (if applicable). Plots can also be downloaded as a separate file. Hover over the top right corner of the plot to see the interactive options

This tab summarizes the identified miRNA and siRNA target peaks from the chimeric reads. The table at the top of this section represents all siRNA target peaks, while the rest of the plots capture only off target siRNA peaks as well as miRNA peaks where indicated. The siRNA is labeled as "APP-01_05" in the plots on this tab.

siRNA Target Peak Information Table

siRNA target clusters are found using the peak calling tool CLIPper. These clusters are identified using chimeric reads. To assess reproducibility, we calculate the modified coefficient of variation (MCV) on the logarithm of the normalized intensity of each peak (i.e., chimeric read counts per siRNA). The method compares the observed MCV (oMCV) values against a theoretical distribution representing reproducible peaks. It then estimates a reproducibility index, calculated as the probability of an oMCV value coming from the distribution of reproducible peaks. Clusters mapped to the target gene are colored teal within the table. All other clusters are considered siRNA off targets.

Since the actual distribution of reproducible peaks is unknown, we use the Empirical Bayes approach to first estimate a vector of mean intensities and a matrix of variance-covariances, where the dimension of these vectors and matrices is equal to the number of replicates in the experiment. Then, these parameters are used to generate intensity values for each peak randomly. The MCV is calculated in each random sample (rMCV) and compared against the oMCV. The proportion of times the oMCV is smaller than rMCV is then used to estimate the reproducibility index (a value between zero and one). A higher value indicates a greater probability that the peak is reproducible. A reproducible siRNA target peak is defined as a peak with ≥ 3 chimeric reads on average and reproducibility index ≥ 0.5.

The chimeric peak information table shows the overlap of chimeric reads of each siRNA with peaks called using chimeric reads. Each entry in the table describes the chimeric reads of a single siRNA that overlap with the peak, so a peak may have multiple entries if more than one siRNA is found to target that region. The number of chimeric reads is calculated using the proportion of the chimeric read that overlaps with the peak (for example, if only 50% of the read overlaps, then a count of 0.5 is added for that entry).

Seed match information was annotated for each siRNA target according to seed match definitions from TargetScan, allowing for up to one mismatch in the seed region.

The following seed matches are classified as "Canonical":

  • 7mer-m8: An exact match to positions 2-8 of the siRNA (the seed + position 8)
  • 7mer-1A: An exact match to positions 2-7 of the siRNA (the seed) followed by an 'A'
  • 8mer: An exact match to positions 2-8 of the siRNA (the seed + position 8) followed by an 'A'
  • 6mer: An exact match to positions 2-7 of the siRNA (the seed)

The following seed matches are classified as "Noncanonical":

  • 6mer offset: An exact match to positions 3-8 of the siRNA
  • A 3' compensatory site is one in which strong 3' pairing (consequential siRNA-target complementarity outside the seed region) compensates for an imperfect seed match (Friedman et al., 2009).
  • A centered site is one that lacks perfect seed pairing and 3'-compensatory pairing but instead has 11-12 contiguous Watson-Crick pairs to siRNA positions 4-15. These are identified only in the reference species and therefore include no information about conservation.

