PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples

Database : the Journal of Biological Databases and Curation
Yiyu ZhengHaiyan Hu

Abstract

PreDREM is a database of DNA regulatory motifs and motifs modules predicted from DNase I hypersensitive sites in 349 human cell and tissue samples. It contains 845-1325 predicted motifs in each sample, which result in a total of 2684 non-redundant motifs. In comparison with seven large collections of known motifs, more than 84% of the 2684 predicted motifs are similar to the known motifs, and 54-76% of the known motifs are similar to the predicted motifs. PreDREM also stores 43 663-20 13 288 motif modules in each sample, which provide the cofactor motifs of each predicted motif. Compared with motifs of known interacting transcription factor (TF) pairs in eight resources, on average, 84% of motif pairs corresponding to known interacting TF pairs are included in the predicted motif modules. Through its web interface, PreDREM allows users to browse motif information by tissues, datasets, individual non-redundant motifs, etc. Users can also search motifs, motif modules, instances of motifs and motif modules in given genomic regions, tissue or cell types a motif occurs, etc. PreDREM thus provides a useful resource for the understanding of cell- and tissue-specific gene regulation in the human genome. Database URL: http://server.cs.u...Continue Reading

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Citations

Mar 10, 2021·BMC Genomics·Amlan TalukderXiaoman Li

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Datasets Mentioned

BETA
GM12878
K562
GM12878-DS10671

Methods Mentioned

BETA
immunoprecipitation
ChIP-seq
K562

Software Mentioned

MySQL
SQLite
STAMP
SIOMICS
JASPAR
TOMTOM
TFBSTools
PreDREM
Apache Tomcat
TRANSFAC

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