AARS
This analysis report summarizes AARS eCLIP data from ENCODE. The current tab provides an overview of the results, and the other tabs list identified peaks and motifs.
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Experiment Summary
| Experiment ID | File ID | Sample | Antibody source | Antibody ID | Antibody lot | Release date | Laboratory | Number of peaks |
|---|---|---|---|---|---|---|---|---|
| ENCSR825SVO | ENCFF128BDG | K562 | Bethyl Labs | A303-475A | 1 | 2016-04-26 | Gene Yeo, UCSD | 49 |
AARS Peak Assignments
The following plots show the assignment of peaks into different genic features:
Introns contain other subdivisions, please see the subsequent plot for a breakdown of those features.
This plot is interactive. You can hover over the bars to see the percentage and number of identified peaks. You can select which features to show by toggling the region names in the legend, and you can download the plot by moving your mouse to the top of the plot and clicking on the camera icon.
AARS Intron Assignments
The following plots show the assignment of peaks into different intronic features:
- 5’ splice site: the peak is within the first 100 bp of an intron (5’ to 3’ direction
- 3’ splice site: the peak is within the last 100 bp of an intron (5’ to 3’ direction)
- Proximal intron: the peak is within 100 bp to 500 bp of the nearest exon
- Distal intron: greater than 500 bp away from the nearest exon
This plot is interactive. You can hover over the bars to see the percentage and number of identified peaks. You can select which features to show by toggling the region names in the legend, and you can download the plot by moving your mouse to the top of the plot and clicking on the camera icon.
AARS Motifs
The following plot shows a summary of the top five motifs by significance in each experiment. Motifs were detected with varying length parameters, you may observe a similar motif with different number of bases included multiple times. A motif present in more peaks and with a higher significance will be in the upper right quadrant of the plot, while the lower left quadrant has motifs that are less significant and in fewer peaks.
This plot is interactive. You can hover over the bars to see the percentage and number of identified peaks. You can select which features to show by toggling the region names in the legend, and you can download the plot by moving your mouse to the top of the plot and clicking on the camera icon.
The following table contains called AARS peaks. To identify peaks, clusters (regions of read enrichment) in the immunoprecipitated (IP) samples were found using the peak calling tool CLIPper. To account for background signal, a cluster was identified as a peak if the log2 fold enrichment over input was ≥ 3 and the p-value ≤ 0.001.
Peaks were annotated using transcript information from GENCODE. Each annotated peak is labeled with specific annotation feature types, first split by coding and non-coding transcripts, then by transcript regions, and then by intron/exon proximity regions. For overlapping transcript regions, the following hierarchy is used to label the region: coding sequence (CDS), 5’ or 3’ untranslated region (UTR), intron, non-coding exon, then non-coding intron. For example, if a peak is in the 5’ UTR of one transcript that overlaps an intron of another transcript, the peak region will be labeled as 5’ UTR. All gene annotations are from GENCODE release v41.
The following columns are included in the table:
- Chromosome: chromosome where the peak is located.
- Peak start: start coordinate for the peak.
- Peak stop: stop coordinate for the peak.
- Strand: strand of DNA where the peak was called.
- -log10(p-value): significance of the cluster call by CLIPper. Values are log transformed so a larger number indicates a greater significance.
- log2(fold change): log transformed fold enrichment of the IP signal over a matched input.
- Gene name: name (symbol) of the gene that overlaps with the peak.
- Ensembl ID: unique identifer of the gene that overlaps with the peak.
- Feature: which part of the listed gene overlaps with the peak.
Please note, this table is interactive. You can search for specific genes or features, and can sort the table by any of the columns.
