Genomics

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Transcription Factor Binding Sites by Motifs Scan


ABSTRACT: Purpose: 224 GSM Samples form GSE32970 and GSE29692 was reanalyzed to find the binding sites of 542 TFs. Methods: 1. iFORM (incorporating Find Occurrence of Regulatory Motifs) is a tool we designed to scan through sequences in search of binding sites that match given motifs. 2. We mapped motif-binding protein information found in TRANSFAC, JASPAR, and UniPROBE databases to 542 coding genes, using GeneCards (Rebhan et al., 1997) and UniProt Knowledgebase (Magrane and Consortium, 2011). The position-specific weight matrices of the 542 TFs, corresponding to 796 motif models, were collected from these databases. 3.We used a uniform set of open chromatin elements (DNaseI hypersensitive sites, DHSs) in 133 ENCODE cell types, based on DNase-seq data produced by the "Open Chromatin" (Duke/UNC/UT-A)(GSE32970) and University of Washington (UW) ENCODE groups (GSE29692)from the project inception in 2007 through the ENCODE January 2011 data freeze. Processing pipeline: Combined all replicates for a given cell type; Subsampled the result at a level of 30 million tags; Ran results through the Stam Lab hotspot pipeline. Hotspots were identified using a relaxed threshold. NarrowPeaks were generated by first thresholding hotspots at FDR 1%, and then locating local maxima of the tag density within the hotspots. The 133 narrowPeaks are base sequences for the given motifs scan. Result: We used our iFORM with a custom library of all 796 motifs to scan for motif instances in 133 ENCODE DHSs cell types separately. Result in 133 files correspond to 133 cell types, each file contains binding sites of 542 TFs in a cell type.

ORGANISM(S): Homo sapiens

PROVIDER: GSE53962 | GEO | 2014/10/12

SECONDARY ACCESSION(S): PRJNA234045

REPOSITORIES: GEO

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