This interactive report provides an overview of eRibo Pro 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 eRibo Pro experiment please contact us.
Experiment Summary
This report summarizes an eRibo Pro experiment where HEK293 cells were treated with either Torin, a translation inhibitor, or a DMSO control. Full methods details are available upon request. The following samples are included in the analysis:
Sample group | RPF | RNA-Seq |
---|---|---|
Treated | RPF_Torin_Rep1, RPF_Torin_Rep2 | RNASeq_Torin_Rep1, RNASeq_Torin_Rep2 |
Untreated | RPF_Untreated_Rep1, RPF_Untreated_Rep2 | RNASeq_Untreated_Rep1, RNASeq_Untreated_Rep2 |
This tab summarizes quality control metrics for the RNA-Seq and ribosome protected footprint (RPF) libraries.
Quality Control Metrics
The following table shows important quality control metrics for each sample. Two libraries are made for each sample, one containing ribosome protected footprints (RPFs) and one from the whole transcriptome (RNA-Seq). For each sample ("Sample"), two rows are included that list the metrics for each library. The identity of the library is included in the "Library" column. The following columns describe the processing of the libraries:
- Initial reads: the number of sequenced reads for each library.
- % 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.
- % 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.
- % 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.
- % 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.
- Final reads: this column lists the number of uniquely mapped, deduplicated reads that were used for this analysis.
Sample | Library | Initial reads | % Pass trim | % Repetitive elements | % Uniquely aligned to the genome | % PCR duplicates | Final reads |
---|---|---|---|---|---|---|---|
RPF_Torin_Rep1 | RPF | 106,375,285 | 87.89 | 42.8 | 62.79 | 28.12 | 24,135,715 |
RPF_Torin_Rep2 | RPF | 96,961,854 | 87.17 | 44.95 | 63.18 | 25.37 | 21,938,930 |
RNASeq_Torin_Rep1 | RNA-Seq | 67,148,202 | 99.17 | 14.51 | 85.78 | 19.02 | 39,548,918 |
RNASeq_Torin_Rep2 | RNA-Seq | 66,921,389 | 99.06 | 14.71 | 85.81 | 20.07 | 38,778,304 |
RPF_Untreated_Rep1 | RPF | 100,440,695 | 88.91 | 37.24 | 63.61 | 27.77 | 25,748,524 |
RPF_Untreated_Rep2 | RPF | 92,265,022 | 89.5 | 36.5 | 62.03 | 27.44 | 23,598,327 |
RNASeq_Untreated_Rep1 | RNA-Seq | 76,244,094 | 99.38 | 15.04 | 85.77 | 20.40 | 43,943,636 |
RNASeq_Untreated_Rep2 | RNA-Seq | 62,247,281 | 99.38 | 15.22 | 85.97 | 19.87 | 36,129,570 |
Gene Coverage Range
Pairs of ribosome protected footprint (RPF) and RNA-Seq libraries were prepared from each sample. The plot below shows the distribution of RPM (reads per million) normalized gene counts in each of the libraries.
RPF Periodicity
This plot shows the location of scaled read ends that have been corrected for their estimated P-site (the second binding site for tRNA in the ribosome) from the ribosome protected footprint (RPF) libraries. This correction is to show where ribosomes are directly binding, as the sequenced read ends have an overhang past the ribosome complex. RPF libraries are expected to show a trinucleotide periodicity.
This tab shows the identified differential genes from the RNA-Seq libraries. The comparison for this analysis is Treated (RNASeq_Torin_Rep1, RNASeq_Torin_Rep2) over Untreated (RNASeq_Untreated_Rep1, RNASeq_Untreated_Rep2). All analyses on this tab were performed on a whole gene level.
RNA-Seq Volcano Plot
The plot below shows a comparison between fold change and significance in RNA-Seq libraries from Treated and Untreated samples. The x-axis shows the fold change ("log2(fold change)") and the x-axis shows significance("-log10(adjusted p-value)"). Red (increased in Treated) and teal (decreased in Treated) dots represent genes that are significantly different between conditions. Gray dots represent genes that are not significant. Hovering your mouse over the volcano plot below will show the gene name, Ensembl gene ID, -log10(adjusted p-value), and log2(fold change) for each point.
RNA-Seq Differential Expression Table
We used a differential expression analysis tool called DESeq2 to compare Treated and Untreated samples. The table below lists significantly up- and downregulated genes along with associated DESeq2 metrics. Genes were identified as significantly different if they have an adjusted p-value cutoff < 0.1 (after multiple testing adjustment) and a log2(fold change) > 1 or < -1. Only genes annotated as protein coding or lncRNA are included in the table. Multimapping reads were removed before the analysis, which may reduce estimates for genes with high pseudogenization or duplication events.
The following columns are included in the table:
- Ensembl ID: Ensembl's unique identifier and version of a gene
- Gene name: common name for the gene.
- baseMean: average DESeq2-normalized counts across all samples and all conditions
- log2(fold change): log2-transformed ratio of expression between the two conditions
- log2(SE): log2-transformed standard error
- P-value: unadjusted measure of significance
- Adjusted p-value: false discovery rate (FDR) adjusted significance
- Up/downregulated: classification of expression change based on the significance and fold change
A copy of the table can be downloaded by clicking the button of the desired format (CSV, Excel or PDF)
Ensembl ID | Gene name | baseMean | log2(fold change) | log2(SE) | P-value | Adjusted p-value | Up/downregulated |
---|---|---|---|---|---|---|---|
ENSG00000135114.14 | OASL | 7.83 | 2.8 | 1.04 | 6.81E-03 | 9.60E-02 | Upregulated |
RNA-Seq Gene Enrichment
The GO term and KEGG pathway enrichment analyses show which functional gene categories and pathways are enriched in up- and downregulated genes from the volcano plot above. GO and KEGG analyses were performed with clusterProfiler's enrichGO and enrichKEGG functions. Within each domain are boxes for each gene ontology or KEGG term, and within each term are the contributing genes. The color of the gene box is the log2 fold change between the two sample conditions while the size of the gene box is based off the -log10(adjusted p-value) for the comparison. The color and size of the term boxes are based off the sum of all contributing genes. You can click on individual GO categories and subcategories to zoom and view their results in more detail. Clicking on the "Analysis" heading will restore the plot to its original appearance. For each gene box, the hover will show the adjusted p-value for the performed comparison and log2 fold change of the listed gene. For each term, the hover will show the adjusted p-value for the enrichment analysis and the average fold-change of all genes included in the box. Significance and fold changes are not provided for the domains.
This tab shows the identified differential genes from the ribosome protected footprint (RPF) libraries. The comparison for this analysis is Treated (RPF_Torin_Rep1, RPF_Torin_Rep2) over Untreated (RPF_Untreated_Rep1, RPF_Untreated_Rep2). All analyses on this tab were performed on a whole gene level.
RPF Volcano Plot
The plot below shows a comparison between fold change and significance in RPF libraries from Treated and Untreated samples. The x-axis shows the fold change ("log2(fold change)") and the x-axis shows significance("-log10(adjusted p-value)"). Red (increased in Treated) and teal (decreased in Treated) dots represent genes that are significantly different between conditions. Gray dots represent genes that are not significant. Hovering your mouse over the volcano plot below will show the gene name, Ensembl gene ID, -log10(adjusted p-value), and log2(fold change) for each point.
RPF Differential Expression Table
We used a differential expression analysis tool called DESeq2 to compare Treated and Untreated samples. The table below lists significantly up- and downregulated genes along with associated DESeq2 metrics. Genes were identified as significantly different if they have an adjusted p-value cutoff < 0.1 (after multiple testing adjustment) and a log2(fold change) > 1 or < -1. Only genes annotated as protein coding or lncRNA are included in the table Multimapping reads were removed before the analysis, which may reduce estimates for genes with high pseudogenization or duplication events.
