MotifViz: an Analysis and Visualization Tool for Motif Discovery

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2004 Jun 25

PMID 15215422

Citations 24

Authors

Yutao Fu

Martin C Frith

Peter M Haverty

Zhiping Weng

Affiliations

Soon will be listed here.

Abstract

Detecting overrepresented known transcription factor binding motifs in a set of promoter sequences of co-regulated genes has become an important approach to deciphering transcriptional regulatory mechanisms. In this paper, we present an interactive web server, MotifViz, for three motif discovery programs, Clover, Rover and Motifish, covering most available flavors of algorithms for achieving this goal. For comparison, we have also implemented the simple motif-matching program Possum. MotifViz provides uniform and intuitive input and output formats for all four programs. It can be accessed at http://biowulf.bu.edu/MotifViz.

Citing Articles

Transcription Factor-Binding Site Identification and Enrichment Analysis.

Guy J, Mor G Methods Mol Biol. 2021; 2255:241-261.

PMID: 34033108 DOI: 10.1007/978-1-0716-1162-3_20.

Improved linking of motifs to their TFs using domain information.

Baumgarten N, Schmidt F, Schulz M Bioinformatics. 2019; 36(6):1655-1662.

PMID: 31742324 PMC: 7703792. DOI: 10.1093/bioinformatics/btz855.

CiiiDER: A tool for predicting and analysing transcription factor binding sites.

Gearing L, Cumming H, Chapman R, Finkel A, Woodhouse I, Luu K PLoS One. 2019; 14(9):e0215495.

PMID: 31483836 PMC: 6726224. DOI: 10.1371/journal.pone.0215495.

Regulation of Cyclin E by transcription factors of the naïve pluripotency network in mouse embryonic stem cells.

Gonnot F, Langer D, Bourillot P, Doerflinger N, Savatier P Cell Cycle. 2019; 18(20):2697-2712.

PMID: 31462142 PMC: 6773236. DOI: 10.1080/15384101.2019.1656475.

Genetic and transcriptional variations in NRAMP-2 and OPAQUE1 genes are associated with salt stress response in wheat.

Oyiga B, Ogbonnaya F, Sharma R, Baum M, Leon J, Ballvora A Theor Appl Genet. 2018; 132(2):323-346.

PMID: 30392081 PMC: 6349800. DOI: 10.1007/s00122-018-3220-5.

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