Partek Flow Documentation

Page tree

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

ChIP-Seq and ATAC-Seq identify enriched regions or peaks in genome. Depending on the assay, the biological meaning of enrichment changes; in ChIP-Seq, enrichment indicates protein binding, while in ATAC-Seq, enrichment indicates open chromatin. To understand the importance of enriched regions in regulating gene expression, we can add information about overlapping or nearby genomic features. 

What is Annotate peaks?

Annotate peaks takes an input set of regions and checks for overlap between those regions and a gene/feature annotation. This gives regulatory context for enriched regions.

Running Annotate peaks

The input for Annotate peaks is a Peaks type data node. 

...

  • Choose a gene/feature annotation from the drop-down menu
  • Click Finish to run

Annotate peaks output

Annotate peaks produces an Annotated peaks data node. The Annotated peaks task report adds a Gene section breakdown pie chart and adds columns with information about the Gene IDs, Transcript IDs, Gene section, Distance to TSS, and Distance to TTS of each peak to the standard Peaks report  (Figure 1). If run with the option to report all gene sections selected, each peak will have a row for each gene section it overlaps. If run with the option to report one gene section selected, each peak will have one row with the gene section it overlaps chosen using the order of precedence. 

...

Clicking the  button at the bottom of the task report generates a Filtered peaks data node containing only the peaks currently included in the table. 

Gene sections

TSS

Transcription start site (TSS) is -1000bp and +100bp from the TSS for a transcript

TTS

Transcription termination site (TTS) is -100bp and +1000bp from the TTS for a transcript 

CDS Exon 

Coding sequence (CDS) Exon is overlapping a coding exon in a transcript

5' UTR Exon

5' Untranslated Region (UTR) Exon is overlapping an exon in the 5' UTR of a transcript

3' UTR Exon

3' Untranslated Region (UTR) Exon is overlapping an exon in the 3' UTR of a transcript

Intron

Intron is overlapping an intron in a transcript 

Intergenic

Intergenic is not located within 1000bp of a transcript

Annotate peaks vs. Annotate regions

Annotate regions is almost identical to Annotate peaks. Annotate regions takes Region counts data as the input and outputs Annotated region counts. One important difference is that you cannot filter the Annotated region counts from the task report. 

...