ENCSR825SVO (K562) Peaks
| Chromosome | Peak start | Peak stop | Strand | -log10(p-value) | log2(fold change) | Gene name | Ensembl ID | Feature |
|---|---|---|---|---|---|---|---|---|
| chr21 | 8,401,778 | 8,401,840 | + | 53.762 | 8.606 | ENSG00000280441 | ENSG00000280441.3 | ncRNA |
| chr19 | 4,035,770 | 4,035,869 | + | 22.039 | 5.130 | PIAS4 | ENSG00000105229.7 | Distal intron |
| chr11 | 93,721,690 | 93,721,719 | + | 16.285 | 4.164 | SCARNA9 | ENSG00000254911.3 | ncRNA |
| chr19 | 2,270,224 | 2,270,300 | + | 8.836 | 3.171 | OAZ1 | ENSG00000104904.12 | 5' UTR |
| chrM | 12,167 | 12,208 | + | 400.000 | 4.086 | MT-TH|MT-TS2 | ENSG00000210176.1||ENSG00000210184.1 | ncRNA |
| chr16 | 2,760,062 | 2,760,143 | + | 10.191 | 3.491 | SRRM2 | ENSG00000167978.17 | Proximal intron |
| chr2 | 148,881,731 | 148,881,770 | - | 400.000 | 3.751 | ENSG00000289474 | ENSG00000289474.2 | ncRNA |
| chrM | 14,351 | 14,374 | - | 67.720 | 5.199 | MT-ND6 | ENSG00000198695.2 | CDS |
| chrM | 14,321 | 14,351 | - | 64.246 | 5.145 | MT-ND6 | ENSG00000198695.2 | CDS |
| chrM | 14,313 | 14,321 | - | 45.293 | 4.976 | MT-ND6 | ENSG00000198695.2 | CDS |
| chrM | 14,374 | 14,402 | - | 41.138 | 4.838 | MT-ND6 | ENSG00000198695.2 | CDS |
| chr8 | 9,770,984 | 9,771,045 | + | 13.714 | 6.975 | TNKS | ENSG00000173273.16 | Distal intron |
| chr19 | 2,270,084 | 2,270,156 | + | 11.835 | 4.324 | OAZ1 | ENSG00000104904.12 | Proximal intron |
| chr2 | 96,894,241 | 96,894,287 | - | 17.739 | 4.838 | FAM178B | ENSG00000168754.15 | Proximal intron |
| chrM | 624 | 643 | + | 49.346 | 3.767 | MT-TF | ENSG00000210049.1 | ncRNA |
| chrM | 4,291 | 4,329 | + | 400.000 | 5.302 | MT-TI | ENSG00000210100.1 | ncRNA |
| chr11 | 65,425,001 | 65,425,114 | + | 83.199 | 3.321 | NEAT1 | ENSG00000245532.11 | ncRNA |
| chr11 | 65,422,993 | 65,423,040 | + | 400.000 | 3.986 | NEAT1 | ENSG00000245532.11 | ncRNA |
| chr11 | 65,422,971 | 65,422,993 | + | 400.000 | 3.577 | NEAT1 | ENSG00000245532.11 | ncRNA |
| chrM | 1,523 | 1,562 | + | 400.000 | 3.112 | MT-RNR1 | ENSG00000211459.2 | ncRNA |
| chrM | 4,456 | 4,459 | + | 400.000 | 6.473 | MT-TM | ENSG00000210112.1 | ncRNA |
| chrM | 4,417 | 4,444 | + | 400.000 | 5.268 | MT-TM | ENSG00000210112.1 | ncRNA |
| chr3 | 160,514,906 | 160,514,909 | - | 17.764 | 6.892 | SCARNA7 | ENSG00000238741.1 | ncRNA |
| chr13 | 91,348,191 | 91,348,263 | + | 11.952 | 3.726 | MIR17HG | ENSG00000215417.13 | ncRNA |
| chr21 | 8,218,740 | 8,218,767 | + | 42.271 | 7.415 | ENSG00000278996 | ENSG00000278996.1 | ncRNA |
| chr21 | 8,218,767 | 8,218,781 | + | 400.000 | 7.385 | ENSG00000278996 | ENSG00000278996.1 | ncRNA |
| chr21 | 8,218,781 | 8,218,825 | + | 33.782 | 5.873 | ENSG00000278996 | ENSG00000278996.1 | ncRNA |
| chr11 | 65,427,351 | 65,427,386 | + | 29.860 | 3.074 | NEAT1 | ENSG00000245532.11 | ncRNA |
| chrM | 14,263 | 14,274 | - | 46.689 | 5.273 | MT-ND6 | ENSG00000198695.2 | CDS |