The following columns are included in the table:
- Ensembl ID: Ensembl's unique identifier and version of a gene
- Gene name: common name for the gene.
- baseMean: average DESeq2-normalized counts across all samples and all conditions
- log2(fold change): log2-transformed ratio of expression between the two conditions
- log2(SE): log2-transformed standard error
- P-value: unadjusted measure of significance
- Adjusted p-value: false discovery rate (FDR) adjusted significance
- Up/downregulated: classification of expression change based on the significance and fold change
A copy of the table can be downloaded by clicking the button of the desired format (CSV, Excel or PDF)
Ensembl ID | Gene name | baseMean | log2(fold change) | log2(SE) | P-value | Adjusted p-value | Up/downregulated |
---|---|---|---|---|---|---|---|
ENSG00000005022.6 | SLC25A5 | 15767.99 | -1.49 | 0.03 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000005206.17 | SPPL2B | 519.23 | -1.09 | 0.12 | 4.60E-21 | 1.24E-19 | Downregulated |
ENSG00000008988.11 | RPS20 | 693.25 | -1.73 | 0.1 | 2.07E-62 | 2.19E-60 | Downregulated |
ENSG00000009307.17 | CSDE1 | 10876.56 | -1.06 | 0.04 | 1.32E-181 | 6.45E-179 | Downregulated |
ENSG00000011028.14 | MRC2 | 443.39 | -1.48 | 0.13 | 3.32E-30 | 1.39E-28 | Downregulated |
ENSG00000026025.16 | VIM | 21849.69 | -1.82 | 0.03 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000030582.18 | GRN | 6762.64 | -1.02 | 0.04 | 3.80E-120 | 1.03E-117 | Downregulated |
ENSG00000049860.14 | HEXB | 2003.02 | -1.06 | 0.06 | 3.84E-66 | 4.24E-64 | Downregulated |
ENSG00000050555.19 | LAMC3 | 221.58 | -1.31 | 0.17 | 4.66E-14 | 7.76E-13 | Downregulated |
ENSG00000054793.14 | ATP9A | 504.87 | -1.13 | 0.11 | 9.79E-23 | 2.90E-21 | Downregulated |
ENSG00000060138.13 | YBX3 | 3519.84 | -1.16 | 0.05 | 3.28E-118 | 8.58E-116 | Downregulated |
ENSG00000062524.16 | LTK | 47.02 | -1.11 | 0.36 | 2.17E-03 | 8.53E-03 | Downregulated |
ENSG00000062582.14 | MRPS24 | 1752.56 | -1.04 | 0.07 | 1.04E-56 | 9.41E-55 | Downregulated |
ENSG00000063177.13 | RPL18 | 8962.39 | -1.34 | 0.08 | 2.72E-57 | 2.53E-55 | Downregulated |
ENSG00000064666.15 | CNN2 | 441.0 | -1.19 | 0.12 | 9.94E-22 | 2.79E-20 | Downregulated |
ENSG00000065150.21 | IPO5 | 9578.8 | -1.22 | 0.04 | 7.38E-228 | 5.49E-225 | Downregulated |
ENSG00000065427.15 | KARS1 | 4534.75 | -1.05 | 0.05 | 1.03E-114 | 2.47E-112 | Downregulated |
ENSG00000065978.19 | YBX1 | 2029.87 | -1.43 | 0.06 | 1.39E-113 | 3.23E-111 | Downregulated |
ENSG00000070756.17 | PABPC1 | 3828.69 | -3.04 | 0.06 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000070915.10 | SLC12A3 | 23.21 | -2.08 | 0.56 | 2.02E-04 | 1.01E-03 | Downregulated |
ENSG00000071082.11 | RPL31 | 1681.15 | -1.71 | 0.07 | 7.57E-130 | 2.33E-127 | Downregulated |
ENSG00000074181.9 | NOTCH3 | 1162.44 | -1.62 | 0.08 | 4.44E-81 | 6.60E-79 | Downregulated |
ENSG00000078053.17 | AMPH | 309.12 | -1.11 | 0.15 | 4.82E-14 | 8.01E-13 | Downregulated |
ENSG00000079739.17 | PGM1 | 3214.18 | -1.21 | 0.05 | 2.26E-116 | 5.82E-114 | Downregulated |
ENSG00000083845.9 | RPS5 | 5307.49 | -1.74 | 0.05 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000089157.16 | RPLP0 | 1420.84 | -1.97 | 0.08 | 7.95E-140 | 2.68E-137 | Downregulated |
ENSG00000089327.15 | FXYD5 | 605.87 | -1.31 | 0.11 | 2.71E-33 | 1.27E-31 | Downregulated |
ENSG00000089351.15 | GRAMD1A | 787.12 | -1.13 | 0.1 | 2.95E-31 | 1.28E-29 | Downregulated |
ENSG00000092445.12 | TYRO3 | 306.87 | -1.12 | 0.15 | 3.89E-14 | 6.50E-13 | Downregulated |
ENSG00000095585.18 | BLNK | 525.67 | -1.06 | 0.12 | 4.06E-18 | 9.10E-17 | Downregulated |
ENSG00000099617.4 | EFNA2 | 32.9 | -1.07 | 0.44 | 1.41E-02 | 4.38E-02 | Downregulated |
ENSG00000100258.18 | LMF2 | 1219.01 | -1.16 | 0.08 | 1.89E-48 | 1.38E-46 | Downregulated |
ENSG00000100979.15 | PLTP | 1937.65 | -1.06 | 0.07 | 6.06E-57 | 5.52E-55 | Downregulated |
ENSG00000101210.13 | EEF1A2 | 2576.73 | -1.09 | 0.06 | 3.16E-72 | 4.03E-70 | Downregulated |
ENSG00000101444.13 | AHCY | 6402.39 | -1.61 | 0.04 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000101680.16 | LAMA1 | 1632.35 | -1.04 | 0.07 | 2.42E-52 | 1.94E-50 | Downregulated |
ENSG00000101911.13 | PRPS2 | 2295.79 | -1.24 | 0.06 | 2.91E-98 | 5.56E-96 | Downregulated |
ENSG00000103226.19 | NOMO3 | 118.42 | -1.07 | 0.23 | 3.19E-06 | 2.17E-05 | Downregulated |
ENSG00000103257.9 | SLC7A5 | 4714.69 | -1.04 | 0.05 | 8.38E-116 | 2.12E-113 | Downregulated |
ENSG00000103512.16 | NOMO1 | 478.99 | -1.33 | 0.12 | 3.47E-29 | 1.40E-27 | Downregulated |
ENSG00000103811.18 | CTSH | 769.89 | -1.03 | 0.09 | 1.61E-27 | 6.04E-26 | Downregulated |
ENSG00000104529.19 | EEF1D | 2369.02 | -1.28 | 0.06 | 3.15E-102 | 6.54E-100 | Downregulated |
ENSG00000104774.13 | MAN2B1 | 700.73 | -1.27 | 0.1 | 2.69E-34 | 1.30E-32 | Downregulated |
ENSG00000104853.16 | CLPTM1 | 2267.38 | -2.08 | 0.07 | 9.32E-223 | 6.59E-220 | Downregulated |
ENSG00000104863.12 | LIN7B | 34.48 | -1.02 | 0.42 | 1.56E-02 | 4.79E-02 | Downregulated |
ENSG00000105193.9 | RPS16 | 6212.19 | -1.33 | 0.04 | 3.31E-203 | 1.95E-200 | Downregulated |
ENSG00000105372.8 | RPS19 | 4108.77 | -1.5 | 0.05 | 2.07E-215 | 1.39E-212 | Downregulated |
ENSG00000105409.19 | ATP1A3 | 1712.31 | -1.04 | 0.07 | 1.04E-56 | 9.39E-55 | Downregulated |
ENSG00000105429.13 | MEGF8 | 1270.38 | -1.01 | 0.08 | 1.20E-39 | 6.83E-38 | Downregulated |
ENSG00000105649.10 | RAB3A | 150.9 | -1.12 | 0.2 | 4.54E-08 | 4.00E-07 | Downregulated |
ENSG00000105726.17 | ATP13A1 | 1833.11 | -1.1 | 0.07 | 1.25E-61 | 1.28E-59 | Downregulated |
ENSG00000106554.13 | CHCHD3 | 2869.09 | -1.3 | 0.05 | 8.30E-124 | 2.44E-121 | Downregulated |
ENSG00000107331.18 | ABCA2 | 505.21 | -1.16 | 0.12 | 5.01E-22 | 1.44E-20 | Downregulated |
ENSG00000108107.15 | RPL28 | 2701.12 | -1.75 | 0.06 | 7.81E-187 | 4.09E-184 | Downregulated |
ENSG00000109475.17 | RPL34 | 1049.96 | -1.24 | 0.08 | 4.54E-49 | 3.38E-47 | Downregulated |
ENSG00000109971.14 | HSPA8 | 12607.21 | -1.85 | 0.04 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000111640.15 | GAPDH | 18332.79 | -2.08 | 0.03 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000112333.12 | NR2E1 | 30.6 | 1.02 | 0.45 | 2.39E-02 | 6.86E-02 | Upregulated |
ENSG00000113504.21 | SLC12A7 | 619.07 | -1.09 | 0.1 | 2.37E-25 | 7.83E-24 | Downregulated |
ENSG00000114391.13 | RPL24 | 3787.34 | -1.09 | 0.05 | 1.26E-93 | 2.28E-91 | Downregulated |
ENSG00000115380.20 | EFEMP1 | 121.32 | -1.37 | 0.23 | 3.42E-09 | 3.48E-08 | Downregulated |
ENSG00000115457.10 | IGFBP2 | 1587.65 | -1.01 | 0.07 | 2.46E-45 | 1.68E-43 | Downregulated |
ENSG00000116251.11 | RPL22 | 295.95 | -1.29 | 0.15 | 1.14E-17 | 2.48E-16 | Downregulated |
ENSG00000116852.15 | KIF21B | 90.78 | -1.06 | 0.26 | 5.42E-05 | 3.05E-04 | Downregulated |
ENSG00000116962.15 | NID1 | 7915.94 | -1.05 | 0.04 | 5.62E-146 | 2.09E-143 | Downregulated |
ENSG00000118816.11 | CCNI | 2795.39 | -1.31 | 0.06 | 1.16E-123 | 3.35E-121 | Downregulated |
ENSG00000123143.13 | PKN1 | 1605.97 | -1.06 | 0.07 | 1.70E-53 | 1.42E-51 | Downregulated |
ENSG00000124155.19 | PIGT | 1648.45 | -1.06 | 0.07 | 5.57E-57 | 5.12E-55 | Downregulated |
ENSG00000125743.11 | SNRPD2 | 6913.68 | -1.14 | 0.04 | 2.94E-175 | 1.38E-172 | Downregulated |
ENSG00000125912.11 | NCLN | 1844.15 | -1.02 | 0.06 | 1.95E-58 | 1.89E-56 | Downregulated |
ENSG00000127022.16 | CANX | 19.08 | -1.51 | 0.59 | 9.86E-03 | 3.20E-02 | Downregulated |
ENSG00000129946.11 | SHC2 | 17.83 | -2.05 | 0.63 | 1.20E-03 | 5.08E-03 | Downregulated |
ENSG00000130005.13 | GAMT | 694.18 | -1.22 | 0.1 | 7.28E-35 | 3.60E-33 | Downregulated |
ENSG00000130203.10 | APOE | 404.69 | -1.15 | 0.13 | 1.88E-18 | 4.30E-17 | Downregulated |
ENSG00000130226.17 | DPP6 | 14.24 | 1.47 | 0.68 | 3.06E-02 | 8.45E-02 | Upregulated |