Chromosome Start End Strand Gene name Ensembl ID Feature Sample Average chimeric reads Reproducibility Seed match
chr1 9,729,205 9,729,317 - CLSTN1 ENSG00000171603.18 3' UTR APP-01-Unmod 5.500 0.703 compensatory region (1 mismatch)
chr1 21,172,327 21,172,412 - EIF4G3 ENSG00000075151.20 Intron APP-01-Unmod 14.000 0.941 6mer (1 mismatch)
chr1 22,095,724 22,095,810 + CDC42 ENSG00000070831.17 3' UTR APP-01-Unmod 16.500 0.931 7mer m8 (Perfect match)
chr1 26,790,604 26,790,687 + PIGV ENSG00000060642.11 Intron APP-01-Unmod 10.000 0.861 8mer (Perfect match)
chr1 28,507,458 28,507,556 + SNORA73A|SNHG3 ENSG00000242125.3||ENSG00000274266.1 Other APP-01-Unmod 3.500 0.584 No seed match
chr1 31,912,852 31,912,927 - PTP4A2 ENSG00000184007.22 Intron APP-01-Unmod 7.000 0.762 6mer offset (Perfect match)
chr1 35,442,161 35,442,233 - KIAA0319L ENSG00000142687.18 Intron APP-01-Unmod 6.000 0.713 8mer (Perfect match)
chr1 40,983,343 40,983,402 + CTPS1 ENSG00000171793.16 CDS APP-01-Unmod 4.000 0.505 6mer (1 mismatch)
chr1 42,229,081 42,229,160 - FOXJ3 ENSG00000198815.9 Intron APP-01-Unmod 4.000 0.634 7mer m8 (Perfect match)
chr1 43,958,962 43,959,031 + IPO13 ENSG00000117408.11 Intron APP-01-Unmod 12.000 0.901 7mer m8 (Perfect match)
chr1 44,776,489 44,776,499 + SNORD46 ENSG00000200913.1 Other APP-01-Unmod 25.500 0.980 No seed match
chr1 44,776,503 44,776,543 + SNORD46 ENSG00000200913.1 Other APP-01-Unmod 92.500 0.990 6mer offset (1 mismatch)
chr1 44,776,543 44,776,551 + SNORD46 ENSG00000200913.1 Other APP-01-Unmod 15.500 0.950 No seed match
chr1 50,921,058 50,921,149 - FAF1 ENSG00000185104.20 Intron APP-01-Unmod 8.000 0.891 8mer (Perfect match)
chr1 70,354,192 70,354,242 - ANKRD13C ENSG00000118454.13 CDS APP-01-Unmod 5.000 0.693 No seed match
chr1 70,354,247 70,354,301 - ANKRD13C ENSG00000118454.13 CDS APP-01-Unmod 26.500 0.980 8mer (Perfect match)
chr1 70,354,660 70,354,710 - ANKRD13C ENSG00000118454.13 5' UTR APP-01-Unmod 5.500 0.703 No seed match
chr1 71,144,910 71,144,968 + ZRANB2-AS2 ENSG00000229956.11 Other APP-01-Unmod 4.500 0.703 7mer m8 (Perfect match)
chr1 75,787,492 75,787,537 + RABGGTB ENSG00000137955.16 CDS APP-01-Unmod 3.500 0.535 6mer (1 mismatch)
chr1 77,801,153 77,801,213 + MIGA1 ENSG00000180488.15 Intron APP-01-Unmod 8.500 0.822 7mer m8 (Perfect match)
chr1 86,957,061 86,957,128 + HS2ST1 ENSG00000153936.17 Intron APP-01-Unmod 6.000 0.762 6mer offset (Perfect match)
chr1 91,010,770 91,010,829 - ZNF644 ENSG00000122482.21 Intron APP-01-Unmod 4.000 0.564 8mer (Perfect match)
chr1 91,331,028 91,331,095 - HFM1 ENSG00000162669.16 Intron APP-01-Unmod 4.000 0.515 8mer (Perfect match)
chr1 99,923,925 99,924,013 + AGL ENSG00000162688.17 3' UTR APP-01-Unmod 19.500 0.970 6mer (Perfect match)
chr1 108,787,482 108,787,557 + STXBP3 ENSG00000116266.11 Intron APP-01-Unmod 16.000 0.921 8mer (Perfect match)
chr1 111,172,436 111,172,580 + CEPT1 ENSG00000134255.14 Intron APP-01-Unmod 5.000 0.743 7mer m8 (Perfect match)
chr1 113,721,438 113,721,484 - PHTF1 ENSG00000116793.16 Intron APP-01-Unmod 3.000 0.584 7mer m8 (Perfect match)
chr1 113,787,825 113,787,907 - RSBN1 ENSG00000081019.13 Intron APP-01-Unmod 5.500 0.624 7mer m8 (Perfect match)
chr1 150,496,326 150,496,398 + TARS2 ENSG00000143374.17 Intron APP-01-Unmod 4.500 0.584 6mer offset (Perfect match)
chr1 151,400,276 151,400,348 + PSMB4 ENSG00000159377.11 Intron APP-01-Unmod 3.500 0.525 7mer m8 (1 mismatch)
chr1 168,295,841 168,295,907 + TBX19 ENSG00000143178.13 Intron APP-01-Unmod 3.500 0.564 7mer m8 (Perfect match)
chr1 178,157,015 178,157,115 + RASAL2 ENSG00000075391.17 Intron APP-01-Unmod 17.000 0.970 7mer A1 (Perfect match)
chr1 183,025,810 183,025,889 + LAMC1 ENSG00000135862.6 Intron APP-01-Unmod 5.000 0.554 6mer offset (Perfect match)
chr1 184,073,853 184,073,931 + TSEN15 ENSG00000198860.13 3' UTR APP-01-Unmod 3.500 0.564 7mer m8 (Perfect match)
chr1 220,058,635 220,058,704 - BPNT1 ENSG00000162813.18 3' UTR APP-01-Unmod 7.000 0.653 6mer (Perfect match)
chr1 223,813,198 223,813,279 - TP53BP2 ENSG00000143514.17 Intron APP-01-Unmod 5.500 0.733 6mer (Perfect match)
chr1 225,408,211 225,408,302 - LBR ENSG00000143815.15 Intron APP-01-Unmod 5.000 0.663 7mer A1 (Perfect match)
chr1 226,989,920 226,989,991 - CDC42BPA ENSG00000143776.18 3' UTR APP-01-Unmod 5.000 0.564 7mer A1 (1 mismatch)
chr1 227,255,826 227,255,893 - CDC42BPA ENSG00000143776.18 Intron APP-01-Unmod 3.500 0.604 8mer (Perfect match)
chr1 229,624,284 229,624,350 - TAF5L ENSG00000135801.9 Intron APP-01-Unmod 4.000 0.624 7mer m8 (Perfect match)
chr1 234,606,604 234,606,728 - IRF2BP2 ENSG00000168264.10 3' UTR APP-01-Unmod 27.500 0.970 6mer offset (Perfect match)
chr1 236,143,189 236,143,254 + GPR137B ENSG00000077585.14 Intron APP-01-Unmod 3.000 0.525 8mer (Perfect match)
chr1 236,816,447 236,816,526 + MTR ENSG00000116984.14 CDS APP-01-Unmod 56.500 0.990 7mer m8 (Perfect match)
chr1 241,309,866 241,309,933 - RGS7 ENSG00000182901.17 Intron APP-01-Unmod 5.500 0.713 7mer A1 (Perfect match)
chr1 243,552,866 243,552,918 - AKT3 ENSG00000117020.18 CDS APP-01-Unmod 5.500 0.762 7mer m8 (Perfect match)
chr10 5,807,565 5,807,642 - GDI2 ENSG00000057608.17 Intron APP-01-Unmod 10.000 0.881 7mer A1 (Perfect match)
chr10 21,654,035 21,654,110 + MLLT10 ENSG00000078403.17 Intron APP-01-Unmod 6.500 0.743 7mer A1 (Perfect match)
chr10 28,589,423 28,589,493 + WAC ENSG00000095787.23 Intron APP-01-Unmod 27.500 0.980 7mer m8 (Perfect match)
chr10 42,812,484 42,812,549 + BMS1 ENSG00000165733.8 Intron APP-01-Unmod 6.500 0.762 7mer m8 (Perfect match)
chr10 51,675,929 51,676,020 + PRKG1 ENSG00000185532.20 Intron APP-01-Unmod 13.000 0.950 7mer m8 (Perfect match)
chr10 68,483,597 68,483,640 - SLC25A16 ENSG00000122912.15 Intron APP-01-Unmod 4.000 0.574 6mer (1 mismatch)
chr10 68,699,783 68,699,860 + AL513534.2 ENSG00000260400.1 Other APP-01-Unmod 5.500 0.723 8mer (1 mismatch)
chr10 74,874,262 74,874,332 + KAT6B ENSG00000156650.14 Intron APP-01-Unmod 18.000 0.941 8mer (Perfect match)
chr10 84,518,184 84,518,250 + CCSER2 ENSG00000107771.17 3' UTR APP-01-Unmod 7.000 0.713 6mer (Perfect match)
chr10 92,555,097 92,555,169 - IDE ENSG00000119912.17 Intron APP-01-Unmod 4.500 0.535 7mer m8 (Perfect match)
chr10 94,565,769 94,565,841 + HELLS ENSG00000119969.15 Intron APP-01-Unmod 61.000 0.990 8mer (Perfect match)
chr10 100,536,595 100,536,668 + HIF1AN ENSG00000166135.14 CDS APP-01-Unmod 21.000 0.980 6mer (1 mismatch)
chr10 100,540,631 100,540,718 + HIF1AN ENSG00000166135.14 CDS APP-01-Unmod 51.000 0.980 7mer m8 (Perfect match)
chr10 110,728,715 110,728,810 + RBM20 ENSG00000203867.8 Intron APP-01-Unmod 6.500 0.772 7mer A1 (Perfect match)
chr10 110,931,339 110,931,426 + SHOC2 ENSG00000108061.12 Intron APP-01-Unmod 11.000 0.931 7mer m8 (1 mismatch)
chr10 113,112,887 113,112,981 + TCF7L2 ENSG00000148737.17 Intron APP-01-Unmod 5.500 0.673 7mer m8 (Perfect match)
chr10 119,852,301 119,852,376 - MCMBP ENSG00000197771.13 Intron APP-01-Unmod 8.500 0.802 8mer (1 mismatch)
chr10 125,098,311 125,098,396 - CTBP2 ENSG00000175029.17 Intron APP-01-Unmod 13.000 0.931 7mer m8 (Perfect match)
chr11 931,071 931,139 + AP2A2 ENSG00000183020.14 Intron APP-01-Unmod 18.000 0.960 7mer A1 (Perfect match)
chr11 2,394,089 2,394,172 + CD81 ENSG00000110651.12 CDS APP-01-Unmod 27.500 0.980 6mer (Perfect match)
chr11 2,991,682 2,991,763 - NAP1L4 ENSG00000205531.13 Intron APP-01-Unmod 5.500 0.703 7mer m8 (Perfect match)
chr11 6,497,504 6,497,563 + DNHD1 ENSG00000179532.13 Intron APP-01-Unmod 3.000 0.525 6mer (1 mismatch)
chr11 6,964,053 6,964,128 + ZNF215 ENSG00000149054.16 Intron APP-01-Unmod 7.500 0.752 8mer (Perfect match)
chr11 14,296,303 14,296,380 - RRAS2 ENSG00000133818.14 Intron APP-01-Unmod 9.000 0.891 8mer (Perfect match)
chr11 16,974,819 16,974,881 - AC116533.1 ENSG00000244398.1 Other APP-01-Unmod 5.000 0.673 compensatory region (1 mismatch)
chr11 18,082,067 18,082,158 - SAAL1 ENSG00000166788.10 Intron APP-01-Unmod 18.500 0.941 7mer A1 (Perfect match)
chr11 18,407,181 18,407,364 + LDHA ENSG00000134333.14 CDS APP-01-Unmod 5.000 0.614 7mer A1 (Perfect match)
chr11 43,855,821 43,855,891 - AC087521.2 ENSG00000246250.3 Other APP-01-Unmod 5.500 0.693 7mer A1 (1 mismatch)
chr11 47,778,849 47,779,030 - NUP160 ENSG00000030066.13 3' UTR APP-01-Unmod 5.500 0.515 6mer offset (1 mismatch)
chr11 61,302,639 61,302,712 - DDB1 ENSG00000167986.14 CDS APP-01-Unmod 33.000 0.960 6mer offset (Perfect match)
chr11 62,677,971 62,678,035 - UBXN1 ENSG00000162191.14 CDS APP-01-Unmod 3.000 0.505 6mer offset (Perfect match)
chr11 65,502,085 65,502,153 + MALAT1 ENSG00000251562.8 Other APP-01-Unmod 31.500 0.950 7mer A1 (Perfect match)
chr11 69,064,752 69,064,819 + TPCN2 ENSG00000162341.18 Intron APP-01-Unmod 10.500 0.871 6mer (1 mismatch)
chr11 70,436,283 70,436,377 + CTTN ENSG00000085733.16 CDS APP-01-Unmod 4.500 0.574 6mer (1 mismatch)
chr11 73,404,460 73,404,523 - FAM168A ENSG00000054965.10 3' UTR APP-01-Unmod 7.500 0.762 7mer A1 (Perfect match)
chr11 74,998,163 74,998,218 + NEU3 ENSG00000162139.10 Intron APP-01-Unmod 11.000 0.931 8mer (Perfect match)
chr11 86,042,503 86,042,550 - PICALM ENSG00000073921.18 Intron APP-01-Unmod 10.000 0.921 7mer m8 (Perfect match)
chr11 94,963,460 94,963,526 - CWC15 ENSG00000150316.12 CDS APP-01-Unmod 4.500 0.644 7mer m8 (1 mismatch)
chr11 95,804,506 95,804,581 + CEP57 ENSG00000166037.11 Intron APP-01-Unmod 7.500 0.792 6mer offset (Perfect match)
chr11 109,005,666 109,005,690 - AP003123.1 ENSG00000255528.1 Other APP-01-Unmod 3.000 0.545 8mer (Perfect match)
chr11 111,838,247 111,838,318 - AP001781.2|ALG9 ENSG00000086848.15||ENSG00000258529.5 CDS APP-01-Unmod 4.000 0.515 7mer m8 (Perfect match)
chr11 117,032,618 117,032,706 - SIK3 ENSG00000160584.16 Intron APP-01-Unmod 8.000 0.792 7mer A1 (Perfect match)
chr12 4,654,417 4,654,447 + AC005833.1|NDUFA9 ENSG00000255639.3||ENSG00000139180.11 CDS APP-01-Unmod 5.000 0.614 No seed match
chr12 11,002,450 11,002,501 - PRH1|AC018630.2 ENSG00000275778.2||ENSG00000231887.7 Intron APP-01-Unmod 4.000 0.634 7mer m8 (Perfect match)
chr12 12,521,083 12,521,154 - DUSP16 ENSG00000111266.9 CDS APP-01-Unmod 5.500 0.693 7mer m8 (Perfect match)
chr12 20,551,420 20,551,466 + PDE3A ENSG00000172572.7 Intron APP-01-Unmod 9.500 0.812 6mer offset (1 mismatch)
chr12 49,759,217 49,759,280 + TMBIM6 ENSG00000139644.13 CDS APP-01-Unmod 4.500 0.604 7mer m8 (1 mismatch)
chr12 56,644,787 56,644,867 - ATP5F1B ENSG00000110955.9 CDS APP-01-Unmod 9.000 0.911 6mer (Perfect match)
chr12 56,665,005 56,665,104 - PTGES3 ENSG00000110958.16 Intron APP-01-Unmod 8.000 0.772 6mer offset (Perfect match)
chr12 57,534,538 57,534,608 - DCTN2 ENSG00000175203.16 Intron APP-01-Unmod 6.000 0.752 6mer (Perfect match)
chr12 76,046,708 76,046,799 - NAP1L1 ENSG00000187109.15 3' UTR APP-01-Unmod 24.500 0.990 7mer m8 (Perfect match)
chr12 101,830,546 101,830,626 - GNPTAB ENSG00000111670.16 CDS APP-01-Unmod 4.500 0.653 6mer offset (Perfect match)
chr12 121,781,097 121,781,148 + TMEM120B ENSG00000188735.13 3' UTR APP-01-Unmod 5.000 0.723 7mer A1 (1 mismatch)
chr12 131,932,818 131,932,870 + PUS1 ENSG00000177192.14 CDS APP-01-Unmod 7.500 0.802 6mer offset (Perfect match)
chr13 24,912,936 24,913,006 - CENPJ ENSG00000151849.15 CDS APP-01-Unmod 5.000 0.604 6mer (1 mismatch)
chr13 28,262,486 28,262,563 + PAN3 ENSG00000152520.14 Intron APP-01-Unmod 6.500 0.733 8mer (Perfect match)
chr13 37,038,488 37,038,521 - SUPT20H ENSG00000102710.20 Intron APP-01-Unmod 3.500 0.683 7mer m8 (Perfect match)
chr13 39,751,841 39,751,922 + COG6 ENSG00000133103.17 3' UTR APP-01-Unmod 4.500 0.604 8mer (Perfect match)
chr13 45,982,050 45,982,120 - ZC3H13 ENSG00000123200.16 Intron APP-01-Unmod 7.500 0.752 8mer (Perfect match)
