The Functional Consequences of Variation in Transcription Factor Binding
Transcriptomics Dataset
FAIR Metrics
2 evaluations
General Information
AccessionGSE50588
TitleThe Functional Consequences of Variation in Transcription Factor Binding
DescriptionOne goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene expression data with transcription factor binding data (based on ChIP-seq and DNase-seq) within 10 kb of the transcription start sites of expressed genes. This combination of data allowed us to infer functional TF binding. Using this approach, we found that only a small subset of genes bound by a factor were differentially expressed following the knockdown of that factor, suggesting that most interactions between TF and chromatin do not result in measurable changes in gene expression levels of putative target genes. We found that functional TF binding is enriched in regulatory elements that harbor a large number of TF binding sites, at sites with predicted higher binding affinity, and at sites that are enriched in genomic regions annotated as active enhancers.
Landing Pagehttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50588
RepositoryGene Expression Omnibus
Tools used to analyze the dataset

Keyword
Dataset Accession

Enrichr
Published May 2016
A comprehensive gene set enrichment analysis web server 2016 update
7759
65
Characteristic Direction
Published March 2014
A geometrical multivariate approach to identify differentially expressed genes
26829
L1000CDS2
Published August 2016
An ultra-fast LINCS L1000 Characteristic Direction signature search engine
7756
GeneMANIA
Published June 2010
Biological network integration for gene prioritization and predicting gene function
7435
PAEA
Published November 2015
Enrichment analysis tool implementing the principal angle method
3879
Canned Analyses generated with the dataset

Dataset Accession
Tool Name
Direction
Hs Gene Symbol
Mm Gene Symbol
Geneset

Small molecules which mimic E2F1 KD
The L1000 database was queried in order to identify small molecule perturbations which mim...
Small molecules which reverse E2F1 KD
The L1000 database was queried in order to identify small molecule perturbations which rev...
Small molecules which mimic CLOCK KD
The L1000 database was queried in order to identify small molecule perturbations which mim...
Small molecules which reverse CLOCK KD
The L1000 database was queried in order to identify small molecule perturbations which rev...
Small molecules which mimic CEBPG KD
The L1000 database was queried in order to identify small molecule perturbations which mim...
Small molecules which reverse CEBPG KD
The L1000 database was queried in order to identify small molecule perturbations which rev...
Small molecules which mimic ARNTL2 KD
The L1000 database was queried in order to identify small molecule perturbations which mim...
Small molecules which reverse ARNTL2 KD
The L1000 database was queried in order to identify small molecule perturbations which rev...
Small molecules which mimic IRF7 KD
The L1000 database was queried in order to identify small molecule perturbations which mim...
Small molecules which reverse IRF7 KD
The L1000 database was queried in order to identify small molecule perturbations which rev...
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