ENSG00000130313.7 | PGLS | 973.5 | -1.03 | 0.09 | 4.72E-33 | 2.18E-31 | Downregulated |
ENSG00000130702.15 | LAMA5 | 1122.12 | -2.37 | 0.09 | 4.94E-155 | 2.11E-152 | Downregulated |
ENSG00000130707.18 | ASS1 | 570.96 | -1.27 | 0.11 | 1.89E-29 | 7.70E-28 | Downregulated |
ENSG00000130741.11 | EIF2S3 | 3265.55 | -1.18 | 0.06 | 2.69E-100 | 5.28E-98 | Downregulated |
ENSG00000131067.17 | GGT7 | 810.66 | -1.12 | 0.09 | 2.80E-33 | 1.31E-31 | Downregulated |
ENSG00000132182.13 | NUP210 | 6402.1 | -1.51 | 0.04 | 8.63E-279 | 8.71E-276 | Downregulated |
ENSG00000132470.14 | ITGB4 | 46.61 | -1.35 | 0.37 | 2.69E-04 | 1.31E-03 | Downregulated |
ENSG00000132938.22 | MTUS2 | 160.72 | -1.55 | 0.2 | 2.68E-14 | 4.52E-13 | Downregulated |
ENSG00000133243.10 | BTBD2 | 1031.28 | -1.6 | 0.09 | 4.95E-72 | 6.24E-70 | Downregulated |
ENSG00000134419.15 | RPS15A | 1302.7 | -1.33 | 0.08 | 3.32E-70 | 4.05E-68 | Downregulated |
ENSG00000135318.12 | NT5E | 22.03 | -1.53 | 0.55 | 5.28E-03 | 1.86E-02 | Downregulated |
ENSG00000135390.21 | ATP5MC2 | 7700.41 | -1.23 | 0.04 | 4.49E-209 | 2.89E-206 | Downregulated |
ENSG00000135636.16 | DYSF | 52.18 | -1.13 | 0.35 | 1.21E-03 | 5.11E-03 | Downregulated |
ENSG00000137154.13 | RPS6 | 10920.84 | -1.15 | 0.04 | 7.77E-229 | 6.10E-226 | Downregulated |
ENSG00000137404.15 | NRM | 579.59 | -1.1 | 0.11 | 1.28E-24 | 4.14E-23 | Downregulated |
ENSG00000137809.17 | ITGA11 | 9.99 | -1.81 | 0.82 | 2.84E-02 | 7.96E-02 | Downregulated |
ENSG00000138326.21 | RPS24 | 4573.99 | -1.35 | 0.05 | 1.55E-185 | 7.83E-183 | Downregulated |
ENSG00000138430.16 | OLA1 | 1055.64 | -1.06 | 0.08 | 1.90E-36 | 9.83E-35 | Downregulated |
ENSG00000138587.6 | MNS1 | 48.3 | -1.01 | 0.37 | 5.56E-03 | 1.95E-02 | Downregulated |
ENSG00000141756.19 | FKBP10 | 4646.94 | -1.0 | 0.05 | 1.94E-101 | 3.97E-99 | Downregulated |
ENSG00000142156.16 | COL6A1 | 2029.43 | -1.08 | 0.06 | 7.94E-69 | 9.36E-67 | Downregulated |
ENSG00000142173.16 | COL6A2 | 1126.38 | -1.38 | 0.08 | 3.40E-65 | 3.73E-63 | Downregulated |
ENSG00000142534.7 | RPS11 | 9056.51 | -1.45 | 0.04 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000142541.18 | RPL13A | 1326.28 | -1.24 | 0.08 | 3.18E-55 | 2.79E-53 | Downregulated |
ENSG00000142676.14 | RPL11 | 8389.68 | -1.32 | 0.04 | 1.70E-258 | 1.60E-255 | Downregulated |
ENSG00000142694.7 | EVA1B | 42.59 | -1.29 | 0.39 | 8.61E-04 | 3.76E-03 | Downregulated |
ENSG00000142798.20 | HSPG2 | 810.38 | -2.85 | 0.11 | 7.70E-154 | 3.20E-151 | Downregulated |
ENSG00000143162.9 | CREG1 | 885.39 | -1.1 | 0.09 | 2.24E-35 | 1.13E-33 | Downregulated |
ENSG00000143545.10 | RAB13 | 281.16 | -1.45 | 0.16 | 5.05E-20 | 1.27E-18 | Downregulated |
ENSG00000143632.15 | ACTA1 | 58.79 | -1.01 | 0.32 | 1.92E-03 | 7.64E-03 | Downregulated |
ENSG00000144713.13 | RPL32 | 1002.27 | -1.24 | 0.09 | 5.21E-43 | 3.35E-41 | Downregulated |
ENSG00000147100.11 | SLC16A2 | 789.28 | -1.07 | 0.09 | 2.48E-30 | 1.04E-28 | Downregulated |
ENSG00000147677.12 | EIF3H | 2835.09 | -1.14 | 0.06 | 2.42E-90 | 4.27E-88 | Downregulated |
ENSG00000148730.7 | EIF4EBP2 | 414.02 | -1.01 | 0.13 | 1.30E-14 | 2.24E-13 | Downregulated |
ENSG00000148908.15 | RGS10 | 272.01 | -1.55 | 0.16 | 4.77E-22 | 1.37E-20 | Downregulated |
ENSG00000149131.17 | SERPING1 | 43.14 | -1.08 | 0.39 | 5.27E-03 | 1.86E-02 | Downregulated |
ENSG00000149273.15 | RPS3 | 9771.89 | -1.08 | 0.04 | 4.32E-188 | 2.35E-185 | Downregulated |
ENSG00000151176.8 | PLBD2 | 1120.91 | -1.2 | 0.08 | 2.53E-51 | 1.94E-49 | Downregulated |
ENSG00000152936.11 | LMNTD1 | 36.55 | -1.32 | 0.43 | 2.02E-03 | 7.99E-03 | Downregulated |
ENSG00000156508.19 | EEF1A1 | 1056.15 | -1.73 | 0.09 | 1.74E-82 | 2.74E-80 | Downregulated |
ENSG00000159640.17 | ACE | 47.09 | -1.05 | 0.38 | 6.58E-03 | 2.25E-02 | Downregulated |
ENSG00000161016.18 | RPL8 | 27234.61 | -1.39 | 0.04 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000162244.12 | RPL29 | 2039.96 | -1.4 | 0.06 | 1.84E-113 | 4.20E-111 | Downregulated |
ENSG00000163453.11 | IGFBP7 | 33.7 | -1.32 | 0.44 | 2.44E-03 | 9.45E-03 | Downregulated |
ENSG00000163584.18 | RPL22L1 | 818.87 | -1.14 | 0.09 | 1.31E-35 | 6.68E-34 | Downregulated |
ENSG00000163754.18 | GYG1 | 958.24 | -1.02 | 0.09 | 3.94E-33 | 1.83E-31 | Downregulated |
ENSG00000163931.17 | TKT | 13153.7 | -1.41 | 0.04 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000164687.11 | FABP5 | 29.64 | -1.53 | 0.48 | 1.38E-03 | 5.71E-03 | Downregulated |
ENSG00000166033.13 | HTRA1 | 404.4 | -1.56 | 0.13 | 1.37E-31 | 5.99E-30 | Downregulated |
ENSG00000167123.20 | CERCAM | 528.44 | -1.07 | 0.11 | 2.04E-21 | 5.63E-20 | Downregulated |
ENSG00000167600.14 | CYP2S1 | 101.74 | -1.3 | 0.26 | 3.83E-07 | 2.96E-06 | Downregulated |
ENSG00000167658.16 | EEF2 | 48433.54 | -1.85 | 0.03 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000168268.11 | NT5DC2 | 2195.59 | -1.26 | 0.06 | 1.74E-95 | 3.23E-93 | Downregulated |
ENSG00000168356.13 | SCN11A | 7.46 | 2.29 | 1.01 | 2.25E-02 | 6.54E-02 | Upregulated |
ENSG00000169710.9 | FASN | 23941.3 | -1.12 | 0.03 | 2.74E-232 | 2.28E-229 | Downregulated |
ENSG00000169919.17 | GUSB | 1047.86 | -1.35 | 0.08 | 2.51E-60 | 2.48E-58 | Downregulated |
ENSG00000170275.15 | CRTAP | 1276.79 | -1.86 | 0.08 | 1.47E-120 | 4.08E-118 | Downregulated |
ENSG00000170889.14 | RPS9 | 2033.69 | -1.48 | 0.06 | 5.82E-125 | 1.75E-122 | Downregulated |
ENSG00000171298.13 | GAA | 2581.22 | -1.5 | 0.06 | 3.52E-151 | 1.38E-148 | Downregulated |
ENSG00000171551.12 | ECEL1 | 99.21 | -1.35 | 0.26 | 1.32E-07 | 1.08E-06 | Downregulated |
ENSG00000171858.18 | RPS21 | 3547.33 | -1.32 | 0.05 | 1.89E-151 | 7.64E-149 | Downregulated |
ENSG00000172487.4 | OR8J1 | 90.74 | -1.5 | 0.27 | 2.74E-08 | 2.50E-07 | Downregulated |
ENSG00000172889.16 | EGFL7 | 426.47 | -1.05 | 0.21 | 5.02E-07 | 3.80E-06 | Downregulated |
ENSG00000174080.12 | CTSF | 252.45 | -1.04 | 0.16 | 1.06E-10 | 1.30E-09 | Downregulated |
ENSG00000175018.13 | TEX36 | 3103.64 | -1.03 | 0.05 | 1.66E-80 | 2.42E-78 | Downregulated |
ENSG00000175390.15 | EIF3F | 833.2 | -1.39 | 0.09 | 1.70E-51 | 1.31E-49 | Downregulated |
ENSG00000177600.9 | RPLP2 | 5089.02 | -1.7 | 0.05 | 5.04E-303 | 5.48E-300 | Downregulated |
ENSG00000178403.4 | NEUROG2 | 18.01 | -1.59 | 0.61 | 9.34E-03 | 3.05E-02 | Downregulated |
ENSG00000179163.12 | FUCA1 | 725.12 | -1.02 | 0.1 | 1.69E-25 | 5.69E-24 | Downregulated |
ENSG00000180096.13 | SEPTIN1 | 66.45 | -1.22 | 0.31 | 9.12E-05 | 4.91E-04 | Downregulated |
ENSG00000180574.4 | EIF2S3B | 931.58 | -1.27 | 0.09 | 5.89E-49 | 4.36E-47 | Downregulated |
ENSG00000180879.14 | SSR4 | 6129.71 | -1.24 | 0.05 | 2.51E-159 | 1.11E-156 | Downregulated |
ENSG00000182054.10 | IDH2 | 1372.44 | -1.04 | 0.07 | 2.47E-45 | 1.68E-43 | Downregulated |
ENSG00000182774.13 | RPS17 | 1174.68 | -1.01 | 0.14 | 5.27E-13 | 8.10E-12 | Downregulated |
ENSG00000182871.16 | COL18A1 | 1370.02 | -1.98 | 0.08 | 1.37E-135 | 4.40E-133 | Downregulated |
ENSG00000184009.13 | ACTG1 | 43552.48 | -1.09 | 0.03 | 1.59E-235 | 1.40E-232 | Downregulated |
ENSG00000184110.15 | EIF3C | 67.14 | -1.42 | 0.31 | 5.79E-06 | 3.82E-05 | Downregulated |
ENSG00000185055.11 | EFCAB10 | 99.94 | -1.02 | 0.25 | 4.51E-05 | 2.57E-04 | Downregulated |
ENSG00000185164.15 | NOMO2 | 227.64 | -1.21 | 0.17 | 9.89E-13 | 1.49E-11 | Downregulated |
ENSG00000185624.16 | P4HB | 10363.63 | -1.08 | 0.04 | 2.09E-189 | 1.18E-186 | Downregulated |
ENSG00000186468.13 | RPS23 | 3272.44 | -1.32 | 0.05 | 2.37E-135 | 7.43E-133 | Downregulated |
ENSG00000186501.15 | TMEM222 | 3351.45 | -1.16 | 0.05 | 8.45E-101 | 1.68E-98 | Downregulated |
ENSG00000187109.15 | NAP1L1 | 3505.93 | -1.14 | 0.05 | 8.85E-111 | 1.95E-108 | Downregulated |
ENSG00000187244.12 | BCAM | 250.07 | -1.04 | 0.17 | 1.24E-09 | 1.32E-08 | Downregulated |
ENSG00000188157.15 | AGRN | 1026.98 | -2.14 | 0.09 | 9.33E-120 | 2.49E-117 | Downregulated |
ENSG00000188385.13 | JAKMIP3 | 7.4 | 2.3 | 1.01 | 2.32E-02 | 6.70E-02 | Upregulated |
ENSG00000188846.14 | RPL14 | 2589.2 | -1.46 | 0.06 | 8.19E-143 | 2.89E-140 | Downregulated |