chr13 48,391,244 48,391,311 + RB1 ENSG00000139687.16 Intron APP-01-Unmod 9.000 0.812 8mer (Perfect match)
chr13 50,097,163 50,097,230 + DLEU1 ENSG00000176124.15 Other APP-01-Unmod 10.500 0.861 6mer offset (Perfect match)
chr13 79,386,480 79,386,552 - RBM26 ENSG00000139746.16 Intron APP-01-Unmod 13.000 0.911 7mer m8 (Perfect match)
chr13 91,350,757 91,350,780 + hsa-mir-18a MI0000072 miRNA APP-01-Unmod 21.000 0.901 No seed match
chr13 95,097,016 95,097,088 - ABCC4 ENSG00000125257.16 Intron APP-01-Unmod 6.500 0.792 8mer (Perfect match)
chr13 95,205,310 95,205,332 - ABCC4 ENSG00000125257.16 Intron APP-01-Unmod 6.000 0.564 8mer (Perfect match)
chr13 98,518,947 98,519,026 - STK24 ENSG00000102572.14 Intron APP-01-Unmod 7.000 0.772 7mer m8 (Perfect match)
chr13 113,626,987 113,627,066 + TFDP1 ENSG00000198176.13 Intron APP-01-Unmod 7.500 0.752 7mer m8 (Perfect match)
chr14 30,568,041 30,568,134 + G2E3 ENSG00000092140.16 Intron APP-01-Unmod 9.500 0.762 7mer m8 (Perfect match)
chr14 35,604,878 35,604,959 - RALGAPA1 ENSG00000174373.16 Intron APP-01-Unmod 29.000 0.970 8mer (Perfect match)
chr14 39,160,990 39,161,047 - TRAPPC6B ENSG00000182400.15 Intron APP-01-Unmod 4.000 0.673 7mer m8 (Perfect match)
chr14 45,133,111 45,133,166 - FKBP3 ENSG00000100442.11 Intron APP-01-Unmod 3.000 0.515 7mer m8 (1 mismatch)
chr14 58,278,496 58,278,546 - PSMA3-AS1|ARMH4 ENSG00000139971.15||ENSG00000257621.8 Other APP-01-Unmod 4.500 0.624 7mer m8 (Perfect match)
chr14 64,743,460 64,743,520 + PLEKHG3 ENSG00000126822.17 CDS APP-01-Unmod 4.500 0.673 7mer m8 (Perfect match)
chr14 67,991,991 67,992,058 + RAD51B ENSG00000182185.18 Intron APP-01-Unmod 6.000 0.752 7mer m8 (Perfect match)
chr14 69,769,923 69,770,006 + SRSF5 ENSG00000100650.16 Intron APP-01-Unmod 4.500 0.604 6mer (Perfect match)
chr14 102,681,766 102,681,850 + RCOR1 ENSG00000089902.10 Intron APP-01-Unmod 13.000 0.941 6mer (Perfect match)
chr14 105,010,792 105,010,854 - CDCA4 ENSG00000170779.11 3' UTR APP-01-Unmod 4.000 0.624 8mer (1 mismatch)
chr15 22,853,228 22,853,291 + NIPA2 ENSG00000140157.15 CDS APP-01-Unmod 3.500 0.574 6mer (1 mismatch)
chr15 22,875,632 22,875,695 - CYFIP1 ENSG00000273749.5 Intron APP-01-Unmod 4.500 0.594 8mer (Perfect match)
chr15 36,941,385 36,941,508 - MEIS2 ENSG00000134138.20 Intron APP-01-Unmod 12.500 0.921 7mer m8 (1 mismatch)
chr15 42,414,447 42,414,512 - ZNF106 ENSG00000103994.17 3' UTR APP-01-Unmod 7.000 0.822 8mer (Perfect match)
chr15 48,726,529 48,726,593 - CEP152 ENSG00000103995.14 Other APP-01-Unmod 4.000 0.624 6mer (1 mismatch)
chr15 50,628,594 50,628,657 - TRPM7 ENSG00000092439.16 Intron APP-01-Unmod 4.500 0.624 7mer A1 (Perfect match)
chr15 61,121,340 61,121,404 - RORA ENSG00000069667.16 Intron APP-01-Unmod 3.500 0.554 6mer (1 mismatch)
chr15 71,915,486 71,915,554 - MYO9A ENSG00000066933.16 Intron APP-01-Unmod 6.500 0.782 6mer (Perfect match)
chr15 84,669,807 84,669,869 - SEC11A ENSG00000140612.14 3' UTR APP-01-Unmod 5.500 0.723 compensatory region (1 mismatch)
chr15 85,548,323 85,548,402 + AKAP13 ENSG00000170776.22 Intron APP-01-Unmod 7.000 0.861 8mer (Perfect match)
chr15 92,949,266 92,949,360 + CHD2 ENSG00000173575.22 Intron APP-01-Unmod 81.500 0.960 8mer (Perfect match)
chr15 98,723,508 98,723,549 + IGF1R ENSG00000140443.15 Intron APP-01-Unmod 4.000 0.634 7mer m8 (Perfect match)
chr15 98,743,661 98,743,728 + IGF1R ENSG00000140443.15 Intron APP-01-Unmod 5.000 0.634 7mer A1 (Perfect match)
chr15 100,289,863 100,289,934 - ADAMTS17 ENSG00000140470.14 Intron APP-01-Unmod 3.000 0.535 8mer (Perfect match)
chr16 1,359,782 1,359,821 + GNPTG ENSG00000090581.10 Intron APP-01-Unmod 3.000 0.515 7mer m8 (Perfect match)
chr16 9,103,384 9,103,481 + C16orf72 ENSG00000182831.12 3' UTR APP-01-Unmod 10.000 0.881 6mer (1 mismatch)
chr16 24,569,310 24,569,388 + RBBP6 ENSG00000122257.20 CDS APP-01-Unmod 11.500 0.911 7mer A1 (1 mismatch)
chr16 30,429,940 30,430,009 - DCTPP1 ENSG00000179958.9 CDS APP-01-Unmod 8.500 0.842 compensatory region (Perfect match)
chr16 57,440,252 57,440,304 - CIAPIN1 ENSG00000005194.15 Intron APP-01-Unmod 3.500 0.584 8mer (Perfect match)
chr16 74,909,778 74,909,830 - WDR59 ENSG00000103091.15 CDS APP-01-Unmod 6.000 0.743 7mer A1 (Perfect match)
chr16 78,223,832 78,223,919 + WWOX ENSG00000186153.17 Intron APP-01-Unmod 23.500 0.970 7mer m8 (Perfect match)
chr16 81,326,609 81,326,673 + GAN ENSG00000261609.8 Intron APP-01-Unmod 6.000 0.752 7mer m8 (Perfect match)
chr17 1,897,158 1,897,233 + RPA1 ENSG00000132383.12 CDS APP-01-Unmod 4.000 0.515 No seed match
chr17 5,435,299 5,435,346 - C1QBP ENSG00000108561.8 Intron APP-01-Unmod 6.500 0.703 6mer (1 mismatch)
chr17 5,442,728 5,442,775 - DHX33 ENSG00000005100.13 3' UTR APP-01-Unmod 3.000 0.525 7mer m8 (Perfect match)
chr17 7,320,755 7,320,819 - NEURL4 ENSG00000215041.10 CDS APP-01-Unmod 8.000 0.851 7mer m8 (Perfect match)
chr17 7,402,779 7,402,850 - TMEM256-PLSCR3 ENSG00000262481.5 Other APP-01-Unmod 10.500 0.901 7mer A1 (1 mismatch)
chr17 15,663,327 15,663,395 - TRIM16 ENSG00000221926.13 Intron APP-01-Unmod 8.000 0.832 7mer A1 (Perfect match)
chr17 16,024,833 16,024,902 + TTC19 ENSG00000011295.16 Intron APP-01-Unmod 5.500 0.653 6mer (1 mismatch)
chr17 16,441,873 16,441,957 + SNHG29 ENSG00000175061.18 Other APP-01-Unmod 11.500 0.802 7mer A1 (1 mismatch)
chr17 28,564,069 28,564,108 - PIGS ENSG00000087111.21 Intron APP-01-Unmod 3.000 0.525 6mer (Perfect match)
chr17 29,551,770 29,551,836 + TAOK1 ENSG00000160551.11 3' UTR APP-01-Unmod 3.000 0.653 6mer offset (Perfect match)
chr17 29,573,481 29,573,557 - GIT1 ENSG00000108262.16 3' UTR APP-01-Unmod 13.500 0.960 6mer (Perfect match)
chr17 30,816,903 30,816,988 - CRLF3 ENSG00000176390.12 Intron APP-01-Unmod 15.000 0.960 7mer m8 (Perfect match)
chr17 31,852,104 31,852,107 - COPRS ENSG00000172301.11 3' UTR APP-01-Unmod 14.000 0.921 No seed match
chr17 31,852,107 31,852,177 - COPRS ENSG00000172301.11 CDS APP-01-Unmod 126.500 0.980 compensatory region (Perfect match)
chr17 40,302,825 40,302,907 + CDC6 ENSG00000094804.12 3' UTR APP-01-Unmod 8.500 0.772 7mer A1 (1 mismatch)
chr17 41,817,098 41,817,172 + FKBP10 ENSG00000141756.19 CDS APP-01-Unmod 3.500 0.505 6mer (1 mismatch)
chr17 41,896,186 41,896,258 - ACLY ENSG00000131473.17 Intron APP-01-Unmod 7.000 0.762 6mer (1 mismatch)
chr17 47,656,779 47,656,837 + KPNB1 ENSG00000108424.10 Intron APP-01-Unmod 3.000 0.535 6mer offset (1 mismatch)
chr17 49,051,018 49,051,099 + IGF2BP1 ENSG00000159217.10 3' UTR APP-01-Unmod 5.000 0.644 6mer offset (1 mismatch)
chr17 57,972,291 57,972,344 - VEZF1 ENSG00000136451.9 3' UTR APP-01-Unmod 6.000 0.723 7mer A1 (1 mismatch)
chr17 64,041,492 64,041,552 - ERN1 ENSG00000178607.16 3' UTR APP-01-Unmod 3.000 0.525 7mer m8 (Perfect match)
chr17 66,107,227 66,107,282 - CEP112 ENSG00000154240.17 Intron APP-01-Unmod 6.500 0.812 8mer (Perfect match)
chr17 74,772,582 74,772,670 - NAT9 ENSG00000109065.12 Intron APP-01-Unmod 4.500 0.594 8mer (Perfect match)
chr17 75,778,002 75,778,075 - H3-3B ENSG00000132475.10 3' UTR APP-01-Unmod 24.500 0.960 No seed match
chr17 76,397,948 76,398,007 - UBE2O ENSG00000175931.13 Intron APP-01-Unmod 3.000 0.535 6mer offset (Perfect match)
chr17 80,379,796 80,379,853 + RNF213 ENSG00000173821.19 Intron APP-01-Unmod 4.000 0.574 7mer A1 (Perfect match)
chr17 82,892,738 82,892,810 + TBCD ENSG00000141556.21 Intron APP-01-Unmod 9.000 0.812 7mer m8 (Perfect match)
chr18 23,540,474 23,540,542 - NPC1 ENSG00000141458.13 CDS APP-01-Unmod 4.500 0.644 6mer (Perfect match)
chr18 32,068,394 32,068,487 + RNF125 ENSG00000101695.9 3' UTR APP-01-Unmod 4.500 0.644 6mer offset (Perfect match)
chr18 39,387,882 39,387,961 - MIR924HG ENSG00000267374.2 Other APP-01-Unmod 9.500 0.881 8mer (Perfect match)
chr18 56,722,137 56,722,231 + WDR7 ENSG00000091157.13 Intron APP-01-Unmod 7.000 0.851 8mer (Perfect match)
chr18 77,084,394 77,084,419 - MBP ENSG00000197971.16 Intron APP-01-Unmod 4.500 0.564 7mer m8 (1 mismatch)
chr19 2,271,464 2,271,528 + OAZ1 ENSG00000104904.12 CDS APP-01-Unmod 19.000 0.980 6mer offset (1 mismatch)
chr19 2,835,663 2,835,731 + ZNF554 ENSG00000172006.12 3' UTR APP-01-Unmod 8.000 0.743 6mer (Perfect match)
chr19 10,172,041 10,172,134 - DNMT1 ENSG00000130816.16 Intron APP-01-Unmod 13.500 0.911 8mer (Perfect match)
chr19 12,692,989 12,693,051 - FBXW9 ENSG00000132004.13 Intron APP-01-Unmod 4.500 0.614 compensatory region (1 mismatch)
chr19 19,006,229 19,006,304 - SUGP2 ENSG00000064607.17 Intron APP-01-Unmod 3.000 0.515 8mer (Perfect match)
chr19 22,694,813 22,694,852 - AC024563.1 ENSG00000268981.5 Other APP-01-Unmod 3229.000 0.990 6mer offset (1 mismatch)
chr19 22,694,852 22,694,860 - AC024563.1 ENSG00000268981.5 Other APP-01-Unmod 656.500 0.990 No seed match
chr19 34,384,431 34,384,492 + GPI ENSG00000105220.17 Intron APP-01-Unmod 5.000 0.545 6mer offset (Perfect match)
chr2 8,982,557 8,982,625 - MBOAT2 ENSG00000143797.12 Intron APP-01-Unmod 4.500 0.693 7mer A1 (Perfect match)
chr2 32,736,746 32,736,818 + TTC27 ENSG00000018699.13 CDS APP-01-Unmod 15.000 0.921 7mer m8 (Perfect match)
chr2 45,684,055 45,684,122 + PRKCE ENSG00000171132.14 Intron APP-01-Unmod 3.500 0.683 6mer offset (Perfect match)
chr2 63,684,526 63,684,577 - WDPCP ENSG00000143951.16 Other APP-01-Unmod 6.000 0.782 No seed match
chr2 64,016,144 64,016,205 - VPS54 ENSG00000143952.20 Intron APP-01-Unmod 20.500 0.950 7mer m8 (Perfect match)
chr2 65,005,284 65,005,348 - LINC02245 ENSG00000237638.2 Other APP-01-Unmod 3.000 0.535 8mer (Perfect match)
chr2 66,569,362 66,569,448 + MEIS1 ENSG00000143995.20 3' UTR APP-01-Unmod 7.500 0.822 8mer (Perfect match)
chr2 77,529,662 77,529,787 - LRRTM4 ENSG00000176204.13 Intron APP-01-Unmod 7.500 0.693 8mer (Perfect match)
chr2 85,542,315 85,542,417 + MAT2A ENSG00000168906.13 CDS APP-01-Unmod 132.000 0.990 6mer (Perfect match)
chr2 96,186,476 96,186,551 - STARD7 ENSG00000084090.13 3' UTR APP-01-Unmod 27.500 0.980 8mer (Perfect match)
chr2 96,273,903 96,274,010 + CIAO1 ENSG00000144021.3 3' UTR APP-01-Unmod 3.000 0.525 6mer (1 mismatch)
chr2 96,299,015 96,299,109 - SNRNP200 ENSG00000144028.15 Intron APP-01-Unmod 12.500 0.911 6mer offset (Perfect match)
chr2 99,355,364 99,355,430 + EIF5B ENSG00000158417.11 Intron APP-01-Unmod 8.500 0.851 7mer m8 (Perfect match)
chr2 118,089,586 118,089,608 + INSIG2 ENSG00000125629.15 Intron APP-01-Unmod 4.500 0.644 No seed match
chr2 134,956,983 134,957,045 + CCNT2 ENSG00000082258.13 3' UTR APP-01-Unmod 7.500 0.713 7mer m8 (Perfect match)
chr2 135,534,654 135,534,710 + R3HDM1 ENSG00000048991.16 Intron APP-01-Unmod 7.500 0.644 6mer (1 mismatch)
chr2 147,979,011 147,979,087 - ORC4 ENSG00000115947.14 Intron APP-01-Unmod 5.500 0.554 7mer m8 (Perfect match)
chr2 151,420,181 151,420,283 + RIF1 ENSG00000080345.18 CDS APP-01-Unmod 39.000 0.990 8mer (1 mismatch)
chr2 169,946,318 169,946,396 + UBR3 ENSG00000144357.17 CDS APP-01-Unmod 8.000 0.842 No seed match
chr2 169,947,523 169,947,599 + UBR3 ENSG00000144357.17 CDS APP-01-Unmod 46.500 0.990 7mer m8 (Perfect match)
chr2 173,366,271 173,366,323 + CDCA7 ENSG00000144354.14 CDS APP-01-Unmod 5.000 0.653 7mer m8 (Perfect match)
chr2 174,119,861 174,119,979 - OLA1 ENSG00000138430.16 Intron APP-01-Unmod 5.000 0.653 8mer (1 mismatch)
chr2 175,953,039 175,953,101 - LNPK ENSG00000144320.14 Intron APP-01-Unmod 4.000 0.624 8mer (Perfect match)
chr2 208,288,850 208,288,949 + PIKFYVE ENSG00000115020.17 Intron APP-01-Unmod 45.000 0.990 8mer (Perfect match)
chr2 216,506,240 216,506,309 + RPL37A ENSG00000197756.10 Intron APP-01-Unmod 6.500 0.713 7mer m8 (Perfect match)
chr2 232,838,035 232,838,084 + GIGYF2 ENSG00000204120.15 Intron APP-01-Unmod 5.000 0.634 6mer (Perfect match)
chr2 233,291,851 233,291,896 + ATG16L1 ENSG00000085978.22 Intron APP-01-Unmod 14.000 0.950 7mer m8 (Perfect match)