| chrM | 14,254 | 14,263 | - | 38.171 | 5.071 | MT-ND6 | ENSG00000198695.2 | CDS |
| chrM | 14,274 | 14,301 | - | 61.229 | 4.925 | MT-ND6 | ENSG00000198695.2 | CDS |
| chr8 | 1,833,311 | 1,833,409 | + | 8.514 | 7.123 | ARHGEF10 | ENSG00000104728.16 | Distal intron |
| chr19 | 893,560 | 893,589 | + | 33.051 | 7.103 | RNU6-9 | ENSG00000207507.1 | ncRNA |
| chr13 | 91,348,438 | 91,348,497 | + | 9.690 | 3.620 | MIR17HG | ENSG00000215417.13 | ncRNA |
| chr13 | 91,348,342 | 91,348,417 | + | 11.225 | 3.449 | MIR17HG | ENSG00000215417.13 | ncRNA |
| chr8 | 9,772,234 | 9,772,330 | + | 18.251 | 5.155 | TNKS | ENSG00000173273.16 | 3' splice site |
| chr11 | 62,854,629 | 62,854,648 | - | 13.225 | 3.579 | SNORD28|SNHG1 | ENSG00000274544.1||ENSG00000255717.9 | ncRNA |
| chr19 | 34,392,525 | 34,392,584 | + | 18.045 | 3.194 | GPI | ENSG00000105220.17 | Distal intron |
| chr8 | 9,772,110 | 9,772,176 | + | 14.624 | 7.906 | TNKS | ENSG00000173273.16 | Proximal intron |
| chrM | 14,465 | 14,499 | - | 84.641 | 5.561 | MT-ND6 | ENSG00000198695.2 | CDS |
| chr19 | 34,391,905 | 34,391,928 | + | 13.154 | 4.037 | GPI | ENSG00000105220.17 | Distal intron |
| chr11 | 65,425,114 | 65,425,194 | + | 59.469 | 3.125 | NEAT1 | ENSG00000245532.11 | ncRNA |
| chr6 | 132,815,315 | 132,815,376 | + | 9.886 | 3.192 | SNORD101 | ENSG00000206754.1 | ncRNA |
| chr14 | 39,180,832 | 39,180,881 | + | 9.538 | 4.603 | PNN | ENSG00000100941.9 | CDS |
| chrM | 3,192 | 3,219 | + | 400.000 | 3.870 | MT-RNR2 | ENSG00000210082.2 | ncRNA |
| chrM | 3,183 | 3,192 | + | 400.000 | 3.280 | MT-RNR2 | ENSG00000210082.2 | ncRNA |
| chr6 | 28,658,233 | 28,658,267 | - | 12.810 | 4.623 | tRNA-Ala-AGC-4-1 | tRNA-Ala-AGC-4-1 | tRNA |
| chr19 | 45,478,597 | 45,478,622 | - | 28.199 | 8.243 | tRNA-SeC-TCA-1-1 | tRNA-SeC-TCA-1-1 | tRNA |
| chr19 | 45,478,622 | 45,478,653 | - | 5.298 | 4.058 | tRNA-SeC-TCA-1-1 | tRNA-SeC-TCA-1-1 | tRNA |
The following table contains identified motifs, where a motif is a short sequence of nucleotides that is significantly enriched in called peaks. Motifs were identified using HOMER's findMotifsGenome.pl tool. Motifs were called at multiple lengths, and results from all examined lengths are aggregated in the table.
The following columns are included in the table:
- Motif: logo plot for the identified motif.
- IUPAC: sequence of motif in IUPAC code.
- Motif length: length of the called motif.
- P-value: Significance of the called motif.
- -log10(p-value): log transformed significance, a larger number indicates a greater significance.
- % Peaks: percent of examined peaks with the identified motif.
- % Background: percent of non-peak background regions with the motif.
Please note, this table is interactive. You can search for specific sequences, and can sort the table by any of the columns. The search buttons at thr bottom of the table allow for specific filtering by sequence or motif length.