ENSG00000196756.15 | SNHG17 | 4572.8 | 1.02 | 0.05 | 2.01E-84 | 3.23E-82 | Upregulated |
ENSG00000196787.4 | H2AC11 | 12007.95 | -1.06 | 0.04 | 8.47E-150 | 3.23E-147 | Downregulated |
ENSG00000196961.13 | AP2A1 | 2449.4 | -1.38 | 0.06 | 2.80E-122 | 7.90E-120 | Downregulated |
ENSG00000197111.16 | PCBP2 | 2110.66 | -1.18 | 0.06 | 3.65E-83 | 5.80E-81 | Downregulated |
ENSG00000197585.10 | ENSG00000197585 | 86.64 | -1.32 | 0.28 | 2.04E-06 | 1.42E-05 | Downregulated |
ENSG00000197756.10 | RPL37A | 4406.61 | -1.38 | 0.05 | 9.53E-163 | 4.34E-160 | Downregulated |
ENSG00000198673.11 | TAFA2 | 227.2 | -1.45 | 0.17 | 2.49E-17 | 5.31E-16 | Downregulated |
ENSG00000198755.11 | RPL10A | 2586.19 | -1.01 | 0.06 | 1.01E-70 | 1.24E-68 | Downregulated |
ENSG00000198816.7 | ZNF358 | 221.72 | -1.59 | 0.18 | 3.19E-18 | 7.18E-17 | Downregulated |
ENSG00000203907.10 | OOEP | 244.39 | -1.0 | 0.16 | 9.90E-10 | 1.07E-08 | Downregulated |
ENSG00000204390.10 | HSPA1L | 87.63 | -1.39 | 0.27 | 4.02E-07 | 3.09E-06 | Downregulated |
ENSG00000204628.12 | RACK1 | 40145.87 | -1.2 | 0.03 | 2.48E-307 | 2.92E-304 | Downregulated |
ENSG00000205846.4 | CLEC6A | 65.81 | -1.34 | 0.32 | 2.30E-05 | 1.37E-04 | Downregulated |
ENSG00000213585.11 | VDAC1 | 1209.53 | -1.17 | 0.08 | 9.47E-53 | 7.69E-51 | Downregulated |
ENSG00000213614.11 | HEXA | 2299.18 | -1.05 | 0.06 | 2.99E-71 | 3.71E-69 | Downregulated |
ENSG00000221983.8 | UBA52 | 5047.17 | -1.4 | 0.05 | 6.99E-208 | 4.30E-205 | Downregulated |
ENSG00000223598.1 | ENSG00000223598 | 30.84 | -1.71 | 0.48 | 3.38E-04 | 1.61E-03 | Downregulated |
ENSG00000224063.6 | CALCRL-AS1 | 60.63 | -1.46 | 0.34 | 1.34E-05 | 8.37E-05 | Downregulated |
ENSG00000225914.5 | TSBP1-AS1 | 18.71 | -1.38 | 0.59 | 1.86E-02 | 5.56E-02 | Downregulated |
ENSG00000226784.3 | PGAM4 | 64.77 | -1.08 | 0.31 | 4.99E-04 | 2.30E-03 | Downregulated |
ENSG00000227240.2 | ENSG00000227240 | 96.38 | -1.98 | 0.28 | 1.07E-12 | 1.60E-11 | Downregulated |
ENSG00000231090.2 | MIR4422HG | 83.0 | -1.1 | 0.29 | 1.60E-04 | 8.18E-04 | Downregulated |
ENSG00000231236.2 | ENSG00000231236 | 97.78 | -1.29 | 0.26 | 5.72E-07 | 4.29E-06 | Downregulated |
ENSG00000231427.6 | LINC01445 | 78.38 | -1.43 | 0.29 | 1.05E-06 | 7.58E-06 | Downregulated |
ENSG00000231718.1 | LINC02789 | 76.48 | -1.65 | 0.31 | 1.07E-07 | 8.89E-07 | Downregulated |
ENSG00000232712.6 | KIZ-AS1 | 9.76 | -1.99 | 0.86 | 2.08E-02 | 6.11E-02 | Downregulated |
ENSG00000233087.8 | RAB6D | 26.57 | 1.54 | 0.51 | 2.85E-03 | 1.08E-02 | Upregulated |
ENSG00000233420.2 | ENSG00000233420 | 121.01 | -1.57 | 0.24 | 4.26E-11 | 5.40E-10 | Downregulated |
ENSG00000235979.9 | ENSG00000235979 | 381.3 | -1.6 | 0.14 | 4.41E-31 | 1.89E-29 | Downregulated |
ENSG00000236830.8 | CBR3-AS1 | 24.88 | -1.38 | 0.51 | 7.14E-03 | 2.41E-02 | Downregulated |
ENSG00000240038.7 | AMY2B | 37.18 | -1.04 | 0.41 | 1.22E-02 | 3.88E-02 | Downregulated |
ENSG00000244509.4 | APOBEC3C | 19.1 | -1.34 | 0.61 | 2.68E-02 | 7.55E-02 | Downregulated |
ENSG00000249856.1 | ENSG00000249856 | 6.03 | -2.34 | 1.12 | 3.62E-02 | 9.67E-02 | Downregulated |
ENSG00000251600.8 | ENSG00000251600 | 18.12 | -1.34 | 0.61 | 2.89E-02 | 8.07E-02 | Downregulated |
ENSG00000253626.4 | EIF5AL1 | 724.43 | 1.18 | 0.1 | 1.20E-33 | 5.66E-32 | Upregulated |
ENSG00000254266.6 | PKIA-AS1 | 8.97 | -2.06 | 0.9 | 2.19E-02 | 6.37E-02 | Downregulated |
ENSG00000254772.10 | EEF1G | 1870.28 | -1.38 | 0.07 | 4.59E-98 | 8.65E-96 | Downregulated |
ENSG00000257407.1 | ENSG00000257407 | 36.69 | -1.34 | 0.42 | 1.32E-03 | 5.52E-03 | Downregulated |
ENSG00000257443.2 | LRIG3-DT | 8.51 | -1.98 | 0.92 | 3.03E-02 | 8.39E-02 | Downregulated |
ENSG00000257595.3 | LINC02356 | 86.96 | -1.62 | 0.28 | 4.68E-09 | 4.69E-08 | Downregulated |
ENSG00000259240.1 | MIR4713HG | 17.03 | 1.37 | 0.62 | 2.77E-02 | 7.79E-02 | Upregulated |
ENSG00000259843.2 | HEATR3-AS1 | 122.86 | -1.44 | 0.23 | 8.86E-10 | 9.64E-09 | Downregulated |
ENSG00000260983.2 | ENSG00000260983 | 73.14 | -1.2 | 0.32 | 1.59E-04 | 8.17E-04 | Downregulated |
ENSG00000270379.6 | HEATR9 | 41.59 | -1.18 | 0.42 | 4.64E-03 | 1.66E-02 | Downregulated |
ENSG00000277586.4 | NEFL | 1021.97 | -1.03 | 0.08 | 1.24E-35 | 6.32E-34 | Downregulated |
ENSG00000280560.3 | LINC01374 | 259.2 | -1.17 | 0.16 | 4.03E-13 | 6.27E-12 | Downregulated |
ENSG00000286377.1 | ENSG00000286377 | 54.46 | -1.48 | 0.35 | 2.18E-05 | 1.31E-04 | Downregulated |
ENSG00000288920.1 | RPSAP58 | 123.66 | -1.21 | 0.24 | 2.58E-07 | 2.03E-06 | Downregulated |
RPF Gene Enrichment
The GO term and KEGG pathway enrichment analyses show which functional gene categories and pathways are enriched in up- and downregulated genes from the volcano plot above. GO and KEGG analyses were performed with clusterProfiler's enrichGO and enrichKEGG functions. Within each domain are boxes for each gene ontology or KEGG term, and within each term are the contributing genes. The color of the gene box is the log2 fold change between the two sample conditions while the size of the gene box is based off the -log10(adjusted p-value) for the comparison. The color and size of the term boxes are based off the sum of all contributing genes. You can click on individual GO categories and subcategories to zoom and view their results in more detail. Clicking on the "Analysis" heading will restore the plot to its original appearance. For each gene box, the hover will show the adjusted p-value for the performed comparison and log2 fold change of the listed gene. For each term, the hover will show the adjusted p-value for the enrichment analysis and the average fold change of all genes included in the box. Significance and fold changes are not provided for the domains.
Two libraries were generated from each sample: a ribosome protected footprint (RPF) library and an RNA-Seq library. This tab shows the differences in ribosome occupancy (RO, also called translational efficiency or TE) between two sample groups, where RO is defined as the RPF counts over the RNA-Seq library counts for each gene. Please refer to the per sample reports for tables of RO values per gene for each individual sample. The comparison for this analysis is Treated over Untreated. All analyses on this tab were performed on a whole gene level.
RO Volcano Plot
The plot below shows a comparison between fold change and significance in ribosome occupancy between Treated and Untreated samples. The x-axis shows the fold change ("log2(fold change)") and the x-axis shows significance("-log10(adjusted p-value)"). Red (increased in Treated) and teal (decreased in Treated) dots represent genes that are significantly different between conditions. Gray dots represent genes that are not significant. Hovering your mouse over the volcano plot below will show the gene name, Ensembl gene ID, -log10(adjusted p-value), and log2(fold change) for each point.
Differential RO Table
We used a differential expression analysis tool called DESeq2 to compare Treated and Untreated samples. The table below lists the average normalized expression in the RPF and RNA-Seq libraries, as well as the fold change differences in ribosome occupancy (RO). The significance of the RO difference was determined by extending DESeq2 models to include RO fold change as an interaction between the experimental condition and the library type. The adjusted p-values of these interactions were used to identify genes with significant RO fold change between conditions. Genes with a RO log2(fold change) > 1 and an adjusted p-value < 0.1 were defined as having upregulated RO. Genes with a RO log 2(fold change) < -1 and an adjusted p-value < 0.1 were defined as having downregulated RO. Only genes annotated as protein coding or lncRNA are included in the table. Multimapping reads were removed before the analysis, which may reduce estimates for genes with high pseudogenization or duplication events.
The following columns are included in the table:
- Ensembl ID: Ensembl's unique identifier and version of a gene
- Gene name: common name for the gene.