chr20 2,118,340 2,118,367 + STK35 ENSG00000125834.13 Intron APP-01-Unmod 3.000 0.594 compensatory region (Perfect match)
chr20 25,379,052 25,379,118 - ABHD12 ENSG00000100997.20 Intron APP-01-Unmod 3.500 0.515 6mer (1 mismatch)
chr20 35,907,752 35,907,843 + PHF20 ENSG00000025293.17 Intron APP-01-Unmod 5.000 0.673 7mer m8 (Perfect match)
chr20 41,137,667 41,137,772 + PLCG1 ENSG00000124181.14 CDS APP-01-Unmod 7.000 0.743 6mer (1 mismatch)
chr20 49,253,734 49,253,793 - ZNFX1 ENSG00000124201.15 CDS APP-01-Unmod 5.000 0.604 8mer (Perfect match)
chr20 62,163,826 62,163,884 + SS18L1 ENSG00000184402.15 Intron APP-01-Unmod 3.500 0.564 7mer m8 (Perfect match)
chr20 62,387,851 62,387,911 + RPS21 ENSG00000171858.18 CDS APP-01-Unmod 4.000 0.624 No seed match
chr20 62,388,454 62,388,518 + RPS21 ENSG00000171858.18 CDS APP-01-Unmod 32.000 0.980 8mer (Perfect match)
chr20 63,214,463 63,214,537 - YTHDF1 ENSG00000149658.18 Intron APP-01-Unmod 6.000 0.634 6mer offset (Perfect match)
chr20 63,712,566 63,712,603 + ZGPAT ENSG00000197114.12 Intron APP-01-Unmod 5.000 0.733 7mer m8 (Perfect match)
chr21 15,734,170 15,734,245 + USP25 ENSG00000155313.15 Intron APP-01-Unmod 19.000 0.960 8mer (Perfect match)
chr21 25,891,790 25,891,803 - APP ENSG00000142192.21 CDS APP-01-Unmod 10.000 0.931 7mer A1 (Perfect match)
chr21 25,891,803 25,891,859 - APP ENSG00000142192.21 CDS APP-01-Unmod 18.000 0.960 compensatory region (Perfect match)
chr21 32,744,012 32,744,066 - PAXBP1 ENSG00000159086.15 Intron APP-01-Unmod 5.000 0.604 7mer m8 (Perfect match)
chr21 45,515,055 45,515,148 - SLC19A1 ENSG00000173638.19 CDS APP-01-Unmod 7.500 0.861 7mer m8 (Perfect match)
chr21 46,289,883 46,290,035 + YBEY ENSG00000182362.14 Intron APP-01-Unmod 18.500 0.960 8mer (Perfect match)
chr22 17,894,992 17,895,012 - MICAL3 ENSG00000243156.9 Intron APP-01-Unmod 4.000 0.614 No seed match
chr22 19,463,603 19,463,652 - UFD1 ENSG00000070010.19 Intron APP-01-Unmod 5.500 0.733 7mer m8 (Perfect match)
chr22 20,492,523 20,492,603 - KLHL22 ENSG00000099910.17 Intron APP-01-Unmod 32.500 0.970 7mer m8 (Perfect match)
chr22 23,825,323 23,825,392 + SMARCB1 ENSG00000099956.20 CDS APP-01-Unmod 5.000 0.634 6mer offset (Perfect match)
chr22 28,366,214 28,366,282 - TTC28 ENSG00000100154.14 Intron APP-01-Unmod 4.500 0.574 7mer A1 (Perfect match)
chr22 29,837,483 29,837,531 - ASCC2 ENSG00000100325.15 Intron APP-01-Unmod 5.500 0.663 7mer m8 (1 mismatch)
chr22 39,319,071 39,319,102 - RPL3 ENSG00000100316.16 CDS APP-01-Unmod 4.000 0.743 No seed match
chr22 40,285,629 40,285,696 + TNRC6B ENSG00000100354.21 CDS APP-01-Unmod 7.000 0.762 7mer m8 (1 mismatch)
chr22 41,621,988 41,622,064 + XRCC6 ENSG00000196419.13 CDS APP-01-Unmod 8.500 0.851 7mer A1 (1 mismatch)
chr22 44,847,866 44,847,941 + PRR5-ARHGAP8|ARHGAP8 ENSG00000241484.9||ENSG00000248405.10 Intron APP-01-Unmod 4.500 0.574 7mer A1 (Perfect match)
chr22 44,850,703 44,850,790 + PRR5-ARHGAP8|ARHGAP8 ENSG00000248405.10||ENSG00000241484.9 Intron APP-01-Unmod 7.000 0.762 8mer (Perfect match)
chr22 44,986,067 44,986,151 - PHF21B ENSG00000056487.16 Intron APP-01-Unmod 5.500 0.644 8mer (Perfect match)
chr3 13,405,837 13,405,961 - NUP210 ENSG00000132182.12 Intron APP-01-Unmod 10.500 0.861 7mer A1 (Perfect match)
chr3 23,338,118 23,338,209 + UBE2E2 ENSG00000182247.10 Intron APP-01-Unmod 26.000 0.990 6mer (1 mismatch)
chr3 37,984,344 37,984,435 + CTDSPL ENSG00000144677.15 3' UTR APP-01-Unmod 6.000 0.851 6mer offset (Perfect match)
chr3 40,813,832 40,813,836 + AC099560.1 ENSG00000231873.2 Other APP-01-Unmod 4.000 0.574 No seed match
chr3 40,813,836 40,813,854 + AC099560.1 ENSG00000231873.2 Other APP-01-Unmod 11.500 0.911 No seed match
chr3 41,758,132 41,758,186 - ULK4 ENSG00000168038.11 Intron APP-01-Unmod 4.500 0.594 8mer (Perfect match)
chr3 45,394,467 45,394,520 + LARS2 ENSG00000011376.12 CDS APP-01-Unmod 57.000 0.980 No seed match
chr3 45,394,520 45,394,565 + LARS2 ENSG00000011376.12 CDS APP-01-Unmod 63.000 0.980 6mer (Perfect match)
chr3 47,054,612 47,054,687 - SETD2 ENSG00000181555.21 Intron APP-01-Unmod 9.000 0.871 7mer m8 (1 mismatch)
chr3 47,841,961 47,842,031 + DHX30 ENSG00000132153.15 Intron APP-01-Unmod 4.500 0.673 6mer offset (Perfect match)
chr3 49,683,428 49,683,498 + APEH ENSG00000164062.13 3' UTR APP-01-Unmod 14.000 0.901 8mer (1 mismatch)
chr3 61,022,850 61,022,909 - FHIT ENSG00000189283.10 Intron APP-01-Unmod 3.500 0.525 8mer (Perfect match)
chr3 61,597,627 61,597,708 + PTPRG ENSG00000144724.20 Intron APP-01-Unmod 8.500 0.891 6mer (Perfect match)
chr3 72,431,466 72,431,541 - RYBP ENSG00000163602.10 Intron APP-01-Unmod 17.000 0.941 8mer (Perfect match)
chr3 75,558,932 75,558,955 - AC133041.1 ENSG00000272710.2 Other APP-01-Unmod 4.500 0.594 6mer offset (1 mismatch)
chr3 121,460,435 121,460,493 - POLQ ENSG00000051341.14 Intron APP-01-Unmod 3.500 0.525 6mer (1 mismatch)
chr3 123,492,774 123,492,833 - HACD2 ENSG00000206527.10 3' UTR APP-01-Unmod 4.500 0.545 7mer m8 (Perfect match)
chr3 125,362,858 125,362,909 - ZNF148 ENSG00000163848.20 Intron APP-01-Unmod 4.000 0.594 6mer (Perfect match)
chr3 127,630,153 127,630,254 + PODXL2 ENSG00000114631.11 Intron APP-01-Unmod 4.500 0.515 7mer A1 (1 mismatch)
chr3 128,182,912 128,182,934 + EEFSEC ENSG00000132394.11 Intron APP-01-Unmod 4.000 0.525 6mer offset (1 mismatch)
chr3 129,170,511 129,170,582 - CNBP ENSG00000169714.17 CDS APP-01-Unmod 3.500 0.574 7mer m8 (1 mismatch)
chr3 136,401,040 136,401,108 - STAG1 ENSG00000118007.13 Intron APP-01-Unmod 3.500 0.525 7mer A1 (Perfect match)
chr3 149,651,120 149,651,160 - WWTR1 ENSG00000018408.15 Intron APP-01-Unmod 3.000 0.535 7mer m8 (Perfect match)
chr3 154,279,788 154,279,855 - DHX36 ENSG00000174953.14 Intron APP-01-Unmod 25.500 0.980 6mer (1 mismatch)
chr3 154,308,441 154,308,517 - DHX36 ENSG00000174953.14 Intron APP-01-Unmod 5.000 0.733 8mer (Perfect match)
chr3 169,349,530 169,349,598 - MECOM ENSG00000085276.19 Intron APP-01-Unmod 3.500 0.574 7mer m8 (Perfect match)
chr3 183,920,043 183,920,104 - ABCC5 ENSG00000114770.17 3' UTR APP-01-Unmod 8.500 0.871 6mer (Perfect match)
chr3 195,903,802 195,903,852 - TNK2 ENSG00000061938.19 Intron APP-01-Unmod 3.000 0.574 6mer (Perfect match)
chr3 196,075,287 196,075,368 - TFRC ENSG00000072274.13 CDS APP-01-Unmod 6.000 0.762 8mer (Perfect match)
chr3 196,936,093 196,936,180 - NCBP2 ENSG00000114503.11 3' UTR APP-01-Unmod 6.500 0.861 8mer (Perfect match)
chr3 197,169,143 197,169,215 - DLG1 ENSG00000075711.21 Intron APP-01-Unmod 8.500 0.812 8mer (1 mismatch)
chr4 487,291 487,356 - ZNF721 ENSG00000182903.16 Intron APP-01-Unmod 8.000 0.881 8mer (Perfect match)
chr4 7,737,707 7,737,730 + SORCS2 ENSG00000184985.16 Intron APP-01-Unmod 5.000 0.594 No seed match
chr4 13,602,081 13,602,184 - BOD1L1 ENSG00000038219.13 CDS APP-01-Unmod 8.500 0.851 6mer offset (Perfect match)
chr4 20,493,695 20,493,750 + SLIT2 ENSG00000145147.20 Intron APP-01-Unmod 3.500 0.515 6mer offset (Perfect match)
chr4 20,620,207 20,620,247 + SLIT2 ENSG00000145147.20 3' UTR APP-01-Unmod 55.500 0.980 No seed match
chr4 20,620,247 20,620,268 + SLIT2 ENSG00000145147.20 3' UTR APP-01-Unmod 22.500 0.960 7mer A1 (Perfect match)
chr4 30,721,827 30,721,851 + PCDH7 ENSG00000169851.15 CDS APP-01-Unmod 9.000 0.851 No seed match
chr4 30,721,828 30,721,851 - AC098595.1 ENSG00000286596.1 Other APP-01-Unmod 8.500 0.762 7mer m8 (1 mismatch)
chr4 55,434,068 55,434,138 - CLOCK ENSG00000134852.15 3' UTR APP-01-Unmod 4.000 0.574 6mer (Perfect match)
chr4 70,768,573 70,768,655 + RUFY3 ENSG00000018189.13 CDS APP-01-Unmod 5.500 0.713 6mer (Perfect match)
chr4 75,644,002 75,644,083 - G3BP2 ENSG00000138757.14 3' UTR APP-01-Unmod 5.000 0.683 6mer (Perfect match)
chr4 87,341,045 87,341,140 - HSD17B11 ENSG00000198189.11 Intron APP-01-Unmod 8.000 0.762 7mer A1 (Perfect match)
chr4 90,193,864 90,193,981 + CCSER1 ENSG00000184305.15 Intron APP-01-Unmod 8.000 0.861 7mer m8 (1 mismatch)
chr4 102,276,988 102,277,040 - SLC39A8 ENSG00000138821.13 Intron APP-01-Unmod 4.000 0.713 8mer (Perfect match)
chr4 102,796,087 102,796,168 - UBE2D3 ENSG00000109332.20 3' UTR APP-01-Unmod 19.500 0.960 7mer m8 (Perfect match)
chr4 119,248,031 119,248,097 + USP53 ENSG00000145390.11 Intron APP-01-Unmod 3.500 0.564 8mer (Perfect match)
chr4 151,297,336 151,297,406 - SH3D19 ENSG00000109686.18 Intron APP-01-Unmod 7.000 0.723 7mer A1 (Perfect match)
chr4 154,535,439 154,535,508 - PLRG1 ENSG00000171566.12 3' UTR APP-01-Unmod 5.000 0.634 6mer offset (Perfect match)
chr4 173,333,617 173,333,683 - HMGB2 ENSG00000164104.12 CDS APP-01-Unmod 7.500 0.574 6mer (1 mismatch)
chr4 186,620,235 186,620,328 - FAT1 ENSG00000083857.14 CDS APP-01-Unmod 13.500 0.911 6mer (Perfect match)
chr5 14,442,561 14,442,642 + TRIO ENSG00000038382.20 Intron APP-01-Unmod 6.000 0.743 8mer (Perfect match)
chr5 31,527,871 31,527,944 - DROSHA ENSG00000113360.16 Intron APP-01-Unmod 4.000 0.644 6mer (1 mismatch)
chr5 36,952,883 36,952,962 + NIPBL ENSG00000164190.19 Intron APP-01-Unmod 6.500 0.743 7mer A1 (Perfect match)
chr5 37,198,680 37,198,770 - CPLANE1 ENSG00000197603.15 CDS APP-01-Unmod 57.500 0.980 7mer m8 (1 mismatch)
chr5 59,145,309 59,145,324 - PDE4D ENSG00000113448.19 Intron APP-01-Unmod 17.500 0.970 No seed match
chr5 59,145,324 59,145,341 - PDE4D ENSG00000113448.19 Intron APP-01-Unmod 8.000 0.812 No seed match
chr5 62,529,040 62,529,107 + IPO11 ENSG00000086200.17 Intron APP-01-Unmod 4.000 0.554 7mer m8 (Perfect match)
chr5 78,216,078 78,216,175 - AP3B1 ENSG00000132842.14 CDS APP-01-Unmod 12.500 0.941 8mer (Perfect match)
chr5 82,273,725 82,273,774 - RPS23 ENSG00000186468.13 3' UTR APP-01-Unmod 3.500 0.515 7mer A1 (1 mismatch)
chr5 98,855,291 98,855,361 - CHD1 ENSG00000153922.11 3' UTR APP-01-Unmod 12.500 0.931 7mer A1 (1 mismatch)
chr5 98,930,078 98,930,148 + LINC02062 ENSG00000248489.2 Other APP-01-Unmod 6.500 0.743 7mer m8 (Perfect match)
chr5 131,643,457 131,643,554 - FNIP1 ENSG00000217128.12 3' UTR APP-01-Unmod 12.000 0.891 6mer offset (1 mismatch)
chr5 137,946,035 137,946,101 - FAM13B ENSG00000031003.10 Intron APP-01-Unmod 18.500 0.960 6mer (1 mismatch)
chr5 139,305,101 139,305,179 + MATR3 ENSG00000015479.20||ENSG00000280987.4 Intron APP-01-Unmod 8.500 0.832 7mer m8 (Perfect match)
chr5 140,551,075 140,551,130 - SRA1 ENSG00000213523.10 CDS APP-01-Unmod 5.000 0.683 6mer offset (Perfect match)
chr5 151,490,273 151,490,315 + SLC36A1 ENSG00000123643.13 3' UTR APP-01-Unmod 3.000 0.554 6mer (Perfect match)
chr6 2,771,483 2,771,548 + WRNIP1 ENSG00000124535.16 Intron APP-01-Unmod 6.500 0.782 6mer offset (Perfect match)
chr6 3,340,419 3,340,484 - SLC22A23 ENSG00000137266.14 Intron APP-01-Unmod 4.500 0.624 8mer (Perfect match)
chr6 13,419,335 13,419,400 - GFOD1 ENSG00000145990.11 Intron APP-01-Unmod 6.000 0.733 6mer (Perfect match)
chr6 15,308,259 15,308,331 + JARID2 ENSG00000008083.14 Intron APP-01-Unmod 7.000 0.723 compensatory region (Perfect match)
chr6 16,705,056 16,705,116 - ATXN1 ENSG00000124788.19 Intron APP-01-Unmod 4.000 0.545 7mer A1 (Perfect match)
chr6 20,493,386 20,493,445 + E2F3 ENSG00000112242.15 3' UTR APP-01-Unmod 5.000 0.733 6mer offset (Perfect match)
chr6 26,285,412 26,285,509 - H4C8 ENSG00000158406.5 CDS APP-01-Unmod 5.000 0.743 7mer m8 (1 mismatch)
chr6 31,535,862 31,535,936 - DDX39B ENSG00000198563.14 Intron APP-01-Unmod 6.000 0.832 7mer A1 (Perfect match)
chr6 31,829,870 31,830,001 + HSPA1B ENSG00000204388.7 CDS APP-01-Unmod 5.000 0.693 6mer (Perfect match)
chr6 34,956,457 34,956,516 + ANKS1A ENSG00000064999.15 Intron APP-01-Unmod 3.500 0.515 6mer offset (Perfect match)
chr6 42,211,309 42,211,386 - MRPS10 ENSG00000048544.6 Intron APP-01-Unmod 18.500 0.931 8mer (Perfect match)
chr6 45,192,935 45,193,014 - SUPT3H ENSG00000196284.17 Intron APP-01-Unmod 6.500 0.812 8mer (1 mismatch)
