APEX1

The following table contains called APEX1 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.

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.