- RPF baseMean: average DESeq2-normalized counts across all samples and all conditions in the RPF libraries
- RNA-Seq baseMean: average DESeq2-normalized counts across all samples and all conditions in the RNA-Seq libraries
- log2(fold change): log2-transformed ratio of RO between the two conditions
- log2(SE): log2-transformed standard error
- P-value: unadjusted measure of significance
- Adjusted p-value: false discovery rate (FDR) adjusted significance
- Up/downregulated: classification of expression change based on the significance and fold change
A copy of the table can be downloaded by clicking the button of the desired format (CSV, Excel or PDF)
Ensembl ID | Gene name | RPF baseMean | RNA-Seq baseMean | log2(fold change) | log2(SE) | P-value | Adjusted p-value | Up/downregulated |
---|---|---|---|---|---|---|---|---|
ENSG00000005022.6 | SLC25A5 | 15767.99 | 25540.59 | -1.57 | 0.04 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000005206.17 | SPPL2B | 519.23 | 2210.03 | -1.15 | 0.11 | 1.05E-26 | 4.85E-25 | Downregulated |
ENSG00000007952.18 | NOX1 | 445.69 | 21.53 | -1.03 | 0.36 | 4.41E-03 | 1.67E-02 | Downregulated |
ENSG00000008988.11 | RPS20 | 693.25 | 16209.14 | -1.75 | 0.08 | 4.95E-102 | 1.21E-99 | Downregulated |
ENSG00000009307.17 | CSDE1 | 10876.56 | 41535.6 | -1.1 | 0.04 | 1.06E-135 | 4.14E-133 | Downregulated |
ENSG00000011028.14 | MRC2 | 443.39 | 1684.73 | -1.34 | 0.12 | 1.03E-28 | 5.29E-27 | Downregulated |
ENSG00000026025.16 | VIM | 21849.69 | 37001.86 | -1.95 | 0.04 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000030582.18 | GRN | 6762.64 | 9163.74 | -1.07 | 0.06 | 2.40E-80 | 4.41E-78 | Downregulated |
ENSG00000037042.9 | TUBG2 | 186.72 | 331.16 | -1.02 | 0.21 | 8.08E-07 | 6.95E-06 | Downregulated |
ENSG00000050555.19 | LAMC3 | 221.58 | 967.67 | -1.34 | 0.16 | 1.60E-17 | 4.38E-16 | Downregulated |
ENSG00000060138.13 | YBX3 | 3519.84 | 10749.47 | -1.29 | 0.06 | 4.58E-120 | 1.41E-117 | Downregulated |
ENSG00000062582.14 | MRPS24 | 1752.56 | 3613.78 | -1.04 | 0.07 | 6.41E-46 | 5.70E-44 | Downregulated |
ENSG00000063177.13 | RPL18 | 8962.39 | 37218.15 | -1.39 | 0.06 | 3.81E-132 | 1.42E-129 | Downregulated |
ENSG00000064666.15 | CNN2 | 441.0 | 1535.7 | -1.37 | 0.12 | 1.91E-29 | 1.02E-27 | Downregulated |
ENSG00000065150.21 | IPO5 | 9578.8 | 34010.38 | -1.24 | 0.04 | 1.04E-178 | 7.01E-176 | Downregulated |
ENSG00000065427.15 | KARS1 | 4534.75 | 7711.71 | -1.08 | 0.05 | 5.27E-89 | 1.10E-86 | Downregulated |
ENSG00000065978.19 | YBX1 | 2029.87 | 16543.42 | -1.56 | 0.06 | 1.23E-144 | 5.80E-142 | Downregulated |
ENSG00000070756.17 | PABPC1 | 3828.69 | 22946.36 | -3.19 | 0.07 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000070915.10 | SLC12A3 | 23.21 | 57.48 | -2.26 | 0.57 | 8.37E-05 | 5.01E-04 | Downregulated |
ENSG00000071082.11 | RPL31 | 1681.15 | 27627.07 | -1.73 | 0.06 | 2.14E-171 | 1.32E-168 | Downregulated |
ENSG00000074181.9 | NOTCH3 | 1162.44 | 5034.18 | -1.44 | 0.08 | 5.93E-67 | 8.37E-65 | Downregulated |
ENSG00000078053.17 | AMPH | 309.12 | 840.18 | -1.11 | 0.15 | 5.06E-14 | 1.04E-12 | Downregulated |
ENSG00000079739.17 | PGM1 | 3214.18 | 3341.99 | -1.32 | 0.07 | 3.04E-76 | 5.31E-74 | Downregulated |
ENSG00000083444.17 | PLOD1 | 2493.85 | 5664.77 | -1.02 | 0.06 | 3.79E-59 | 4.74E-57 | Downregulated |
ENSG00000083845.9 | RPS5 | 5307.49 | 15880.77 | -1.86 | 0.06 | 1.07E-184 | 7.94E-182 | Downregulated |
ENSG00000089157.16 | RPLP0 | 1420.84 | 27604.25 | -1.96 | 0.07 | 4.13E-193 | 3.43E-190 | Downregulated |
ENSG00000089327.15 | FXYD5 | 605.87 | 326.12 | -1.41 | 0.16 | 4.27E-19 | 1.30E-17 | Downregulated |
ENSG00000089351.15 | GRAMD1A | 787.12 | 3250.5 | -1.16 | 0.09 | 9.39E-37 | 6.57E-35 | Downregulated |
ENSG00000092445.12 | TYRO3 | 306.87 | 2773.77 | -1.04 | 0.12 | 2.84E-18 | 8.12E-17 | Downregulated |
ENSG00000095585.18 | BLNK | 525.67 | 61.02 | -1.07 | 0.48 | 2.63E-02 | 7.43E-02 | Downregulated |
ENSG00000100258.18 | LMF2 | 1219.01 | 3196.65 | -1.15 | 0.09 | 9.14E-40 | 6.87E-38 | Downregulated |
ENSG00000100979.15 | PLTP | 1937.65 | 1352.72 | -1.07 | 0.09 | 1.77E-32 | 1.05E-30 | Downregulated |
ENSG00000101115.13 | SALL4 | 15.06 | 54.41 | -1.39 | 0.6 | 2.01E-02 | 5.95E-02 | Downregulated |
ENSG00000101210.13 | EEF1A2 | 2576.73 | 3504.41 | -1.15 | 0.07 | 1.76E-57 | 2.09E-55 | Downregulated |
ENSG00000101444.13 | AHCY | 6402.39 | 19356.3 | -1.62 | 0.05 | 1.37E-258 | 3.24E-255 | Downregulated |
ENSG00000101911.13 | PRPS2 | 2295.79 | 5349.74 | -1.27 | 0.06 | 1.09E-87 | 2.22E-85 | Downregulated |
ENSG00000102030.16 | NAA10 | 2457.38 | 5864.2 | -1.11 | 0.06 | 1.55E-70 | 2.35E-68 | Downregulated |
ENSG00000102882.12 | MAPK3 | 2181.6 | 3720.79 | -1.0 | 0.07 | 8.91E-50 | 8.69E-48 | Downregulated |
ENSG00000103226.19 | NOMO3 | 118.42 | 385.07 | -1.16 | 0.22 | 1.29E-07 | 1.27E-06 | Downregulated |
ENSG00000103257.9 | SLC7A5 | 4714.69 | 23564.67 | -1.17 | 0.05 | 8.14E-112 | 2.30E-109 | Downregulated |
ENSG00000103512.16 | NOMO1 | 478.99 | 2069.68 | -1.44 | 0.11 | 1.68E-40 | 1.29E-38 | Downregulated |
ENSG00000104529.19 | EEF1D | 2369.02 | 12291.52 | -1.3 | 0.06 | 2.35E-110 | 6.39E-108 | Downregulated |
ENSG00000104774.13 | MAN2B1 | 700.73 | 3267.34 | -1.26 | 0.1 | 1.14E-39 | 8.55E-38 | Downregulated |
ENSG00000104805.16 | NUCB1 | 2349.01 | 4210.73 | -1.03 | 0.07 | 4.04E-54 | 4.36E-52 | Downregulated |
ENSG00000104853.16 | CLPTM1 | 2267.38 | 4856.59 | -2.11 | 0.07 | 5.60E-195 | 5.28E-192 | Downregulated |
ENSG00000104863.12 | LIN7B | 34.48 | 158.25 | -1.27 | 0.37 | 6.68E-04 | 3.22E-03 | Downregulated |
ENSG00000105193.9 | RPS16 | 6212.19 | 23986.75 | -1.38 | 0.05 | 9.18E-175 | 5.90E-172 | Downregulated |
ENSG00000105220.17 | GPI | 15923.77 | 21990.9 | -1.11 | 0.04 | 4.16E-147 | 2.03E-144 | Downregulated |
ENSG00000105372.8 | RPS19 | 4108.77 | 53387.3 | -1.54 | 0.05 | 2.61E-249 | 5.26E-246 | Downregulated |
ENSG00000105409.19 | ATP1A3 | 1712.31 | 2338.45 | -1.12 | 0.08 | 1.43E-44 | 1.23E-42 | Downregulated |
ENSG00000105613.10 | MAST1 | 255.8 | 644.29 | -1.19 | 0.16 | 1.11E-13 | 2.19E-12 | Downregulated |
ENSG00000105726.17 | ATP13A1 | 1833.11 | 3612.85 | -1.24 | 0.08 | 9.48E-59 | 1.18E-56 | Downregulated |
ENSG00000105750.15 | ZNF85 | 17.95 | 59.29 | 1.19 | 0.55 | 3.16E-02 | 8.64E-02 | Upregulated |
ENSG00000106554.13 | CHCHD3 | 2869.09 | 37697.68 | -1.28 | 0.05 | 9.64E-144 | 4.39E-141 | Downregulated |
ENSG00000107331.18 | ABCA2 | 505.21 | 3521.37 | -1.13 | 0.1 | 1.76E-28 | 8.93E-27 | Downregulated |
ENSG00000108107.15 | RPL28 | 2701.12 | 3857.21 | -1.86 | 0.08 | 7.66E-130 | 2.58E-127 | Downregulated |
ENSG00000109475.17 | RPL34 | 1049.96 | 11351.07 | -1.16 | 0.16 | 1.80E-13 | 3.51E-12 | Downregulated |
ENSG00000109736.15 | MFSD10 | 909.03 | 2512.76 | -1.03 | 0.09 | 9.70E-31 | 5.42E-29 | Downregulated |
ENSG00000109971.14 | HSPA8 | 12607.21 | 24144.88 | -1.81 | 0.05 | 2.17E-245 | 3.40E-242 | Downregulated |
ENSG00000110700.7 | RPS13 | 5770.42 | 13991.37 | -1.08 | 0.05 | 4.10E-111 | 1.14E-108 | Downregulated |
ENSG00000111640.15 | GAPDH | 18332.79 | 60144.21 | -2.21 | 0.04 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000113504.21 | SLC12A7 | 619.07 | 1644.06 | -1.17 | 0.11 | 2.57E-27 | 1.24E-25 | Downregulated |
ENSG00000114391.13 | RPL24 | 3787.34 | 12611.47 | -1.09 | 0.06 | 1.50E-80 | 2.83E-78 | Downregulated |
ENSG00000115380.20 | EFEMP1 | 121.32 | 140.21 | -1.47 | 0.28 | 2.16E-07 | 2.05E-06 | Downregulated |
ENSG00000116251.11 | RPL22 | 295.95 | 6581.25 | -1.32 | 0.11 | 2.46E-33 | 1.50E-31 | Downregulated |
ENSG00000116852.15 | KIF21B | 90.78 | 638.26 | -1.13 | 0.21 | 1.18E-07 | 1.16E-06 | Downregulated |
ENSG00000116962.15 | NID1 | 7915.94 | 4966.17 | -1.19 | 0.05 | 3.55E-104 | 8.81E-102 | Downregulated |
ENSG00000118816.11 | CCNI | 2795.39 | 13964.69 | -1.34 | 0.06 | 2.12E-130 | 7.70E-128 | Downregulated |
ENSG00000123143.13 | PKN1 | 1605.97 | 6444.86 | -1.09 | 0.07 | 3.53E-58 | 4.30E-56 | Downregulated |
ENSG00000124155.19 | PIGT | 1648.45 | 3402.9 | -1.12 | 0.08 | 1.27E-47 | 1.18E-45 | Downregulated |
ENSG00000124721.18 | DNAH8 | 22.12 | 25.65 | 1.89 | 0.65 | 3.69E-03 | 1.43E-02 | Upregulated |
ENSG00000125743.11 | SNRPD2 | 6913.68 | 11660.02 | -1.2 | 0.05 | 2.50E-130 | 8.85E-128 | Downregulated |