chr6 72,721,971 72,722,035 + KCNQ5 ENSG00000185760.16 Intron APP-01-Unmod 14.500 0.960 6mer (Perfect match)
chr6 118,059,325 118,059,400 + SLC35F1 ENSG00000196376.11 Intron APP-01-Unmod 11.000 0.842 8mer (Perfect match)
chr6 127,312,561 127,312,666 - ECHDC1 ENSG00000093144.19 Intron APP-01-Unmod 179.000 0.990 8mer (Perfect match)
chr6 127,312,676 127,312,702 - ECHDC1 ENSG00000093144.19 Intron APP-01-Unmod 9.000 0.812 No seed match
chr6 142,202,707 142,202,773 + VTA1 ENSG00000009844.16 Intron APP-01-Unmod 5.500 0.713 7mer A1 (Perfect match)
chr6 156,809,793 156,809,934 + ARID1B ENSG00000049618.24 Intron APP-01-Unmod 27.000 0.990 7mer m8 (Perfect match)
chr6 169,703,564 169,703,671 + C6orf120 ENSG00000185127.6 3' UTR APP-01-Unmod 93.000 0.970 8mer (Perfect match)
chr6 170,398,847 170,398,939 + FAM120B ENSG00000112584.14 Intron APP-01-Unmod 5.500 0.634 7mer A1 (Perfect match)
chr7 2,188,247 2,188,269 - MAD1L1 ENSG00000002822.15 Intron APP-01-Unmod 9.000 0.812 7mer m8 (1 mismatch)
chr7 7,705,696 7,705,755 + UMAD1 ENSG00000219545.11 Intron APP-01-Unmod 4.500 0.614 6mer (Perfect match)
chr7 22,940,958 22,941,037 - FAM126A ENSG00000122591.12 3' UTR APP-01-Unmod 9.500 0.881 8mer (Perfect match)
chr7 27,169,526 27,169,547 - hsa-mir-196b MI0001150 miRNA APP-01-Unmod 5.500 0.624 No seed match
chr7 33,720,493 33,720,556 + BBS9 ENSG00000122507.21 Other APP-01-Unmod 6.500 0.832 7mer A1 (Perfect match)
chr7 35,891,305 35,891,395 + SEPTIN7 ENSG00000122545.20 Intron APP-01-Unmod 4.000 0.683 7mer m8 (Perfect match)
chr7 67,173,277 67,173,354 + TYW1 ENSG00000198874.13 Intron APP-01-Unmod 10.500 0.960 7mer m8 (Perfect match)
chr7 70,234,067 70,234,139 + AUTS2 ENSG00000158321.18 Intron APP-01-Unmod 11.000 0.911 7mer A1 (1 mismatch)
chr7 70,450,715 70,450,769 + AUTS2 ENSG00000158321.18 Intron APP-01-Unmod 3.000 0.545 8mer (Perfect match)
chr7 76,570,632 76,570,687 + AC004980.1 ENSG00000205485.13 Other APP-01-Unmod 5.000 0.693 6mer offset (Perfect match)
chr7 87,163,330 87,163,453 + DMTF1 ENSG00000135164.19 5' UTR APP-01-Unmod 28.000 0.980 7mer m8 (Perfect match)
chr7 87,872,497 87,872,567 - SLC25A40 ENSG00000075303.13 Intron APP-01-Unmod 4.000 0.564 6mer offset (Perfect match)
chr7 93,755,515 93,755,561 + GNGT1 ENSG00000127928.13 Intron APP-01-Unmod 5.500 0.653 8mer (Perfect match)
chr7 99,559,613 99,559,701 + ZNF655 ENSG00000197343.11 Intron APP-01-Unmod 16.500 0.990 7mer A1 (Perfect match)
chr7 105,272,098 105,272,169 - SRPK2 ENSG00000135250.17 Intron APP-01-Unmod 12.500 0.950 6mer (Perfect match)
chr7 110,800,279 110,800,348 - IMMP2L ENSG00000184903.10 Intron APP-01-Unmod 4.500 0.634 7mer m8 (Perfect match)
chr7 129,302,391 129,302,467 + AHCYL2 ENSG00000158467.16 Intron APP-01-Unmod 7.000 0.752 7mer m8 (Perfect match)
chr7 133,024,470 133,024,528 - CHCHD3 ENSG00000106554.13 Intron APP-01-Unmod 4.000 0.584 8mer (Perfect match)
chr7 135,560,525 135,560,595 + NUP205 ENSG00000155561.15 Intron APP-01-Unmod 7.000 0.693 7mer A1 (Perfect match)
chr7 139,369,747 139,369,823 + FMC1-LUC7L2|LUC7L2 ENSG00000146963.18||ENSG00000269955.2 Intron APP-01-Unmod 5.000 0.762 7mer m8 (Perfect match)
chr7 141,743,570 141,743,639 + SSBP1 ENSG00000106028.11 CDS APP-01-Unmod 6.500 0.762 6mer (1 mismatch)
chr7 149,244,965 149,245,030 + ZNF212 ENSG00000170260.9 Intron APP-01-Unmod 5.000 0.604 8mer (Perfect match)
chr7 152,148,059 152,148,159 - KMT2C ENSG00000055609.19 CDS APP-01-Unmod 54.000 0.990 7mer m8 (Perfect match)
chr7 155,301,614 155,301,687 + INSIG1 ENSG00000186480.13 CDS APP-01-Unmod 24.000 0.970 6mer (Perfect match)
chr7 155,308,877 155,308,911 + INSIG1 ENSG00000186480.13 3' UTR APP-01-Unmod 7.000 0.792 7mer m8 (Perfect match)
chr7 157,388,947 157,389,033 + DNAJB6 ENSG00000105993.15 Intron APP-01-Unmod 42.000 0.980 7mer m8 (Perfect match)
chr7 158,632,011 158,632,014 - NCAPG2 ENSG00000146918.20 Intron APP-01-Unmod 5.000 0.663 No seed match
chr7 158,632,014 158,632,036 - NCAPG2 ENSG00000146918.20 Intron APP-01-Unmod 33.000 0.990 No seed match
chr8 17,567,600 17,567,700 + SLC7A2 ENSG00000003989.18 3' UTR APP-01-Unmod 22.000 0.950 6mer (Perfect match)
chr8 22,244,973 22,244,998 - hsa-mir-320a MI0000542 miRNA APP-01-Unmod 4.500 0.663 No seed match
chr8 31,072,415 31,072,491 + WRN ENSG00000165392.11 Intron APP-01-Unmod 6.000 0.693 7mer A1 (1 mismatch)
chr8 43,174,347 43,174,398 + HGSNAT ENSG00000165102.15 Intron APP-01-Unmod 6.500 0.822 No seed match
chr8 43,174,398 43,174,466 + HGSNAT ENSG00000165102.15 Intron APP-01-Unmod 23.500 0.970 8mer (1 mismatch)
chr8 47,773,488 47,773,542 - PRKDC ENSG00000253729.8 3' UTR APP-01-Unmod 3.000 0.505 8mer (1 mismatch)
chr8 61,644,219 61,644,296 - ASPH ENSG00000198363.18 Intron APP-01-Unmod 3.000 0.525 6mer (1 mismatch)
chr8 94,789,749 94,789,790 + DPY19L4 ENSG00000156162.16 CDS APP-01-Unmod 22.500 0.970 6mer offset (1 mismatch)
chr8 94,789,790 94,789,841 + DPY19L4 ENSG00000156162.16 CDS APP-01-Unmod 38.500 0.990 7mer m8 (Perfect match)
chr8 104,578,907 104,578,981 - LRP12 ENSG00000147650.11 Intron APP-01-Unmod 4.500 0.594 8mer (Perfect match)
chr8 130,394,445 130,394,489 - ASAP1 ENSG00000153317.15 Intron APP-01-Unmod 3.500 0.525 7mer m8 (Perfect match)
chr9 5,811,186 5,811,249 - ERMP1 ENSG00000099219.14 CDS APP-01-Unmod 3.500 0.554 7mer m8 (Perfect match)
chr9 32,862,444 32,862,516 - AL157884.3 ENSG00000236796.1 Other APP-01-Unmod 7.500 0.851 8mer (Perfect match)
chr9 74,947,534 74,947,592 - C9orf40 ENSG00000135045.7 3' UTR APP-01-Unmod 3.000 0.515 6mer offset (1 mismatch)
chr9 78,329,238 78,329,306 + PSAT1 ENSG00000135069.14 3' UTR APP-01-Unmod 4.000 0.574 6mer (1 mismatch)
chr9 92,272,962 92,273,021 - IARS1 ENSG00000196305.18 Intron APP-01-Unmod 6.000 0.723 7mer m8 (Perfect match)
chr9 101,542,132 101,542,192 + RNF20 ENSG00000155827.12 Intron APP-01-Unmod 5.500 0.782 6mer offset (Perfect match)
chr9 108,928,778 108,928,847 - ELP1 ENSG00000070061.16 Intron APP-01-Unmod 4.500 0.564 8mer (Perfect match)
chr9 111,450,338 111,450,408 - ECPAS ENSG00000136813.14 Intron APP-01-Unmod 5.000 0.644 8mer (Perfect match)
chr9 120,769,515 120,769,556 - FBXW2 ENSG00000119402.17 Intron APP-01-Unmod 3.500 0.594 7mer A1 (Perfect match)
chr9 122,285,914 122,285,984 + MRRF ENSG00000148187.18 Intron APP-01-Unmod 4.000 0.584 6mer (1 mismatch)
chr9 124,857,888 124,857,965 - RPL35 ENSG00000136942.15 CDS APP-01-Unmod 75.000 0.980 6mer offset (Perfect match)
chr9 128,969,451 128,969,517 + NUP188 ENSG00000095319.14 CDS APP-01-Unmod 6.000 0.703 6mer offset (Perfect match)
chr9 130,086,435 130,086,484 + GPR107 ENSG00000148358.19 CDS APP-01-Unmod 5.500 0.743 6mer (Perfect match)
chr9 133,778,268 133,778,351 - VAV2 ENSG00000160293.17 Intron APP-01-Unmod 5.500 0.792 7mer m8 (Perfect match)
chrM 671 788 + MT-RNR1 ENSG00000211459.2 Other APP-01-Unmod 5.500 0.673 No seed match
chrM 1,387 1,422 + MT-RNR1 ENSG00000211459.2 Other APP-01-Unmod 9.500 0.851 No seed match
chrM 2,389 2,432 + MT-RNR2 ENSG00000210082.2 Other APP-01-Unmod 4.500 0.584 6mer (1 mismatch)
chrX 23,984,597 23,984,679 - KLHL15 ENSG00000174010.9 3' UTR APP-01-Unmod 7.500 0.703 7mer m8 (1 mismatch)
chrX 24,801,090 24,801,170 + POLA1 ENSG00000101868.12 Intron APP-01-Unmod 4.000 0.574 7mer m8 (Perfect match)
chrX 45,747,030 45,747,060 - hsa-mir-222 MI0000299 miRNA APP-01-Unmod 4.500 0.594 No seed match
chrX 45,749,310 45,749,386 - MIR222HG ENSG00000270069.1 Other APP-01-Unmod 29.000 0.980 7mer m8 (Perfect match)
chrX 47,176,562 47,176,644 + RBM10 ENSG00000182872.16 CDS APP-01-Unmod 13.000 0.871 7mer m8 (Perfect match)
chrX 48,575,546 48,575,616 + RBM3 ENSG00000102317.18 CDS APP-01-Unmod 4.500 0.693 6mer offset (Perfect match)
chrX 73,827,255 73,827,311 - XIST ENSG00000229807.12 Other APP-01-Unmod 184.000 0.990 6mer (Perfect match)
chrX 73,827,311 73,827,339 - XIST ENSG00000229807.12 Other APP-01-Unmod 48.500 0.980 No seed match
chrX 73,850,929 73,850,958 - XIST ENSG00000229807.12 Other APP-01-Unmod 5.000 0.673 6mer offset (1 mismatch)
chrX 74,220,197 74,220,269 - FTX ENSG00000230590.11 Other APP-01-Unmod 4.000 0.604 7mer A1 (Perfect match)
chrX 78,118,198 78,118,286 + PGK1 ENSG00000102144.15 Intron APP-01-Unmod 28.000 0.970 8mer (Perfect match)
chrX 118,356,099 118,356,154 + WDR44 ENSG00000131725.14 Intron APP-01-Unmod 3.500 0.614 6mer offset (1 mismatch)
chrX 132,074,571 132,074,643 + STK26 ENSG00000134602.16 3' UTR APP-01-Unmod 5.500 0.693 7mer A1 (1 mismatch)
chrX 134,170,079 134,170,108 - hsa-mir-18b MI0001518 miRNA APP-01-Unmod 4.500 0.574 No seed match
chrX 134,500,278 134,500,333 + HPRT1 ENSG00000165704.15 3' UTR APP-01-Unmod 7.000 0.782 6mer offset (1 mismatch)
chrX 140,766,068 140,766,138 + LINC00632 ENSG00000203930.12 Other APP-01-Unmod 9.500 0.891 6mer (1 mismatch)
chrX 154,770,620 154,770,684 + DKC1 ENSG00000130826.18 Intron APP-01-Unmod 4.500 0.653 6mer (Perfect match)
chr1 75,787,492 75,787,534 + RABGGTB ENSG00000137955.16 CDS APP-05 4.000 0.564 6mer (1 mismatch)
chr1 234,606,620 234,606,678 - IRF2BP2 ENSG00000168264.10 3' UTR APP-05 3.500 0.505 6mer offset (Perfect match)
chr10 51,675,949 51,676,008 + PRKG1 ENSG00000185532.20 Intron APP-05 3.500 0.594 7mer m8 (Perfect match)
chr10 100,540,651 100,540,718 + HIF1AN ENSG00000166135.14 CDS APP-05 6.000 0.723 7mer m8 (Perfect match)
chr11 61,302,645 61,302,714 - DDB1 ENSG00000167986.14 CDS APP-05 8.000 0.594 6mer offset (Perfect match)
chr13 91,350,754 91,350,757 + hsa-mir-18a MI0000072 miRNA APP-05 7.000 0.802 No seed match
chr13 91,350,758 91,350,767 + hsa-mir-18a MI0000072 miRNA APP-05 16.500 0.950 No seed match
chr13 91,350,769 91,350,779 + hsa-mir-18a MI0000072 miRNA APP-05 16.000 0.970 No seed match
chr15 92,949,266 92,949,353 + CHD2 ENSG00000173575.22 Intron APP-05 12.000 0.960 8mer (Perfect match)
chr16 9,103,382 9,103,452 + C16orf72 ENSG00000182831.12 3' UTR APP-05 3.500 0.525 6mer (1 mismatch)
chr19 22,694,816 22,694,846 - AC024563.1 ENSG00000268981.5 Other APP-05 66.500 0.980 6mer offset (1 mismatch)
chr19 22,694,846 22,694,861 - AC024563.1 ENSG00000268981.5 Other APP-05 34.000 0.980 No seed match
chr2 85,542,344 85,542,415 + MAT2A ENSG00000168906.13 CDS APP-05 6.500 0.802 6mer (Perfect match)
chr2 169,947,524 169,947,601 + UBR3 ENSG00000144357.17 CDS APP-05 16.500 0.950 7mer m8 (Perfect match)
chr20 62,388,452 62,388,513 + RPS21 ENSG00000171858.18 CDS APP-05 8.500 0.842 8mer (Perfect match)
chr22 20,492,524 20,492,606 - KLHL22 ENSG00000099910.17 Intron APP-05 8.500 0.802 7mer m8 (Perfect match)
chr5 59,145,309 59,145,341 - PDE4D ENSG00000113448.19 Intron APP-05 9.500 0.891 No seed match
chr6 42,211,316 42,211,382 - MRPS10 ENSG00000048544.6 Intron APP-05 4.500 0.604 8mer (Perfect match)
chr6 127,312,561 127,312,639 - ECHDC1 ENSG00000093144.19 Intron APP-05 5.500 0.693 8mer (Perfect match)
chr6 169,703,575 169,703,671 + C6orf120 ENSG00000185127.6 3' UTR APP-05 23.500 0.970 8mer (Perfect match)
chr7 27,169,514 27,169,547 - hsa-mir-196b MI0001150 miRNA APP-05 5.000 0.743 No seed match
chr7 158,632,014 158,632,019 - NCAPG2 ENSG00000146918.20 Intron APP-05 3.500 0.564 No seed match
chr7 158,632,019 158,632,036 - NCAPG2 ENSG00000146918.20 Intron APP-05 8.000 0.842 No seed match
chr8 22,244,974 22,244,999 - hsa-mir-320a MI0000542 miRNA APP-05 4.500 0.752 No seed match
chr8 94,789,776 94,789,843 + DPY19L4 ENSG00000156162.16 CDS APP-05 6.000 0.752 7mer m8 (Perfect match)
chr9 124,857,885 124,857,983 - RPL35 ENSG00000136942.15 CDS APP-05 7.000 0.792 6mer offset (Perfect match)
chrM 1,395 1,420 + MT-RNR1 ENSG00000211459.2 Other APP-05 4.500 0.683 No seed match
chrX 73,827,258 73,827,326 - XIST ENSG00000229807.12 Other APP-05 23.500 0.970 6mer (Perfect match)
chrX 134,170,081 134,170,109 - hsa-mir-18b MI0001518 miRNA APP-05 6.500 0.703 No seed match

