Method for identifying transcription factor binding sites in yeast

Bioinformatics
Huai-Kuang TsaiWen-Hsiung Li

Abstract

Identifying transcription factor binding sites (TFBSs) is helpful for understanding the mechanism of transcriptional regulation. The abundance and the diversity of genomic data provide an excellent opportunity for identifying TFBSs. Developing methods to integrate various types of data has become a major trend in this pursuit. We develop a TFBS identification method, TFBSfinder, which utilizes several data sources, including DNA sequences, phylogenetic information, microarray data and ChIP-chip data. For a TF, TFBSfinder rigorously selects a set of reliable target genes and a set of non-target genes (as a background set) to find overrepresented and conserved motifs in target genes. A new metric for measuring the degree of conservation at a binding site across species and methods for clustering motifs and for inferring position weight matrices are proposed. For synthetic data and yeast cell cycle TFs, TFBSfinder identifies motifs that are highly similar to known consensuses. Moreover, TFBSfinder outperforms well-known methods. http://cg1.iis.sinica.edu.tw/~TFBSfinder/.

References

Apr 1, 1990·Computer Applications in the Biosciences : CABIOS·G Z HertzG D Stormo
Feb 21, 1998·Nucleic Acids Research·J M CherryD Botstein
Dec 10, 1998·Nucleic Acids Research·H W MewesD Frishman
Sep 17, 1999·Bioinformatics·J Zhu, M Q Zhang
May 17, 2000·Bioinformatics·G D Stormo
Jan 11, 2000·Nucleic Acids Research·E WingenderS Urbach
Oct 26, 2002·Science·Tong Ihn LeeRichard A Young
Aug 26, 2003·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Saurabh Sinha
Aug 30, 2003·BMC Evolutionary Biology·Alan M MosesMichael B Eisen
Nov 25, 2003·Nucleic Acids Research·Nilanjana Banerjee, Michael Q Zhang
Nov 25, 2003·BMC Bioinformatics·Eldon EmberlyEric D Siggia
May 8, 2004·Nature Reviews. Genetics·Wyeth W Wasserman, Albin Sandelin
Aug 4, 2004·Genome Biology·Mamoru KatoMichael Q Zhang
Aug 7, 2004·Journal of Bioinformatics and Computational Biology·Hideo BannaiSatoru Miyano
Sep 3, 2004·Nature·Christopher T HarbisonRichard A Young
May 11, 2005·Proceedings of the National Academy of Sciences of the United States of America·Amos TanayRon Shamir
Sep 6, 2005·Nucleic Acids Research·Cinzia PizziGian Antonio Danieli
Sep 15, 2005·Proceedings of the National Academy of Sciences of the United States of America·Huai-Kuang TsaiWen-Hsiung Li
Oct 7, 2005·Genome Biology·Reut ShalgiYitzhak Pilpel
Nov 23, 2005·Proceedings of the National Academy of Sciences of the United States of America·Ting Wang, Gary D Stormo

❮ Previous
Next ❯

Citations

Feb 15, 2008·Proceedings of the National Academy of Sciences of the United States of America·Chien-Yu ChenWen-Hsiung Li
Oct 28, 2008·Proceedings of the National Academy of Sciences of the United States of America·Yao-Ming ChangArthur Chun-Chieh Shih
Mar 14, 2008·Bioinformatics·Cheng-Long ChuangGrace S Shieh
Jun 1, 2007·Nucleic Acids Research·Huai-Kuang TsaiWen-Hsiung Li
Sep 22, 2009·Nucleic Acids Research·Krishna B S SwamyHuai-Kuang Tsai
Jun 18, 2015·Molecular Microbiology·Chiu-Lien HungWen-Ching Wang
Feb 6, 2017·BMC Bioinformatics·Sinjini Sikdar, Susmita Datta

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Chien-Yu ChenWen-Hsiung Li
Proceedings of the National Academy of Sciences of the United States of America
Huai-Kuang TsaiWen-Hsiung Li
Nucleic Acids Research
J M CherryD Botstein
© 2022 Meta ULC. All rights reserved