ENSG00000125912.11 | NCLN | 1844.15 | 8915.02 | -1.14 | 0.06 | 8.39E-75 | 1.41E-72 | Downregulated |
ENSG00000127022.16 | CANX | 19.08 | 378.42 | -1.55 | 0.42 | 2.66E-04 | 1.41E-03 | Downregulated |
ENSG00000129946.11 | SHC2 | 17.83 | 191.59 | -2.03 | 0.5 | 5.69E-05 | 3.52E-04 | Downregulated |
ENSG00000130005.13 | GAMT | 694.18 | 1671.06 | -1.22 | 0.11 | 7.20E-31 | 4.05E-29 | Downregulated |
ENSG00000130203.10 | APOE | 404.69 | 471.25 | -1.12 | 0.16 | 1.30E-12 | 2.35E-11 | Downregulated |
ENSG00000130702.15 | LAMA5 | 1122.12 | 3547.06 | -2.23 | 0.1 | 2.36E-101 | 5.64E-99 | Downregulated |
ENSG00000130741.11 | EIF2S3 | 3265.55 | 14750.34 | -1.2 | 0.06 | 1.10E-99 | 2.59E-97 | Downregulated |
ENSG00000131067.17 | GGT7 | 810.66 | 2496.75 | -1.06 | 0.09 | 2.70E-29 | 1.43E-27 | Downregulated |
ENSG00000132182.13 | NUP210 | 6402.1 | 18103.29 | -1.49 | 0.05 | 5.35E-201 | 5.81E-198 | Downregulated |
ENSG00000132470.14 | ITGB4 | 46.61 | 97.78 | -1.22 | 0.39 | 1.90E-03 | 8.07E-03 | Downregulated |
ENSG00000132622.11 | HSPA12B | 8.72 | 17.57 | 2.57 | 0.94 | 6.28E-03 | 2.24E-02 | Upregulated |
ENSG00000132938.22 | MTUS2 | 160.72 | 74.7 | -1.87 | 0.31 | 9.04E-10 | 1.19E-08 | Downregulated |
ENSG00000133243.10 | BTBD2 | 1031.28 | 7551.91 | -1.49 | 0.08 | 1.62E-77 | 2.91E-75 | Downregulated |
ENSG00000134243.12 | SORT1 | 1665.91 | 7312.62 | -1.01 | 0.07 | 7.79E-54 | 8.28E-52 | Downregulated |
ENSG00000134419.15 | RPS15A | 1302.7 | 21125.17 | -1.36 | 0.06 | 2.66E-105 | 6.70E-103 | Downregulated |
ENSG00000135114.14 | OASL | 8.09 | 7.83 | -3.09 | 1.28 | 1.59E-02 | 4.88E-02 | Downregulated |
ENSG00000135318.12 | NT5E | 22.03 | 36.84 | -1.39 | 0.61 | 2.39E-02 | 6.87E-02 | Downregulated |
ENSG00000135390.21 | ATP5MC2 | 7700.41 | 3330.19 | -1.42 | 0.11 | 2.22E-36 | 1.54E-34 | Downregulated |
ENSG00000135519.8 | KCNH3 | 14.11 | 130.56 | 1.07 | 0.51 | 3.65E-02 | 9.74E-02 | Upregulated |
ENSG00000135525.19 | MAP7 | 618.26 | 953.17 | -1.04 | 0.12 | 3.16E-18 | 9.01E-17 | Downregulated |
ENSG00000137154.13 | RPS6 | 10920.84 | 73962.34 | -1.16 | 0.04 | 3.95E-148 | 1.99E-145 | Downregulated |
ENSG00000137818.12 | RPLP1 | 3743.15 | 19348.74 | -1.12 | 0.11 | 1.18E-22 | 4.37E-21 | Downregulated |
ENSG00000137955.16 | RABGGTB | 3797.06 | 4723.91 | -1.1 | 0.37 | 2.72E-03 | 1.10E-02 | Downregulated |
ENSG00000138326.21 | RPS24 | 4573.99 | 30286.86 | -1.38 | 0.05 | 5.47E-143 | 2.42E-140 | Downregulated |
ENSG00000138430.16 | OLA1 | 1055.64 | 5936.5 | -1.1 | 0.08 | 2.90E-47 | 2.67E-45 | Downregulated |
ENSG00000138587.6 | MNS1 | 48.3 | 110.67 | -1.24 | 0.38 | 9.69E-04 | 4.46E-03 | Downregulated |
ENSG00000142156.16 | COL6A1 | 2029.43 | 4374.82 | -1.1 | 0.07 | 8.15E-57 | 9.60E-55 | Downregulated |
ENSG00000142173.16 | COL6A2 | 1126.38 | 2585.99 | -1.34 | 0.09 | 1.34E-52 | 1.40E-50 | Downregulated |
ENSG00000142534.7 | RPS11 | 9056.51 | 24906.07 | -1.55 | 0.05 | 9.82E-194 | 8.68E-191 | Downregulated |
ENSG00000142541.18 | RPL13A | 1326.28 | 22369.08 | -1.21 | 0.06 | 1.74E-80 | 3.24E-78 | Downregulated |
ENSG00000142676.14 | RPL11 | 8389.68 | 28519.57 | -1.37 | 0.05 | 1.11E-185 | 8.74E-183 | Downregulated |
ENSG00000142694.7 | EVA1B | 42.59 | 199.33 | -1.24 | 0.34 | 2.54E-04 | 1.36E-03 | Downregulated |
ENSG00000142798.20 | HSPG2 | 810.38 | 1541.39 | -2.75 | 0.12 | 2.57E-113 | 7.42E-111 | Downregulated |
ENSG00000143162.9 | CREG1 | 885.39 | 4228.43 | -1.02 | 0.08 | 1.31E-35 | 8.71E-34 | Downregulated |
ENSG00000143545.10 | RAB13 | 281.16 | 650.24 | -1.3 | 0.17 | 4.86E-15 | 1.08E-13 | Downregulated |
ENSG00000144713.13 | RPL32 | 1002.27 | 24567.7 | -1.27 | 0.07 | 1.61E-74 | 2.67E-72 | Downregulated |
ENSG00000145592.14 | RPL37 | 3597.01 | 18465.23 | -1.04 | 0.05 | 1.41E-80 | 2.69E-78 | Downregulated |
ENSG00000147100.11 | SLC16A2 | 789.28 | 1376.47 | -1.04 | 0.1 | 2.10E-23 | 8.10E-22 | Downregulated |
ENSG00000147408.16 | CSGALNACT1 | 29.61 | 55.07 | 1.33 | 0.5 | 7.30E-03 | 2.54E-02 | Upregulated |
ENSG00000147677.12 | EIF3H | 2835.09 | 6959.06 | -1.23 | 0.07 | 1.22E-73 | 1.98E-71 | Downregulated |
ENSG00000148908.15 | RGS10 | 272.01 | 1633.75 | -1.47 | 0.14 | 2.40E-25 | 1.02E-23 | Downregulated |
ENSG00000149131.17 | SERPING1 | 43.14 | 22.92 | -1.39 | 0.57 | 1.40E-02 | 4.40E-02 | Downregulated |
ENSG00000149273.15 | RPS3 | 9771.89 | 44619.97 | -1.14 | 0.05 | 7.02E-139 | 2.92E-136 | Downregulated |
ENSG00000150990.9 | DHX37 | 1549.0 | 4721.29 | -1.04 | 0.07 | 4.18E-50 | 4.13E-48 | Downregulated |
ENSG00000151176.8 | PLBD2 | 1120.91 | 863.95 | -1.23 | 0.11 | 4.33E-30 | 2.39E-28 | Downregulated |
ENSG00000152936.11 | LMNTD1 | 36.55 | 94.35 | -1.28 | 0.45 | 4.36E-03 | 1.65E-02 | Downregulated |
ENSG00000156508.19 | EEF1A1 | 1056.15 | 21783.24 | -1.71 | 0.07 | 6.26E-130 | 2.16E-127 | Downregulated |
ENSG00000158246.8 | TENT5B | 48.32 | 64.17 | 1.05 | 0.44 | 1.80E-02 | 5.44E-02 | Upregulated |
ENSG00000159905.15 | ZNF221 | 70.96 | 87.89 | 1.05 | 0.36 | 3.99E-03 | 1.53E-02 | Upregulated |
ENSG00000160161.9 | CILP2 | 630.63 | 1304.98 | -1.13 | 0.12 | 1.55E-22 | 5.68E-21 | Downregulated |
ENSG00000161016.18 | RPL8 | 27234.61 | 68344.47 | -1.47 | 0.04 | 4.40E-243 | 6.21E-240 | Downregulated |
ENSG00000161970.15 | RPL26 | 2189.18 | 11883.86 | -1.08 | 0.07 | 3.52E-49 | 3.36E-47 | Downregulated |
ENSG00000162244.12 | RPL29 | 2039.96 | 17977.39 | -1.54 | 0.06 | 2.18E-155 | 1.19E-152 | Downregulated |
ENSG00000163453.11 | IGFBP7 | 33.7 | 73.49 | -1.01 | 0.46 | 2.75E-02 | 7.70E-02 | Downregulated |
ENSG00000163584.18 | RPL22L1 | 818.87 | 2710.91 | -1.4 | 0.09 | 5.76E-55 | 6.46E-53 | Downregulated |
ENSG00000163754.18 | GYG1 | 958.24 | 2380.57 | -1.1 | 0.09 | 9.14E-35 | 5.95E-33 | Downregulated |
ENSG00000163931.17 | TKT | 13153.7 | 25000.21 | -1.48 | 0.04 | 3.71E-248 | 6.55E-245 | Downregulated |
ENSG00000164304.16 | CAGE1 | 1528.85 | 2255.99 | -1.0 | 0.08 | 8.69E-35 | 5.68E-33 | Downregulated |
ENSG00000164687.11 | FABP5 | 29.64 | 472.69 | -1.62 | 0.35 | 3.01E-06 | 2.35E-05 | Downregulated |
ENSG00000164916.11 | FOXK1 | 1557.7 | 13365.88 | -1.08 | 0.06 | 3.26E-62 | 4.22E-60 | Downregulated |
ENSG00000165246.15 | NLGN4Y | 64.3 | 34.95 | 1.0 | 0.46 | 2.75E-02 | 7.71E-02 | Upregulated |
ENSG00000165863.17 | C10orf82 | 23.06 | 59.99 | -1.13 | 0.53 | 3.30E-02 | 8.95E-02 | Downregulated |
ENSG00000166033.13 | HTRA1 | 404.4 | 1012.74 | -1.28 | 0.14 | 2.36E-20 | 7.66E-19 | Downregulated |
ENSG00000167600.14 | CYP2S1 | 101.74 | 146.66 | -1.52 | 0.3 | 3.77E-07 | 3.41E-06 | Downregulated |
ENSG00000167658.16 | EEF2 | 48433.54 | 278130.39 | -1.82 | 0.04 | 0.00E+00 | 0.00E+00 | Downregulated |
ENSG00000167779.9 | IGFBP6 | 25.54 | 38.37 | -1.18 | 0.56 | 3.54E-02 | 9.49E-02 | Downregulated |
ENSG00000168268.11 | NT5DC2 | 2195.59 | 11664.66 | -1.28 | 0.06 | 5.45E-106 | 1.40E-103 | Downregulated |
ENSG00000168356.13 | SCN11A | 7.46 | 58.3 | 2.34 | 0.85 | 5.73E-03 | 2.07E-02 | Upregulated |
ENSG00000169252.6 | ADRB2 | 26.62 | 40.37 | 1.38 | 0.56 | 1.30E-02 | 4.14E-02 | Upregulated |
ENSG00000169710.9 | FASN | 23941.3 | 56069.4 | -1.5 | 0.05 | 5.88E-168 | 3.32E-165 | Downregulated |
ENSG00000169727.13 | GPS1 | 4930.73 | 10080.02 | -1.06 | 0.05 | 2.26E-93 | 4.99E-91 | Downregulated |
ENSG00000169919.17 | GUSB | 1047.86 | 2563.52 | -1.32 | 0.09 | 6.60E-52 | 6.71E-50 | Downregulated |
ENSG00000170275.15 | CRTAP | 1276.79 | 10492.7 | -1.77 | 0.07 | 1.11E-140 | 4.77E-138 | Downregulated |
ENSG00000170889.14 | RPS9 | 2033.69 | 23825.82 | -1.54 | 0.06 | 1.17E-170 | 6.91E-168 | Downregulated |
ENSG00000171298.13 | GAA | 2581.22 | 6283.4 | -1.48 | 0.06 | 3.46E-119 | 1.04E-116 | Downregulated |
ENSG00000171408.14 | PDE7B | 21.33 | 43.81 | 1.41 | 0.58 | 1.51E-02 | 4.68E-02 | Upregulated |
ENSG00000171551.12 | ECEL1 | 99.21 | 537.63 | -1.21 | 0.22 | 3.40E-08 | 3.66E-07 | Downregulated |
ENSG00000171858.18 | RPS21 | 3547.33 | 14803.38 | -1.43 | 0.06 | 5.44E-135 | 2.08E-132 | Downregulated |
ENSG00000172421.10 | EFCAB3 | 278.09 | 566.76 | -1.11 | 0.16 | 7.59E-12 | 1.28E-10 | Downregulated |
ENSG00000172487.4 | OR8J1 | 90.74 | 60.52 | -1.64 | 0.37 | 8.82E-06 | 6.33E-05 | Downregulated |
ENSG00000172733.12 | PURG | 35.33 | 310.55 | 1.23 | 0.34 | 2.61E-04 | 1.39E-03 | Upregulated |
ENSG00000172889.16 | EGFL7 | 426.47 | 1014.1 | -1.06 | 0.14 | 1.31E-13 | 2.58E-12 | Downregulated |