siRNA & miRNA Target Counts

The bar plot below shows the number of peaks detected in each sample, as well as the number of reproducible peaks for each set of replicates. The bars are colored according to whether the peak is a miRNA target or an siRNA off target. siRNA on target peaks are not counted in this plot. Hover over each bars to see the number of peaks in each set. All plots in this report are interactive, meaning you can zoom in/out, pan to a certain location, and select elements from the legend to remove. Plots can also be downloaded as a separate file. Hover over the top right corner of the plot to see the interactive options.

siRNA Off Target Feature Distribution

The following bar plot depicts the feature distribution of siRNA off target peaks in each sample, as well as reproducible siRNA off target peaks for each set of replicates. Peaks are annotated according to the following hierarchy: CDS, 5'UTR or 3'UTR, miRNA, intron, and other. Hover over the bars to see the number of peaks and percentage of peaks per feature in each peak set. All plots in this report are interactive, meaning you can zoom in/out, pan to a certain location, and select elements from the legend to remove. Plots can also be downloaded as a separate file. Hover over the top right corner of the plot to see the interactive options.

siRNA Off Target Seed Match Distribution

The bar plot below shows the seed match distribution of siRNA off target peaks and reproducible siRNA off target peaks for each set of sample conditions. Seed match information was added to each peak according to seed match definitions from TargetScan, allowing for up to one mismatch in the seed region.

The following seed matches are classified as "Canonical":

  • 7mer-m8: An exact match to positions 2-8 of the mature miRNA (the seed + position 8)
  • 7mer-1A: An exact match to positions 2-7 of the mature miRNA (the seed) followed by an 'A'
  • 8mer: An exact match to positions 2-8 of the mature miRNA (the seed + position 8) followed by an 'A'
  • 6mer: An exact match to positions 2-7 of the mature miRNA (the seed)

The following seed matches are classified as "Noncanonical":

  • 6mer offset: An exact match to positions 3-8 of the mature miRNA
  • A 3' compensatory site is one in which strong 3' pairing (consequential miRNA-target complementarity outside the seed region) compensates for an imperfect seed match (Friedman et al., 2009).
  • A centered site is one that lacks perfect seed pairing and 3'-compensatory pairing but instead has 11-12 contiguous Watson-Crick pairs to miRNA positions 4-15. These are identified only in the reference species and therefore include no information about conservation.

Hover over each bar to see the number of peaks and % of peaks containing each type of seed match for each peak set. All plots in this report are interactive, meaning you can zoom in/out, pan to a certain location, and select elements from the legend to remove. Plots can also be downloaded as a separate file. Hover over the top right corner of the plot to see the interactive options.

Top siRNAs & miRNAs in Chimeric Reads

This plot shows the top 5 most abundant siRNAs or miRNAs in chimeric reads in each sample. All other siRNAs or miRNAs are summed to create the "Other" category. Hover over the bar to see the percentage of chimeric reads containing the siRNA or miRNA in each sample. All plots in this report are interactive, meaning you can zoom in/out, pan to a certain location, and select elements from the legend to remove. Plots can also be downloaded as a separate file. Hover over the top right corner of the plot to see the interactive options.

siRNA & miRNA Abundance in Chimeric Reads

The following plot shows the percentage of chimeric reads containing each siRNA or miRNA. Each siRNA or miRNA is depicted as one point for each sample. siRNA points are colored in red, and miRNA points are colored in teal. Hover over a point to see which siRNA or miRNA it corresponds to, and what percentage of chimeric reads contain that siRNA or miRNA. All plots in this report are interactive, meaning you can zoom in/out, pan to a certain location, and select elements from the legend to remove. Plots can also be downloaded as a separate file. Hover over the top right corner of the plot to see the interactive options.

siRNA & miRNA Target Gene Counts

The bar plot below shows the number of genes containing at least one siRNA or miRNA target peak per sample, as well as the number of genes containing at least one siRNA or miRNA target peak for each set of replicates. The bars are colored according to whether the gene is a miRNA target or an siRNA off target. Hover over the bars to see the number of genes in each peak set. All plots in this report are interactive, meaning you can zoom in/out, pan to a certain location, and select elements from the legend to remove. Plots can also be downloaded as a separate file. Hover over the top right corner of the plot to see the interactive options.

siRNA Off Target Gene Enrichment

This wordcloud shows significantly enriched GO terms and KEGG pathways identified using the tool clusterProfiler. This analysis looks for enriched functional types or pathways in the set of genes that contain at least one siRNA off target peak. The GO terms are split into the following three categories: Biological Process, Cell Component, and Molecular Function. The drop down menu in the bottom left corner can be used to navigate between different sets of peaks. For this plot, only motifs called from reproducible peaks are shown (if applicable). Plots can also be downloaded as a separate file. Hover over the top right corner of the plot to see the interactive options.

This tab summarizes differential siRNA (APP-01_05) and miRNA targets identified from miR-eCLIP +siRNA data.


We used DESeq2 to confidently identify statistically significant differences between sample groups. With DESeq2, we first normalize the raw counts by genomic peak across all our libraries, using relative log expression (REL). This helps us account for differences in sequencing depth and other factors that could affect our results. Next, we use information from all the peaks to accurately estimate the variability (dispersion) between samples for each peak in a way that considers the logarithmic nature of miR-eCLIP +siRNA data. This step is essential because it helps us identify the most reliable differences between groups. Finally, we use the dispersions to divide the log2 fold changes between conditions and calculate a statistical test called the "Wald" test. This test helps us determine whether our observed differences are likely real or just due to chance. We also obtain p-values from this test for each peak and adjust them for multiple comparisons using the FDR procedure.

For each differential analysis performed, a table and volcano plot is provided below. The table lists the coordinates of each chimeric peak, and which gene and siRNA or miRNA is associated with the peak. The average columns list the average, normalized chimeric read counts in each sample group. The associated fold change and -log10-transformed significance is shown as well. The volcano plot shows the fold change versus the significance, with genes colored by which sample group they are enriched in.

