Eukaryotic transcription factor binding sites--modeling and integrative search methods

Bioinformatics
Sridhar Hannenhalli

Abstract

A comprehensive knowledge of transcription factor binding sites (TFBS) is important for a mechanistic understanding of transcriptional regulation as well as for inferring gene regulatory networks. Because the DNA motif recognized by a transcription factor is typically short and degenerate, computational approaches for identifying binding sites based only on the sequence motif inevitably suffer from high error rates. Current state-of-the-art techniques for improving computational identification of binding sites can be broadly categorized into two classes: (1) approaches that aim to improve binding motif models by extracting maximal sequence information from experimentally determined binding sites and (2) approaches that supplement binding motif models with additional genomic or other attributes (such as evolutionary conservation). In this review we will discuss recent attempts to improve computational identification of TFBS through these two types of approaches and conclude with thoughts on future development.

References

Nov 20, 1997·Journal of Cellular Physiology·D NiessingH Jäckle
May 26, 1998·Journal of Molecular Biology·W W Wasserman, J W Fickett
Feb 19, 2000·Current Opinion in Biotechnology·J W Fickett, W W Wasserman
May 17, 2000·Bioinformatics·G D Stormo
Sep 27, 2001·Cell·S Lomvardas, D Thanos
Dec 26, 2001·Nucleic Acids Research·Olga V Kel-MargoulisEdgar Wingender
Jan 24, 2002·Proceedings of the National Academy of Sciences of the United States of America·Benjamin P BermanMichael B Eisen
May 25, 2002·Developmental Biology·Hamid Bolouri, Eric H Davidson
Jun 26, 2002·Molecular Biology and Evolution·Emmanouil T Dermitzakis, Andrew G Clark
Jul 11, 2002·Proceedings of the National Academy of Sciences of the United States of America·Mark RebeizJames W Posakony
Oct 5, 2002·Nucleic Acids Research·Sridhar Hannenhalli, Samuel Levy
Oct 9, 2002·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Samuel Levy, Sridhar Hannenhalli
Oct 18, 2002·Nucleic Acids Research·Panayiotis V BenosGary D Stormo
Dec 25, 2002·Bioinformatics·Ji-Hong ZhangXiang-Sun Zhang
Jan 17, 2003·Genome Research·Laura ElnitskiFrancesca Chiaromonte
Feb 4, 2003·Nature Medicine·Shahin Rafii, Mihaela Skobe
Mar 5, 2003·Journal of Molecular Biology·Arun K Ramani, Edward M Marcotte
Jul 12, 2003·Bioinformatics·Saurabh SinhaEric D Siggia
Nov 25, 2003·Nucleic Acids Research·Nilanjana Banerjee, Michael Q Zhang
Nov 25, 2003·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Sridhar Hannenhalli, Samuel Levy
Nov 25, 2003·BMC Bioinformatics·Eldon EmberlyEric D Siggia
Dec 19, 2003·Nucleic Acids Research·Albin SandelinBoris Lenhard
Apr 16, 2004·Cell·Michael A Beer, Saeed Tavazoie
May 8, 2004·Nature Reviews. Genetics·Wyeth W Wasserman, Albin Sandelin
Aug 7, 2004·Proceedings of the National Academy of Sciences of the United States of America·Qing Zhou, Wing H Wong
Oct 7, 2004·Genome Research·William ThompsonCharles E Lawrence
Oct 22, 2004·Proceedings of the National Academy of Sciences of the United States of America·Sharyl L WongFrederick P Roth
Oct 22, 2004·Nature·Marcelo A NóbregaEdward M Rubin
Nov 10, 2004·Proceedings of the National Academy of Sciences of the United States of America·Debopriya DasMichael Q Zhang
May 11, 2005·Proceedings of the National Academy of Sciences of the United States of America·Mayetri Gupta, Jun S Liu
Jun 18, 2005·Bioinformatics·Sridhar Hannenhalli, Li-San Wang
Jun 18, 2005·Bioinformatics·William Stafford NobleJohn Stamatoyannopoulos
Dec 31, 2005·Nucleic Acids Research·V MatysE Wingender

❮ Previous
Next ❯

Citations

Jun 6, 2009·Briefings in Functional Genomics & Proteomics·Leelavati Narlikar, Ivan Ovcharenko
Nov 15, 2008·Bioinformatics·Anton V PersikovMona Singh
May 30, 2009·Bioinformatics·Tobias Marschall, Sven Rahmann
Oct 15, 2009·Bioinformatics·Curtis HuttenhowerHilary A Coller
Sep 8, 2011·Bioinformatics·Shu YangJunwen Wang
Apr 3, 2012·Bioinformatics·Erola PairóAlexandre Perera
Apr 8, 2011·Nucleic Acids Research·Logan J EverettSridhar Hannenhalli
Apr 14, 2011·Nucleic Acids Research·Abha Singh BaisPanayiotis V Benos
Oct 8, 2013·Nucleic Acids Research·Anton V Persikov, Mona Singh
Jun 21, 2011·Genome Research·Michael Schnall-LevinBonnie Berger
Jul 21, 2011·Physiological Genomics·Craig C BensonJoseph M Miano
May 20, 2011·BMC Bioinformatics·Mitja I KurkiPetri Pehkonen
Mar 26, 2013·BMC Bioinformatics·Chih Lee, Chun-Hsi Huang
Jan 16, 2010·BMC Genomics·John E ReidSascha Ott
Jan 11, 2013·BMC Genomics·Yupeng HeChaochun Wei
Sep 7, 2012·Genome Biology·Troy W WhitfieldZhiping Weng
Jan 31, 2009·PLoS Computational Biology·Debopriya DasJoe W Gray
Jun 23, 2012·Journal of Molecular Endocrinology·Gioia Altobelli
Jul 10, 2009·Yi chuan = Hereditas·Lin HouMing-Hua Deng
Feb 25, 2011·Bioinformation·Nidhi Bhargava, Ivan Erill
Sep 25, 2010·Trends in Genetics : TIG·Robin D Dowell
Jun 15, 2010·Comptes rendus biologies·Denis TaguStefano Colella
Jan 20, 2009·Science in China. Series C, Life Sciences·Pei HaoYang Zhong
May 12, 2009·Journal of Biotechnology·Noémie Manuelle Dorval CourchesneChristopher Q Lan
Jan 29, 2013·Genesis : the Journal of Genetics and Development·Mohsin A F KhanClaudio D Stern
Jun 24, 2010·Clinical Genetics·J M ChenD N Cooper
May 23, 2013·IEEE Transactions on Nanobioscience·Elana J FertigMichael F Ochs
Oct 30, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Gang LiKin-Hong Lee

❮ 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.