ENSG00000173638.19 | SLC19A1 | 2266.48 | 6945.38 | -1.03 | 0.07 | 2.58E-55 | 2.92E-53 | Downregulated |
ENSG00000175018.13 | TEX36 | 3103.64 | 470.03 | -1.17 | 0.1 | 2.09E-31 | 1.21E-29 | Downregulated |
ENSG00000175265.19 | GOLGA8A | 8.22 | 259.76 | 1.62 | 0.64 | 1.06E-02 | 3.48E-02 | Upregulated |
ENSG00000175390.15 | EIF3F | 833.2 | 2696.06 | -1.49 | 0.09 | 1.10E-58 | 1.35E-56 | Downregulated |
ENSG00000177600.9 | RPLP2 | 5089.02 | 20369.39 | -1.86 | 0.06 | 9.43E-203 | 1.11E-199 | Downregulated |
ENSG00000179148.10 | ALOXE3 | 49.56 | 64.83 | -1.07 | 0.42 | 9.68E-03 | 3.24E-02 | Downregulated |
ENSG00000180574.4 | EIF2S3B | 931.58 | 3439.25 | -1.26 | 0.09 | 5.32E-45 | 4.64E-43 | Downregulated |
ENSG00000180879.14 | SSR4 | 6129.71 | 9308.91 | -1.24 | 0.06 | 8.95E-107 | 2.39E-104 | Downregulated |
ENSG00000181163.14 | NPM1 | 3264.07 | 22829.57 | -1.04 | 0.05 | 1.15E-98 | 2.65E-96 | Downregulated |
ENSG00000182379.10 | NXPH4 | 448.89 | 421.36 | -1.07 | 0.15 | 1.92E-12 | 3.42E-11 | Downregulated |
ENSG00000182774.13 | RPS17 | 1174.68 | 17441.19 | -1.09 | 0.14 | 1.51E-14 | 3.19E-13 | Downregulated |
ENSG00000182871.16 | COL18A1 | 1370.02 | 6159.62 | -1.99 | 0.08 | 2.04E-136 | 8.23E-134 | Downregulated |
ENSG00000182979.18 | MTA1 | 2150.05 | 10102.19 | -1.03 | 0.06 | 3.02E-59 | 3.81E-57 | Downregulated |
ENSG00000184009.13 | ACTG1 | 43552.48 | 105957.4 | -1.2 | 0.04 | 3.43E-182 | 2.42E-179 | Downregulated |
ENSG00000184110.15 | EIF3C | 67.14 | 464.29 | -1.35 | 0.26 | 1.60E-07 | 1.54E-06 | Downregulated |
ENSG00000185055.11 | EFCAB10 | 99.94 | 3207.9 | -1.14 | 0.17 | 4.43E-11 | 6.83E-10 | Downregulated |
ENSG00000185164.15 | NOMO2 | 227.64 | 773.11 | -1.2 | 0.16 | 9.06E-14 | 1.81E-12 | Downregulated |
ENSG00000185624.16 | P4HB | 10363.63 | 22672.53 | -1.07 | 0.04 | 1.59E-128 | 5.23E-126 | Downregulated |
ENSG00000186468.13 | RPS23 | 3272.44 | 14755.15 | -1.44 | 0.06 | 1.02E-117 | 3.00E-115 | Downregulated |
ENSG00000186501.15 | TMEM222 | 3351.45 | 3735.91 | -1.3 | 0.07 | 3.64E-73 | 5.85E-71 | Downregulated |
ENSG00000186868.17 | MAPT | 483.96 | 1344.14 | -1.05 | 0.12 | 1.87E-19 | 5.79E-18 | Downregulated |
ENSG00000187109.15 | NAP1L1 | 3505.93 | 17854.58 | -1.19 | 0.06 | 1.97E-92 | 4.22E-90 | Downregulated |
ENSG00000187244.12 | BCAM | 250.07 | 351.77 | -1.12 | 0.2 | 4.72E-08 | 4.98E-07 | Downregulated |
ENSG00000188157.15 | AGRN | 1026.98 | 4325.16 | -2.2 | 0.09 | 7.12E-126 | 2.24E-123 | Downregulated |
ENSG00000188385.13 | JAKMIP3 | 7.4 | 29.05 | 2.12 | 0.95 | 2.61E-02 | 7.39E-02 | Upregulated |
ENSG00000188846.14 | RPL14 | 2589.2 | 18874.14 | -1.48 | 0.06 | 4.26E-155 | 2.23E-152 | Downregulated |
ENSG00000196961.13 | AP2A1 | 2449.4 | 6373.73 | -1.43 | 0.07 | 1.84E-94 | 4.12E-92 | Downregulated |
ENSG00000197111.16 | PCBP2 | 2110.66 | 2562.99 | -1.24 | 0.07 | 1.38E-61 | 1.77E-59 | Downregulated |
ENSG00000197585.10 | ENSG00000197585 | 86.64 | 109.75 | -1.42 | 0.33 | 1.49E-05 | 1.03E-04 | Downregulated |
ENSG00000197756.10 | RPL37A | 4406.61 | 15869.43 | -1.51 | 0.11 | 5.71E-41 | 4.53E-39 | Downregulated |
ENSG00000198673.11 | TAFA2 | 227.2 | 809.8 | -1.52 | 0.16 | 5.58E-21 | 1.87E-19 | Downregulated |
ENSG00000198755.11 | RPL10A | 2586.19 | 15375.4 | -1.12 | 0.06 | 3.00E-83 | 5.89E-81 | Downregulated |
ENSG00000198816.7 | ZNF358 | 221.72 | 1120.04 | -1.67 | 0.16 | 1.76E-25 | 7.57E-24 | Downregulated |
ENSG00000203907.10 | OOEP | 244.39 | 17358.24 | -1.04 | 0.11 | 1.04E-21 | 3.64E-20 | Downregulated |
ENSG00000204628.12 | RACK1 | 40145.87 | 104029.24 | -1.23 | 0.04 | 3.15E-214 | 4.05E-211 | Downregulated |
ENSG00000213585.11 | VDAC1 | 1209.53 | 7252.47 | -1.31 | 0.07 | 2.38E-78 | 4.32E-76 | Downregulated |
ENSG00000216490.4 | IFI30 | 1018.63 | 1077.01 | -1.05 | 0.11 | 5.46E-22 | 1.95E-20 | Downregulated |
ENSG00000221983.8 | UBA52 | 5047.17 | 22937.98 | -1.45 | 0.05 | 1.26E-199 | 1.27E-196 | Downregulated |
ENSG00000223561.8 | LINC03007 | 43.31 | 271.47 | -1.04 | 0.31 | 8.82E-04 | 4.12E-03 | Downregulated |
ENSG00000223598.1 | ENSG00000223598 | 30.84 | 496.67 | -1.76 | 0.35 | 4.28E-07 | 3.84E-06 | Downregulated |
ENSG00000224063.6 | CALCRL-AS1 | 60.63 | 45.54 | -1.43 | 0.47 | 2.16E-03 | 9.05E-03 | Downregulated |
ENSG00000225697.13 | SLC26A6 | 1183.32 | 1807.23 | -1.01 | 0.09 | 1.10E-27 | 5.42E-26 | Downregulated |
ENSG00000225806.8 | ENSG00000225806 | 6.92 | 169.98 | 1.85 | 0.72 | 1.02E-02 | 3.37E-02 | Upregulated |
ENSG00000226784.3 | PGAM4 | 64.77 | 22.76 | -1.42 | 0.51 | 5.39E-03 | 1.97E-02 | Downregulated |
ENSG00000227240.2 | ENSG00000227240 | 96.38 | 54.01 | -1.84 | 0.39 | 2.58E-06 | 2.04E-05 | Downregulated |
ENSG00000228412.9 | LNC-LBCS | 116.65 | 31.21 | -1.09 | 0.41 | 7.62E-03 | 2.64E-02 | Downregulated |
ENSG00000231090.2 | MIR4422HG | 83.0 | 46.87 | -1.02 | 0.42 | 1.58E-02 | 4.87E-02 | Downregulated |
ENSG00000231236.2 | ENSG00000231236 | 97.78 | 53.88 | -1.46 | 0.38 | 1.25E-04 | 7.18E-04 | Downregulated |
ENSG00000231427.6 | LINC01445 | 78.38 | 112.85 | -1.25 | 0.34 | 2.01E-04 | 1.10E-03 | Downregulated |
ENSG00000231718.1 | LINC02789 | 76.48 | 9.6 | -1.79 | 0.64 | 5.05E-03 | 1.86E-02 | Downregulated |
ENSG00000232019.1 | ENSG00000232019 | 110.76 | 225.32 | -1.07 | 0.25 | 2.20E-05 | 1.46E-04 | Downregulated |
ENSG00000232712.6 | KIZ-AS1 | 9.76 | 1305.94 | -1.97 | 0.58 | 7.18E-04 | 3.44E-03 | Downregulated |
ENSG00000233087.8 | RAB6D | 26.57 | 106.08 | 1.65 | 0.48 | 6.75E-04 | 3.25E-03 | Upregulated |
ENSG00000233420.2 | ENSG00000233420 | 121.01 | 16.47 | -1.92 | 0.49 | 9.67E-05 | 5.69E-04 | Downregulated |
ENSG00000233635.2 | ENSG00000233635 | 44.24 | 10.7 | 1.96 | 0.69 | 4.36E-03 | 1.65E-02 | Upregulated |
ENSG00000234390.4 | USP27X-DT | 12.8 | 69.24 | 1.46 | 0.61 | 1.62E-02 | 4.97E-02 | Upregulated |
ENSG00000235979.9 | ENSG00000235979 | 381.3 | 21873.64 | -1.62 | 0.1 | 3.85E-63 | 5.03E-61 | Downregulated |
ENSG00000236230.2 | ENSG00000236230 | 10.23 | 8.2 | 2.24 | 1.05 | 3.28E-02 | 8.92E-02 | Upregulated |
ENSG00000236830.8 | CBR3-AS1 | 24.88 | 88.01 | -1.26 | 0.48 | 8.47E-03 | 2.89E-02 | Downregulated |
ENSG00000237250.3 | ENSG00000237250 | 24.32 | 19.19 | -1.47 | 0.69 | 3.35E-02 | 9.07E-02 | Downregulated |
ENSG00000238083.9 | LRRC37A2 | 12.76 | 112.97 | -1.14 | 0.54 | 3.30E-02 | 8.95E-02 | Downregulated |
ENSG00000240038.7 | AMY2B | 37.18 | 408.8 | -1.21 | 0.31 | 1.10E-04 | 6.40E-04 | Downregulated |
ENSG00000242220.9 | TCP10L | 43.21 | 53.78 | 1.15 | 0.47 | 1.50E-02 | 4.65E-02 | Upregulated |
ENSG00000244038.11 | DDOST | 7917.92 | 10530.89 | -1.02 | 0.05 | 7.57E-95 | 1.73E-92 | Downregulated |
ENSG00000244184.1 | PELP1-DT | 20.46 | 87.91 | -1.07 | 0.49 | 2.83E-02 | 7.89E-02 | Downregulated |
ENSG00000244509.4 | APOBEC3C | 19.1 | 130.51 | -1.33 | 0.49 | 6.87E-03 | 2.41E-02 | Downregulated |
ENSG00000246273.9 | SBF2-AS1 | 45.7 | 297.54 | 1.14 | 0.3 | 1.37E-04 | 7.77E-04 | Upregulated |
ENSG00000248079.4 | DPH6-DT | 13.58 | 59.26 | -1.48 | 0.63 | 1.82E-02 | 5.48E-02 | Downregulated |
ENSG00000249738.10 | ENSG00000249738 | 18.29 | 125.48 | 1.27 | 0.48 | 7.85E-03 | 2.70E-02 | Upregulated |
ENSG00000249846.7 | LINC02021 | 9.83 | 86.8 | -1.35 | 0.63 | 3.23E-02 | 8.79E-02 | Downregulated |
ENSG00000249856.1 | ENSG00000249856 | 6.03 | 89.44 | -2.24 | 0.88 | 1.14E-02 | 3.72E-02 | Downregulated |
ENSG00000251165.6 | F11-AS1 | 12.29 | 69.22 | -1.36 | 0.61 | 2.66E-02 | 7.51E-02 | Downregulated |
ENSG00000253626.4 | EIF5AL1 | 724.43 | 2962.9 | 1.07 | 0.09 | 1.23E-31 | 7.15E-30 | Upregulated |
ENSG00000253669.4 | GASAL1 | 15.69 | 54.64 | 1.48 | 0.58 | 1.11E-02 | 3.63E-02 | Upregulated |
ENSG00000254772.10 | EEF1G | 1870.28 | 24608.23 | -1.39 | 0.06 | 4.43E-128 | 1.42E-125 | Downregulated |
ENSG00000254929.6 | ENSG00000254929 | 11.11 | 251.5 | 1.14 | 0.54 | 3.41E-02 | 9.19E-02 | Upregulated |
ENSG00000257407.1 | ENSG00000257407 | 36.69 | 37.55 | -1.41 | 0.54 | 9.48E-03 | 3.18E-02 | Downregulated |
ENSG00000257443.2 | LRIG3-DT | 8.51 | 13.53 | -2.13 | 1.01 | 3.52E-02 | 9.44E-02 | Downregulated |
ENSG00000257595.3 | LINC02356 | 86.96 | 49.81 | -1.5 | 0.4 | 1.96E-04 | 1.08E-03 | Downregulated |
ENSG00000259240.1 | MIR4713HG | 17.03 | 227.56 | 1.2 | 0.46 | 8.62E-03 | 2.93E-02 | Upregulated |