APP-05 vs. APP-01-Unmod Sample Comparisons Volcano Plot

APP-05 vs. APP-01-Unmod Sample Comparisons Table

Chromosome Start End Strand Gene name Ensembl ID Feature siRNA / miRNA Average APP-05 Average APP-01-Unmod Log2 Fold Change -log10(p-value)
chrM 8438 8500 + MT-ATP8 ENSG00000228253.1 CDS hsa-miR-196b-5p 5.23 0.07 1.98 1.15
chr2 70150128 70150205 - C2orf42 ENSG00000115998.7 3' UTR hsa-miR-16-5p 5.79 0.3 1.97 1.15
chrX 124078100 124078187 + STAG2 ENSG00000101972.19 Intron hsa-miR-92a-3p 8.7 1.43 1.9 1.37
chr19 6419207 6419266 - KHSRP ENSG00000088247.17 CDS hsa-miR-423-3p 6.41 0.5 1.86 1.16
chr2 84441275 84441385 - SUCLG1 ENSG00000163541.12 CDS hsa-miR-218-5p 6.31 0.5 1.86 1.16
chr4 75655175 75655225 - G3BP2 ENSG00000138757.14 CDS hsa-miR-24-3p 4.56 0.0 1.86 1.04
chr12 69258905 69258981 + CPSF6 ENSG00000111605.18 CDS hsa-miR-320a-3p 14.29 3.64 1.81 1.84
chr6 52284066 52284129 - MCM3 ENSG00000112118.20 Intron hsa-miR-92a-3p 5.54 0.94 1.73 1.03
chr17 7576623 7576690 + EIF4A1 ENSG00000161960.16 CDS hsa-miR-361-5p 11.35 2.94 1.67 1.38
chr4 77048248 77048362 - CCNI ENSG00000118816.11 CDS hsa-miR-148a-3p 16.97 4.95 1.66 1.88
chr6 44249710 44249798 + HSP90AB1 ENSG00000096384.20 CDS hsa-miR-218-5p 8.63 2.9 1.51 1.05
chr6 142203990 142204074 + VTA1 ENSG00000009844.16 CDS hsa-miR-93-5p 19.45 6.5 1.47 1.77
chr6 26156487 26156547 + H1-4 ENSG00000168298.7 CDS hsa-miR-423-3p 15.61 5.94 1.37 1.4
chr16 46661746 46661835 - VPS35 ENSG00000069329.18 CDS hsa-miR-320a-3p 13.86 5.92 1.24 1.14
chr6 159785382 159785457 - TCP1 ENSG00000120438.12 CDS hsa-miR-103a-3p 11.98 4.97 1.24 1.06
chr4 82857033 82857110 - SEC31A ENSG00000138674.17 CDS hsa-miR-30c-5p 11.87 4.96 1.23 1.05
chr17 75779116 75779183 - H3-3B ENSG00000132475.10 CDS hsa-miR-423-3p 12.97 5.44 1.22 1.1
chr22 29813456 29813542 - ASCC2 ENSG00000100325.15 CDS hsa-miR-17-5p 17.0 7.43 1.2 1.29
chr7 158632014 158632036 - NCAPG2 ENSG00000146918.20 Intron hsa-miR-92a-3p 16.5 7.2 1.16 1.22
chr2 43894714 43894791 - LRPPRC ENSG00000138095.19 Intron hsa-miR-92a-3p 12.28 5.28 1.15 1.0
chr1 11054686 11054760 - SRM ENSG00000116649.10 3' UTR hsa-miR-103a-3p 26.49 12.99 1.15 1.32
chr17 1464924 1464991 - MYO1C ENSG00000197879.17 3' UTR hsa-miR-92a-3p 20.43 10.41 1.07 1.16
chr15 66502629 66502695 - RPL4 ENSG00000174444.15 CDS hsa-miR-652-3p 17.41 8.49 1.07 1.06
chr22 23765980 23766016 - CHCHD10 ENSG00000250479.9 CDS hsa-miR-181a-5p 25.79 13.4 1.02 1.22
chr17 1679022 1679097 - PRPF8 ENSG00000174231.17 CDS hsa-miR-17-5p 18.87 9.68 1.02 1.06
chr1 11908179 11908258 + RNU5E-1|AL021155.4 ENSG00000285646.2||ENSG00000199347.1 Other hsa-miR-484 18.76 45.27 -1.05 1.7
chr14 31700645 31700811 + NUBPL ENSG00000151413.17 Intron hsa-miR-20a-5p 9.76 25.58 -1.06 1.12
chr3 73057605 73057688 + PPP4R2 ENSG00000163605.15 Intron hsa-miR-106b-5p 6.5 18.86 -1.09 1.11
chr7 92235573 92235649 - AC000120.4|KRIT1 ENSG00000285953.1||ENSG00000001631.16 CDS hsa-miR-20a-5p 4.56 15.19 -1.21 1.1
chr6 26055818 26055902 - H1-2 ENSG00000187837.4 CDS hsa-miR-15a-5p 4.42 13.03 -1.27 1.06
chr2 169947523 169947601 + UBR3 ENSG00000144357.17 CDS APP-01_05 16.35 46.17 -1.3 2.33
chr12 113904494 113904573 - RBM19 ENSG00000122965.11 Intron hsa-miR-18a-5p 5.97 20.11 -1.35 1.5
chr10 51675929 51676020 + PRKG1 ENSG00000185532.20 Intron APP-01_05 3.48 12.93 -1.36 1.07
chr7 158632014 158632036 - NCAPG2 ENSG00000146918.20 Intron APP-01_05 9.66 32.27 -1.38 1.88
chr5 98855291 98855361 - CHD1 ENSG00000153922.11 3' UTR APP-01_05 2.89 11.75 -1.41 1.08
chr6 42211309 42211386 - MRPS10 ENSG00000048544.6 Intron APP-01_05 4.5 18.44 -1.47 1.5
chr4 30721827 30721851 + PCDH7 ENSG00000169851.15 CDS APP-01_05 1.5 9.0 -1.48 1.01
chr3 40813836 40813854 + AC099560.1 ENSG00000231873.2 Other APP-01_05 2.42 10.88 -1.5 1.08
chr13 79386480 79386552 - RBM26 ENSG00000139746.16 Intron APP-01_05 2.98 12.61 -1.52 1.21
chr20 62388452 62388518 + RPS21 ENSG00000171858.18 CDS APP-01_05 8.1 31.74 -1.64 2.3
chr11 61302639 61302714 - DDB1 ENSG00000167986.14 CDS APP-01_05 7.95 32.47 -1.65 2.2
chr22 20492523 20492606 - KLHL22 ENSG00000099910.17 Intron APP-01_05 8.46 32.17 -1.66 2.37
chr7 2188247 2188269 - MAD1L1 ENSG00000002822.15 Intron APP-01_05 1.0 9.0 -1.67 1.11
chr4 87341045 87341140 - HSD17B11 ENSG00000198189.11 Intron APP-01_05 0.5 7.79 -1.67 1.01
chr12 131932818 131932870 + PUS1 ENSG00000177192.14 CDS APP-01_05 0.5 7.15 -1.69 1.02
chr12 20551420 20551466 + PDE3A ENSG00000172572.7 Intron APP-01_05 1.62 8.66 -1.69 1.11
chr2 77529662 77529787 - LRRTM4 ENSG00000176204.13 Intron APP-01_05 0.5 7.06 -1.72 1.03
chr4 13602081 13602184 - BOD1L1 ENSG00000038219.13 CDS APP-01_05 1.37 8.24 -1.76 1.1
chr6 169703564 169703671 + C6orf120 ENSG00000185127.6 3' UTR APP-01_05 23.5 92.42 -1.76 6.06
chr3 197169143 197169215 - DLG1 ENSG00000075711.21 Intron APP-01_05 0.5 8.38 -1.8 1.13
chr10 84518184 84518250 + CCSER2 ENSG00000107771.17 3' UTR APP-01_05 0.0 6.78 -1.81 1.01
chr7 67173277 67173354 + TYW1 ENSG00000198874.13 Intron APP-01_05 1.48 10.32 -1.81 1.28
chr22 40285629 40285696 + TNRC6B ENSG00000100354.21 CDS APP-01_05 0.49 6.5 -1.83 1.05
chr2 63684526 63684577 - WDPCP ENSG00000143951.16 Other APP-01_05 0.0 6.0 -1.84 1.06
chr6 15308259 15308331 + JARID2 ENSG00000008083.14 Intron APP-01_05 0.0 6.33 -1.84 1.06
chr7 135560525 135560595 + NUP205 ENSG00000155561.15 Intron APP-01_05 0.0 6.92 -1.84 1.06
chr7 70234067 70234139 + AUTS2 ENSG00000158321.18 Intron APP-01_05 1.0 10.76 -1.85 1.36
chr10 110728715 110728810 + RBM20 ENSG00000203867.8 Intron APP-01_05 0.45 6.43 -1.86 1.07
chr15 42414447 42414512 - ZNF106 ENSG00000103994.17 3' UTR APP-01_05 0.0 6.84 -1.86 1.07
chr7 129302391 129302467 + AHCYL2 ENSG00000158467.16 Intron APP-01_05 0.0 6.7 -1.86 1.07
chr7 155308877 155308911 + INSIG1 ENSG00000186480.13 3' UTR APP-01_05 0.27 6.17 -1.86 1.07
chr4 173333617 173333683 - HMGB2 ENSG00000164104.12 CDS APP-01_05 0.0 7.45 -1.88 1.06
chr4 30721828 30721851 - AC098595.1 ENSG00000286596.1 Other APP-01_05 0.5 8.5 -1.89 1.25
chr1 220058635 220058704 - BPNT1 ENSG00000162813.18 3' UTR APP-01_05 0.46 6.94 -1.89 1.09
chr3 47054612 47054687 - SETD2 ENSG00000181555.21 Intron APP-01_05 0.5 8.51 -1.9 1.27
chr11 73404460 73404523 - FAM168A ENSG00000054965.10 3' UTR APP-01_05 0.0 7.47 -1.9 1.11
chr2 134956983 134957045 + CCNT2 ENSG00000082258.13 3' UTR APP-01_05 0.45 7.45 -1.9 1.11
chr15 85548323 85548402 + AKAP13 ENSG00000170776.22 Intron APP-01_05 0.0 6.6 -1.91 1.13
chr16 24569310 24569388 + RBBP6 ENSG00000122257.20 CDS APP-01_05 1.0 11.12 -1.92 1.46
chr11 95804506 95804581 + CEP57 ENSG00000166037.11 Intron APP-01_05 0.0 7.26 -1.93 1.14
chr9 32862444 32862516 - AL157884.3 ENSG00000236796.1 Other APP-01_05 0.0 7.31 -1.94 1.15
chr18 39387882 39387961 - MIR924HG ENSG00000267374.2 Other APP-01_05 0.5 8.73 -1.95 1.3
chr4 151297336 151297406 - SH3D19 ENSG00000109686.18 Intron APP-01_05 0.0 6.87 -1.95 1.16
chr13 45982050 45982120 - ZC3H13 ENSG00000123200.16 Intron APP-01_05 0.0 7.17 -1.96 1.16
chr11 86042503 86042550 - PICALM ENSG00000073921.18 Intron APP-01_05 0.5 9.83 -1.97 1.36
chr11 117032618 117032706 - SIK3 ENSG00000160584.16 Intron APP-01_05 0.0 7.41 -1.98 1.19
chr19 2835663 2835731 + ZNF554 ENSG00000172006.12 3' UTR APP-01_05 0.0 7.74 -1.98 1.19
chr4 90193864 90193981 + CCSER1 ENSG00000184305.15 Intron APP-01_05 0.49 7.89 -1.98 1.19
chr13 113626987 113627066 + TFDP1 ENSG00000198176.13 Intron APP-01_05 0.0 7.34 -1.99 1.21
chr17 7320755 7320819 - NEURL4 ENSG00000215041.10 CDS APP-01_05 0.48 7.97 -2.0 1.23
chr17 15663327 15663395 - TRIM16 ENSG00000221926.13 Intron APP-01_05 0.0 7.94 -2.0 1.23
chr2 66569362 66569448 + MEIS1 ENSG00000143995.20 3' UTR APP-01_05 0.0 7.43 -2.0 1.23
chr22 44850703 44850790 + PRR5-ARHGAP8|ARHGAP8 ENSG00000241484.9||ENSG00000248405.10 Intron APP-01_05 0.0 7.0 -2.0 1.23
chr1 50921058 50921149 - FAF1 ENSG00000185104.20 Intron APP-01_05 0.0 7.8 -2.02 1.24
chr4 487291 487356 - ZNF721 ENSG00000182903.16 Intron APP-01_05 0.0 7.72 -2.02 1.24
chr1 26790604 26790687 + PIGV ENSG00000060642.11 Intron APP-01_05 0.5 9.81 -2.02 1.43
chr2 32736746 32736818 + TTC27 ENSG00000018699.13 CDS APP-01_05 1.5 14.75 -2.03 1.87
chr3 13405837 13405961 - NUP210 ENSG00000132182.12 Intron APP-01_05 0.5 10.45 -2.03 1.43
chr2 135534654 135534710 + R3HDM1 ENSG00000048991.16 Intron APP-01_05 0.0 7.42 -2.05 1.24
chr11 69064752 69064819 + TPCN2 ENSG00000162341.18 Intron APP-01_05 0.5 10.48 -2.06 1.47
chr1 77801153 77801213 + MIGA1 ENSG00000180488.15 Intron APP-01_05 0.74 8.14 -2.07 1.29
chr10 125098311 125098396 - CTBP2 ENSG00000175029.17 Intron APP-01_05 1.0 12.55 -2.07 1.72
chr13 50097163 50097230 + DLEU1 ENSG00000176124.15 Other APP-01_05 0.89 10.31 -2.08 1.46
chr22 41621988 41622064 + XRCC6 ENSG00000196419.13 CDS APP-01_05 0.0 7.99 -2.08 1.31
chr2 99355364 99355430 + EIF5B ENSG00000158417.11 Intron APP-01_05 0.0 8.48 -2.09 1.32
chr16 30429940 30430009 - DCTPP1 ENSG00000179958.9 CDS APP-01_05 0.0 8.37 -2.1 1.33
chr1 108787482 108787557 + STXBP3 ENSG00000116266.11 Intron APP-01_05 1.5 15.91 -2.12 2.05
chr17 40302825 40302907 + CDC6 ENSG00000094804.12 3' UTR APP-01_05 0.0 8.02 -2.12 1.33
chr3 61597627 61597708 + PTPRG ENSG00000144724.20 Intron APP-01_05 0.0 8.11 -2.12 1.33
chr3 183920043 183920104 - ABCC5 ENSG00000114770.17 3' UTR APP-01_05 0.93 8.27 -2.13 1.32
chr13 48391244 48391311 + RB1 ENSG00000139687.16 Intron APP-01_05 0.0 8.94 -2.13 1.36
chr6 127312676 127312702 - ECHDC1 ENSG00000093144.19 Intron APP-01_05 0.0 8.22 -2.16 1.4
chr11 14296303 14296380 - RRAS2 ENSG00000133818.14 Intron APP-01_05 0.0 8.76 -2.17 1.41
chr10 119852301 119852376 - MCMBP ENSG00000197771.13 Intron APP-01_05 0.98 8.27 -2.19 1.42
chr1 234606604 234606728 - IRF2BP2 ENSG00000168264.10 3' UTR APP-01_05 4.02 26.97 -2.21 3.1
chr1 43958962 43959031 + IPO13 ENSG00000117408.11 Intron APP-01_05 0.87 11.71 -2.22 1.73
chrX 140766068 140766138 + LINC00632 ENSG00000203930.12 Other APP-01_05 0.0 9.04 -2.22 1.48
chr5 131643457 131643554 - FNIP1 ENSG00000217128.12 3' UTR APP-01_05 0.82 11.77 -2.23 1.74
chr17 30816903 30816988 - CRLF3 ENSG00000176390.12 Intron APP-01_05 1.46 14.31 -2.25 2.07
chr5 78216078 78216175 - AP3B1 ENSG00000132842.14 CDS APP-01_05 0.5 12.3 -2.28 1.82
chr7 105272098 105272169 - SRPK2 ENSG00000135250.17 Intron APP-01_05 0.5 12.44 -2.29 1.83
chr21 25891790 25891803 - APP ENSG00000142192.21 CDS APP-01_05 0.6 9.25 -2.3 1.58
chr14 30568041 30568134 + G2E3 ENSG00000092140.16 Intron APP-01_05 0.0 9.1 -2.3 1.47
chr5 137946035 137946101 - FAM13B ENSG00000031003.10 Intron APP-01_05 1.5 18.27 -2.3 2.48
chrX 47176562 47176644 + RBM10 ENSG00000182872.16 CDS APP-01_05 0.5 12.81 -2.3 1.85
chr10 5807565 5807642 - GDI2 ENSG00000057608.17 Intron APP-01_05 0.0 9.82 -2.3 1.59
chr17 29573481 29573557 - GIT1 ENSG00000108262.16 3' UTR APP-01_05 0.5 13.32 -2.37 1.99
chr1 99923925 99924013 + AGL ENSG00000162688.17 3' UTR APP-01_05 1.99 19.41 -2.38 2.69
chr3 49683428 49683498 + APEH ENSG00000164062.13 3' UTR APP-01_05 0.5 13.76 -2.41 2.03
chr10 110931339 110931426 + SHOC2 ENSG00000108061.12 Intron APP-01_05 0.0 10.89 -2.41 1.74
chr2 233291851 233291896 + ATG16L1 ENSG00000085978.22 Intron APP-01_05 0.79 13.52 -2.42 2.08
chr3 72431466 72431541 - RYBP ENSG00000163602.10 Intron APP-01_05 1.0 16.85 -2.42 2.44
chr4 102796087 102796168 - UBE2D3 ENSG00000109332.20 3' UTR APP-01_05 1.5 19.09 -2.42 2.71
chr1 21172327 21172412 - EIF4G3 ENSG00000075151.20 Intron APP-01_05 0.5 13.85 -2.43 2.09
chr17 16441873 16441957 + SNHG29 ENSG00000175061.18 Other APP-01_05 0.42 10.76 -2.43 1.7
chr17 7402779 7402850 - TMEM256-PLSCR3 ENSG00000262481.5 Other APP-01_05 0.0 10.43 -2.44 1.78
chr6 118059325 118059400 + SLC35F1 ENSG00000196376.11 Intron APP-01_05 0.0 10.94 -2.46 1.77
chr2 64016144 64016205 - VPS54 ENSG00000143952.20 Intron APP-01_05 1.5 20.25 -2.46 2.91
chr15 92949266 92949360 + CHD2 ENSG00000173575.22 Intron APP-01_05 11.95 81.13 -2.46 8.02
chr6 156809793 156809934 + ARID1B ENSG00000049618.24 Intron APP-01_05 2.5 26.72 -2.47 3.45
chr6 72721971 72722035 + KCNQ5 ENSG00000185760.16 Intron APP-01_05 0.5 14.28 -2.48 2.19
chr11 74998163 74998218 + NEU3 ENSG00000162139.10 Intron APP-01_05 0.0 10.61 -2.49 1.86
chr17 75778002 75778075 - H3-3B ENSG00000132475.10 3' UTR APP-01_05 2.25 23.98 -2.54 3.34
chr3 154279788 154279855 - DHX36 ENSG00000174953.14 Intron APP-01_05 2.0 25.23 -2.56 3.48
chr8 17567600 17567700 + SLC7A2 ENSG00000003989.18 3' UTR APP-01_05 1.91 21.55 -2.57 3.12
chr2 96299015 96299109 - SNRNP200 ENSG00000144028.15 Intron APP-01_05 0.47 12.26 -2.6 2.04
chr15 36941385 36941508 - MEIS2 ENSG00000134138.20 Intron APP-01_05 0.48 12.09 -2.62 2.05
chr10 100540631 100540718 + HIF1AN ENSG00000166135.14 CDS APP-01_05 5.98 50.61 -2.62 5.68
chr14 102681766 102681850 + RCOR1 ENSG00000089902.10 Intron APP-01_05 0.0 12.83 -2.65 2.12
chr4 186620235 186620328 - FAT1 ENSG00000083857.14 CDS APP-01_05 0.0 12.96 -2.66 2.11
chr8 43174398 43174466 + HGSNAT ENSG00000165102.15 Intron APP-01_05 1.94 22.98 -2.67 3.42
chr19 10172041 10172134 - DNMT1 ENSG00000130816.16 Intron APP-01_05 0.45 13.19 -2.68 2.19
chr7 87163330 87163453 + DMTF1 ENSG00000135164.19 5' UTR APP-01_05 2.49 27.29 -2.7 3.84
chr17 31852104 31852107 - COPRS ENSG00000172301.11 3' UTR APP-01_05 0.32 13.45 -2.75 2.32
chrX 45749310 45749386 - MIR222HG ENSG00000270069.1 Other APP-01_05 2.48 28.86 -2.75 3.96
chr10 74874262 74874332 + KAT6B ENSG00000156650.14 Intron APP-01_05 0.5 17.58 -2.79 2.86
chr11 18082067 18082158 - SAAL1 ENSG00000166788.10 Intron APP-01_05 0.5 18.2 -2.8 2.94
chr4 20620247 20620268 + SLIT2 ENSG00000145147.20 3' UTR APP-01_05 1.61 21.75 -2.82 3.48
chr1 44776543 44776551 + SNORD46 ENSG00000200913.1 Other APP-01_05 0.16 14.82 -2.87 2.54
chr14 35604878 35604959 - RALGAPA1 ENSG00000174373.16 Intron APP-01_05 1.5 28.94 -2.91 4.07
chr8 94789749 94789843 + DPY19L4 ENSG00000156162.16 CDS APP-01_05 5.97 58.8 -2.95 7.09
chr7 99559613 99559701 + ZNF655 ENSG00000197343.11 Intron APP-01_05 0.49 16.23 -2.95 2.72
chr10 100536595 100536668 + HIF1AN ENSG00000166135.14 CDS APP-01_05 0.5 20.85 -2.96 3.31
chr1 22095724 22095810 + CDC42 ENSG00000070831.17 3' UTR APP-01_05 0.0 16.32 -2.96 2.74
chr1 178157015 178157115 + RASAL2 ENSG00000075391.17 Intron APP-01_05 0.0 16.51 -3.02 2.87
chr1 70354247 70354301 - ANKRD13C ENSG00000118454.13 CDS APP-01_05 1.0 26.03 -3.02 3.93
chrX 73827255 73827339 - XIST ENSG00000229807.12 Other APP-01_05 23.7 227.11 -3.02 24.66
chr4 20620207 20620247 + SLIT2 ENSG00000145147.20 3' UTR APP-01_05 4.49 54.83 -3.08 6.95
chr11 931071 931139 + AP2A2 ENSG00000183020.14 Intron APP-01_05 0.0 17.49 -3.08 3.03
chr21 25891803 25891859 - APP ENSG00000142192.21 CDS APP-01_05 0.78 17.34 -3.08 3.03
chr9 124857885 124857983 - RPL35 ENSG00000136942.15 CDS APP-01_05 6.87 75.64 -3.1 9.38
chr21 46289883 46290035 + YBEY ENSG00000182362.14 Intron APP-01_05 0.48 18.38 -3.12 3.12
chrX 78118198 78118286 + PGK1 ENSG00000102144.15 Intron APP-01_05 1.0 27.72 -3.12 4.28
chr7 155301614 155301687 + INSIG1 ENSG00000186480.13 CDS APP-01_05 0.5 23.67 -3.16 3.92
chr19 2271464 2271528 + OAZ1 ENSG00000104904.12 CDS APP-01_05 0.0 18.98 -3.17 3.2
chr2 151420181 151420283 + RIF1 ENSG00000080345.18 CDS APP-01_05 2.47 38.45 -3.18 5.29
chr21 15734170 15734245 + USP25 ENSG00000155313.15 Intron APP-01_05 0.0 18.83 -3.19 3.23
chr12 76046708 76046799 - NAP1L1 ENSG00000187109.15 3' UTR APP-01_05 0.5 24.16 -3.19 4.0
chr2 96186476 96186551 - STARD7 ENSG00000084090.13 3' UTR APP-01_05 0.58 27.02 -3.34 4.38
chr10 28589423 28589493 + WAC ENSG00000095787.23 Intron APP-01_05 0.5 27.29 -3.35 4.41
chr16 78223832 78223919 + WWOX ENSG00000186153.17 Intron APP-01_05 0.0 22.97 -3.48 4.0
chr2 208288850 208288949 + PIKFYVE ENSG00000115020.17 Intron APP-01_05 1.99 44.33 -3.55 6.29
chr1 44776489 44776499 + SNORD46 ENSG00000200913.1 Other APP-01_05 0.27 24.67 -3.55 4.25
chr3 23338118 23338209 + UBE2E2 ENSG00000182247.10 Intron APP-01_05 0.0 25.76 -3.58 4.35
chr10 94565769 94565841 + HELLS ENSG00000119969.15 Intron APP-01_05 2.5 60.19 -3.62 8.33
chr11 2394089 2394172 + CD81 ENSG00000110651.12 CDS APP-01_05 0.0 27.24 -3.65 4.5
chr7 157388947 157389033 + DNAJB6 ENSG00000105993.15 Intron APP-01_05 1.0 41.29 -3.69 6.07
chr11 65502085 65502153 + MALAT1 ENSG00000251562.8 Other APP-01_05 0.34 31.27 -3.85 4.98
chr2 85542315 85542417 + MAT2A ENSG00000168906.13 CDS APP-01_05 6.48 131.22 -3.89 17.52
chr7 152148059 152148159 - KMT2C ENSG00000055609.19 CDS APP-01_05 0.5 53.93 -4.27 7.37
chr1 236816447 236816526 + MTR ENSG00000116984.14 CDS APP-01_05 0.5 56.17 -4.35 7.8
chr5 37198680 37198770 - CPLANE1 ENSG00000197603.15 CDS APP-01_05 0.97 57.39 -4.38 8.04
chr6 127312561 127312666 - ECHDC1 ENSG00000093144.19 Intron APP-01_05 5.5 178.23 -4.44 22.44
chr3 45394467 45394520 + LARS2 ENSG00000011376.12 CDS APP-01_05 0.17 56.15 -4.69 7.78
chr1 44776503 44776543 + SNORD46 ENSG00000200913.1 Other APP-01_05 1.02 92.29 -4.78 11.75
chr3 45394520 45394565 + LARS2 ENSG00000011376.12 CDS APP-01_05 0.34 62.31 -4.84 8.43
chr17 31852107 31852177 - COPRS ENSG00000172301.11 CDS APP-01_05 2.74 126.31 -4.85 16.0
chr19 22694813 22694861 - AC024563.1 ENSG00000268981.5 Other APP-01_05 97.2 3781.51 -5.1 241.14

