Genome-wide measurement of gene expression changes with Bptf knockout in mouse embryonic fibroblasts
Transcriptomics Dataset
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General Information
AccessionGSE48123
TitleGenome-wide measurement of gene expression changes with Bptf knockout in mouse embryonic fibroblasts
DescriptionGene expression frequently requires the action of chromatin remodeling complexes and it is assumed that these complexes have common gene targets across cell-types. Contrary to this belief, we show that Bptf, an essential and unique subunit of the Nucleosome Remodeling Factor (NURF), largely regulates cell-type-restricted gene expression across diverse cell-types. Unexpectedly, cell-type-restricted gene expression is accomplished through both physical and functional interactions between NURF and the ubiquitous multivalent factor Ctcf. We go on to show in these cell types, that Bptf influences the regulatory activity of Ctcf binding sites in a cell type-restricted manner. Detailed studies of Ctcf binding sites in embryonic stem cells (ESC) show that Bptf prevents Klf4 binding upstream of H2-K1, and facilitates RNA polymerase elongation through Ccnd1, to regulate genes important for embryonic development. In total, these studies provide mechanisms by which prominent chromatin remodeling complexes can maintain cell-type-restricted gene expression through ubiquitous factors like Ctcf.
Landing Pagehttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48123
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
GeneMANIA
Published June 2010
Biological network integration for gene prioritization and predicting gene function
7435
L1000CDS2
Published August 2016
An ultra-fast LINCS L1000 Characteristic Direction signature search engine
7756
PAEA
Published November 2015
Enrichment analysis tool implementing the principal angle method
3879
Canned Analyses generated with the dataset
Filters  
Dataset Accession
Tool Name
Direction
Geneset
Small molecules which mimic BPTF KO
L1000CDS2, Characteristic Direction
The L1000 database was queried in order to identify small molecule perturbations which mim...
Small molecules which reverse BPTF KO
L1000CDS2, Characteristic Direction
The L1000 database was queried in order to identify small molecule perturbations which rev...
Enrichment analysis of genes dysregulated in BPTF KO
PAEA, Characteristic Direction
An enrichment analysis was performed on the top most dyresgulated genes determined by appl...
Interaction network and enrichment analysis of genes downregulated in BPTF KO
GeneMANIA, Characteristic Direction
The analysis explores the gene interaction network and pathway enrichment of the top 50 mo...
Interaction network and enrichment analysis of genes upregulated in BPTF KO
GeneMANIA, Characteristic Direction
The analysis explores the gene interaction network and pathway enrichment of the top 50 mo...
Enrichment analysis of genes downregulated in BPTF KO
Enrichr, Characteristic Direction
An enrichment analysis was performed on the top 500 most downregulated genes identified by...
Enrichment analysis of genes upregulated in BPTF KO
Enrichr, Characteristic Direction
An enrichment analysis was performed on the top 500 most upregulated genes identified by a...
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