2020
DOI: 10.3389/fgene.2020.00199
|View full text |Cite
|
Sign up to set email alerts
|

Testing Proximity of Genomic Regions to Transcription Start Sites and Enhancers Complements Gene Set Enrichment Testing

Abstract: Large sets of genomic regions are generated by the initial analysis of various genomewide sequencing data, such as ChIP-seq and ATAC-seq experiments. Gene set enrichment (GSE) methods are commonly employed to determine the pathways associated with them. Given the pathways and other gene sets (e.g., GO terms) of significance, it is of great interest to know the extent to which each is driven by binding near transcription start sites (TSS) or near enhancers. Currently, no tool performs such an analysis. Here, we… Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
1
1
1

Citation Types

0
2
0

Year Published

2020
2020
2024
2024

Publication Types

Select...
4
1

Relationship

2
3

Authors

Journals

citations
Cited by 5 publications
(3 citation statements)
references
References 60 publications
(65 reference statements)
0
2
0
Order By: Relevance
“…Linking enhancers to their target promoters remains a challenging problem [79][80][81][82]. To the best of our knowledge, the most successful approach so far was to link promoters to enhancers based on 100 K distance proximity of chromatin-accessible regions [83][84][85][86][87], without considering possible interference of neighbouring expressed genes. Our approach, which takes into account distance to the nearest transcribed gene, chromatin accessibility, and TAD borders, could allow for the detection of more precise promoter-enhancer links for developmental genes.…”
Section: Discussionmentioning
confidence: 99%
“…Linking enhancers to their target promoters remains a challenging problem [79][80][81][82]. To the best of our knowledge, the most successful approach so far was to link promoters to enhancers based on 100 K distance proximity of chromatin-accessible regions [83][84][85][86][87], without considering possible interference of neighbouring expressed genes. Our approach, which takes into account distance to the nearest transcribed gene, chromatin accessibility, and TAD borders, could allow for the detection of more precise promoter-enhancer links for developmental genes.…”
Section: Discussionmentioning
confidence: 99%
“…1 C: Evaluation of the Enhancer-Target gene Definition), to identify the EnTDefs with greatest concordance. The assumption of this approach, used previously in [ 72 , 73 ], is that TFs tend to the regulate genes in the biological processes to which they belong, and thus greater overlap with TF GO BP annotation indicates more accurate enrichment results, and thus more accurate peak-to-gene assignments. We used the Gene Ontology Biological Process (GO BP) terms that each of the 34 TFs were assigned to by the GO database [ 74 , 75 ], and extracted the GOBP-to-gene assignments from the human annotation Bioconductor package org.Hs.eg.db [ 76 ].…”
Section: Methodsmentioning
confidence: 99%
“…the GOBP terms assigned to the 34 TFs by the GO database, excluding the terms with <15 or >2000 assigned genes) ( Figure 1C: Evaluation of the Enhancer-Target gene Definition), to identify the EnTDefs with greatest concordance. The assumption of this approach, used previously in [70,71], is that TFs tend to the regulate genes in the biological processes to which they belong, and thus greater overlap with TF GO BP annotation indicates more accurate enrichment results, and thus more accurate peak-to-gene assignments. For a full justification of this, see Supplementary Methods.…”
Section: Evaluation Of Enhancer-target Gene Definitionsmentioning
confidence: 99%