Annotate regions

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 regiorns?

Annotate regions 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 regions

The input for Annotate regions is a Regions count type data node. This can be raw data or any filtered or normalized node containing region counts.

• Click a Regions data node

• Click the Regions analysis section in the toolbox

• Click Annotate regions

• Set the Assembly and Annotation model

• Set the Genomic overlaps parameter

The Genomics overlaps parameter lets you choose one of two options (Figure 1).

• Report one gene region per genomic feature (precedence applies) chooses one gene section for each region using the precedence order to settle cases where more than one gene section overlaps a peak. The order of precedence is TSS, TTS, CDS Exon, 5' UTR Exon, 3' UTR Exon, Intron, Intergenic.

• Report all gene regions per feature creates a row for each gene section that overlaps a region in the task report.

Figure 1. Annotate regions task setup page.

• User should define the transcription start site (TSS) and transcription termination site (TTS) limit in the unit of bp

• Click Finish to run

Annotate regions output

Annotate regions produces an Annotated regions data node. The Annotated regions 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 region to the standard Regions report (Figure 2). If run with the option to report all gene sections selected, each region will have a row for each gene section it overlaps. If run with the option to report one gene section selected, each region will have one row with the gene section it overlaps chosen using the order of precedence.

Figure 2. Annotated regions report.

The table can be sorted by any of its columns (Figure 3). Click on the Optional columns on the upper-left corner of the table to add more information on each region

Figure 3. Optional columns in the report table, click the arrows next to the column header to sort it.

Gene sections

TSS

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

TTS

Transcription termination site (TTS) is -100bp and +1000bp (default setting) 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