Finding transcription factor binding motifs for coregulated genes by combining sequence overrepresentation with cross-species conservation

DOI10.1155/2012/830575zbMATH Open1263.62127OpenAlexW2147405530WikidataQ58910993 ScholiaQ58910993MaRDI QIDQ454795FDOQ454795

Authors: Hui Jia, Jinming Li 

Publication date: 10 October 2012

Published in: Journal of Probability and Statistics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1155/2012/830575

Recommendations

• Prediction of motifs based on a repeated-measures model for integrating cross-species sequence and expression data
• A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites
• Coupling hidden Markov models for the discovery of Cis-regulatory modules in multiple species
• An efficient algorithm for deciphering regulatory motifs
• Detection of over-represented motifs corresponding to known TFBSs via motif clustering and matching

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10)

Cites Work

• Title not available (Why is that?)
• Biological Sequence Analysis
• Title not available (Why is that?)

Cited In (9)

• A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites
• Detection of over-represented motifs corresponding to known TFBSs via motif clustering and matching
• Distance conservation of transcription regulatory motifs in human promoters
• Sampling motifs on phylogenetic trees
• Analysis of transcriptional synergy between upstream regions and introns in ribosomal protein genes of yeast
• Evaluation of phylogenetic footprinting and its application for improved prediction of transcription factor binding sites
• Decoding transcriptional regulatory interactions
• Prediction of motifs based on a repeated-measures model for integrating cross-species sequence and expression data
• Heterogeneity in DNA multiple alignments: modeling, inference, and applications in motif finding

Uses Software

• ClustalW
• PhyME

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