This following files are provided along with this analysis:

File Description
fastq.gz Gzipped raw sequencing reads in FASTQ format.
ago2.bam BAM file containing unique AGO2 eCLIP sequence alignments to the genome. Reads aligned to repetitive elements were filtered out and PCR duplicates were removed.
ago2.pos.bw Bigwig file containing RPM normalized AGO2 eCLIP reads aligned to the + strand.
ago2.neg.bw Bigwig file containing RPM normalized AGO2 eCLIP reads aligned to the - strand.
ago2_clusters.bed Input normalized file of AGO2 eCLIP clusters, with tab-separated columns as follows: Chromosome, Start position, Stop position, -log10(P-value), Log2 fold enrichment in eCLIP vs. input, Strand (+ or -).
ago2_idr_peaks.bed This file is only included if the experiment contained 2 or 3 replicate samples. AGO2 eCLIP peaks found to be reproducible and significant in all replicates with the same format as above.
mir_targets.bam Bam file containing unique miRNA target sequence alignments to the genome, after the miRNA portion of the reads has been trimmed. Nonchimeric reads were filtered out and PCR duplicates were removed.
mir_targets.pos.bw Bigwig file containing RPM normalized miRNA target reads aligned to the + strand.
mir_targets.neg.bw Bigwig file containing RPM normalized miRNA target reads aligned to the - strand.
mir_targets_clusters.bed Locations of miRNA target read clusters called using the CLIPper algorithm with the following tab-separated columns: Chromosome, Start position, Stop position, miRNA, RPM coverage of miRNA target reads, Strand.
mir_targets_reproducible_clusters.bed This file is only included if the experiment contained replicate samples. miRNA target clusters found to be reproducible and significant in all replicates with the same format as above.
report.html HTML report containing plots, enriched GO terms and KEGG pathways, HOMER motif analysis, and repetitive element mapping information for enriched peaks.