ENSG00000259803.8 | SLC22A31 | 26.99 | 78.38 | -1.13 | 0.47 | 1.69E-02 | 5.14E-02 | Downregulated |
ENSG00000259843.2 | HEATR3-AS1 | 122.86 | 17.17 | -2.04 | 0.48 | 2.25E-05 | 1.49E-04 | Downregulated |
ENSG00000260167.1 | ENSG00000260167 | 13.87 | 71.16 | -1.23 | 0.59 | 3.72E-02 | 9.88E-02 | Downregulated |
ENSG00000260983.2 | ENSG00000260983 | 73.14 | 1066.63 | -1.26 | 0.22 | 9.77E-09 | 1.13E-07 | Downregulated |
ENSG00000268089.3 | GABRQ | 16.13 | 51.42 | 1.42 | 0.59 | 1.62E-02 | 4.98E-02 | Upregulated |
ENSG00000270379.6 | HEATR9 | 41.59 | 94.43 | -1.24 | 0.42 | 3.32E-03 | 1.31E-02 | Downregulated |
ENSG00000277757.4 | ENSG00000277757 | 15.73 | 148.97 | -1.12 | 0.48 | 2.07E-02 | 6.09E-02 | Downregulated |
ENSG00000280560.3 | LINC01374 | 259.2 | 910.21 | -1.31 | 0.15 | 1.12E-17 | 3.08E-16 | Downregulated |
ENSG00000283777.2 | CANX | 15.73 | 1214.84 | -1.05 | 0.4 | 8.88E-03 | 3.01E-02 | Downregulated |
ENSG00000285372.1 | TNKS | 11.21 | 79.04 | -1.42 | 0.64 | 2.63E-02 | 7.44E-02 | Downregulated |
ENSG00000286046.1 | ENSG00000286046 | 8.01 | 58.6 | -2.07 | 0.77 | 6.96E-03 | 2.44E-02 | Downregulated |
ENSG00000286377.1 | ENSG00000286377 | 54.46 | 10.05 | -2.11 | 0.66 | 1.50E-03 | 6.55E-03 | Downregulated |
ENSG00000287526.1 | ENSG00000287526 | 59.86 | 14.44 | -1.57 | 0.63 | 1.23E-02 | 3.97E-02 | Downregulated |
ENSG00000288920.1 | RPSAP58 | 123.66 | 5253.49 | -1.23 | 0.16 | 2.24E-15 | 5.21E-14 | Downregulated |
RO Gene Enrichment
The GO term and KEGG pathway enrichment analyses show which functional gene categories and pathways are enriched in up- and downregulated genes from the volcano plot above. GO and KEGG analyses were performed with clusterProfiler's enrichGO and enrichKEGG functions. Within each domain are boxes for each gene ontology or KEGG term, and within each term are the contributing genes. The color of the gene box is the log2 fold change between the two sample conditions while the size of the gene box is based off the -log10(adjusted p-value) for the comparison. The color and size of the term boxes are based off the sum of all contributing genes. You can click on individual GO categories and subcategories to zoom and view their results in more detail. Clicking on the "Analysis" heading will restore the plot to its original appearance. For each gene box, the hover will show the adjusted p-value for the performed comparison and log2 fold change of the listed gene. For each term, the hover will show the adjusted p-value for the enrichment analysis and the average fold change of all genes included in the box. Significance and fold changes are not provided for the domains.
This tab summarizes analyses performed on per-transcript basis, including determining codon usage, the detection of open reading frames (ORFs), and the identification of stalls.
ORF Detection
Open reading frames (ORFs) are regions of transcripts that undergo active translation. This barplot shows high confidence ORFs that were identified with ribotricer. For this plot, we required that the read density per ORF was ≥ 10, the read count was ≥ 50, and the ratio of codons with reads to total codons was ≥ 0.75. There are four main categories of reported ORFs:
- Known: the ORF matches the annotated CDS
- Downstream: the ORF is downstream of the annotated CDS and does not overlap the CDS
- Upstream: the ORF is upstream of the annotated CDS and does not overlap the CDS
- Novel: the ORF is located on a lncRNA.
Codon Usage
This scatter plot shows the average codon usage in each condition, where codon usage is defined as the scaled normalized frequency that P-sites were found to be enriched in each codon. Each dot is a different codon, colored by if it is a start, stop, or an amino acid-coding codon. Off-diagonal codons can indicate differential codon usage between the two conditions. Codon usage was determined using riboWaltz. If a gene has multiple transcripts, only the longest transcript is included in this analysis.
Stall Identification
RPF reads will accumulate where a ribosome pauses or stalls during translation. This plot shows putative stall locations for each transcript in the transcriptome, where stalls were detected per Shalgi et al. through the use of a Kolmogorov-Smirnov (KS) test on normalized cumulative P-site densities. Please note, this analysis is performed per transcript so listed distances refer to the distance in transcriptomic space not genomic space. The stall summary in the hover indicates the magnitude of the stall preceding the listed position relative to the coverage after the identified site.
This following files are provided along with this analysis:
File extension | Description | Help |
---|---|---|
.fastq.gz | Gzipped raw sequencing reads in FASTQ format. |
A FASTQ file is a special type of text file that contains the sequencing data. Each read has four lines:
|
.bam .bai |
BAM file containing unique sequence alignments to the genome. Reads aligned to repetitive elements were filtered out and PCR duplicates were removed. Multimapping reads are not included. Alignment indexes are also provided, and are required for visualization in a genome viewer. |
A BAM file is a compressed binary file that contains a header (summarizing the entire file) and the aligned reads (read name, position, and alignment quality). |
.pos.bw .neg.bw |
Normalized bigwig file aligned to the positive (pos) and negative (neg) strand. |
A bigWig track is a binary file that is used to visualize genome alignments. You can view these tracks in a genome browser such as IGV. We provide the data separated by the associated strand. |
deseq_results.tsv | Results and statistics table for differential gene counts analysis using DESeq2 for the RPF and RNA-Seq libraries, and for the calculated ribosome occupancy. |
Differentials were identified per gene, and following columns are provided in the DESeq2 outputs:
|
translating_ORFs.tsv | Identified ORFs for each sample. |
Each sample was analyzed with ribotricer and the unprocessed output file is provided. The following columns are included:
|
codon_usage.tsv | Table containing normalized codon frequency and codon usage for each sample. |
Codon usage was determined using riboWaltz. If a gene has multiple transcripts, only the longest transcript is included in this analysis. The following columns are provided:
|
differential_stall.tsv | Table containing identified stalls within the Treated condition. |
Counts for each codon in each transcript were obtained with riboWaltz. A Kolmogorov-Smirnov test was performed to identify transcripts with putative stalls. The following columns are included:
|
differential_loading.tsv | Table containing transcripts with changes in 5' loading. |
Counts for each codon in each transcript were obtained with riboWaltz. Per Shalgi et al. counts were obtained in the first 16-195 bases of the CDS to the rest of the CDS. Counts were TPM normalized and the ratio between the beginning of the ORF and the end of the ORF was calculated. A pseudocount of 1 is added to both values to avoid divide by zero errors.
|
differential_readthrough.tsv | Table containing transcripts with changes in 3' readthrough. |
Counts for each codon in each transcript were obtained with riboWaltz. Per Dunn et al. counts from the CDS were obtained for +12 bases after the start codon and -15 bases from the stop codon, and 3' UTR counts were obtained for +9 bases after the stop codon. The listed regions were excluded to avoid read contributions from the expected start and stop codon enrichment. Counts were TPM normalized and the ratio between the 3' UTR and the CDS was calculated. A pseudocount of 1 is added to both values to avoid divide by zero errors.
|
report.html | Report comparing libraries from RPF and RNA-Seq libraries for a given sample. |
This interactive report summarizes information on a given sample for both the RNA-Seq and RPF libraries. The report can be viewed in an internet browser such as Google Chrome. |
summary.report.html | Summary report comparing samples from two different conditions. |
This interactive report summarizes information on the entire experiment. The report can be viewed in an internet browser such as Google Chrome. |