TF-finder: a software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base

BMC Bioinformatics
Xiaoqi CuiHairong Wei


Identification of transcription factors (TFs) involved in a biological process is the first step towards a better understanding of the underlying regulatory mechanisms. However, due to the involvement of a large number of genes and complicated interactions in a gene regulatory network (GRN), identification of the TFs involved in a biology process remains to be very challenging. In reality, the recognition of TFs for a given a biological process can be further complicated by the fact that most eukaryotic genomes encode thousands of TFs, which are organized in gene families of various sizes and in many cases with poor sequence conservation except for small conserved domains. This poses a significant challenge for identification of the exact TFs involved or ranking the importance of a set of TFs to a process of interest. Therefore, new methods for recognizing novel TFs are desperately needed. Although a plethora of methods have been developed to infer regulatory genes using microarray data, it is still rare to find the methods that use existing knowledge base in particular the validated genes known to be involved in a process to bait/guide discovery of novel TFs. Such methods can replace the sometimes-arbitrary process of selectio...Continue Reading


Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Sep 29, 1999·Proceedings of the National Academy of Sciences of the United States of America·U SchiefthalerKay Schneitz
Aug 30, 2000·Proceedings of the National Academy of Sciences of the United States of America·M LuoA Chaudhury
Jun 9, 2001·Biochemical and Biophysical Research Communications·R GopalakrishnaM Udaya Kumar
Jan 19, 2002·Biochemical and Biophysical Research Communications·Yoh SakumaKazuko Yamaguchi-Shinozaki
Jun 18, 2002·Plant Physiology·Bin ShuaiPatricia S Springer
Aug 17, 2002·Current Opinion in Plant Biology·Karam SinghLuis Oñate-Sánchez
Sep 12, 2002·Plant Physiology·K. Shinozaki, Kazuko Yamaguchi-Shinozaki
Nov 6, 2002·The Plant Cell·Mande K KumaranVenkatesan Sundaresan
Jan 2, 2003·The Plant Cell·Raymond W KwongJohn J Harada
Jun 6, 2003·The Plant Journal : for Cell and Molecular Biology·Miki NakazawaMinami Matsui
Feb 20, 2004·Development·José R DinnenyDetlef Weigel
Mar 20, 2004·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Hisako OokaShoshi Kikuchi
Apr 17, 2004·The Plant Journal : for Cell and Molecular Biology·Julia C RedmanChristopher D Town
Oct 27, 2004·Proceedings of the National Academy of Sciences of the United States of America·Elena MontePeter H Quail
Nov 18, 2004·The Plant Journal : for Cell and Molecular Biology·Jordan B SottosantoEduardo Blumwald
Jun 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Staffan PerssonChristopher R Somerville
Jun 18, 2005·The Plant Journal : for Cell and Molecular Biology·Gorou HoriguchiHirokazu Tsukaya
Sep 30, 2005·Development·José R DinnenyMartin F Yanofsky
Oct 18, 2005·The Plant Cell·Michael G MasonG Eric Schaller
Aug 22, 2006·Plant Physiology·Hairong WeiAnn Loraine
Oct 13, 2006·Plant Molecular Biology·Matthew RamonBarbara Leyman
Dec 22, 2006·Nature·Lynn Jo PillitteriKeiko U Torii
Mar 23, 2007·The Plant Journal : for Cell and Molecular Biology·Daiqing HuangAdrian J Cutler
Aug 11, 2007·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Lynn Jo Pillitteri, Keiko U Torii
Sep 28, 2007·Plant, Cell & Environment·Simone D CastellarinGabriele DI Gaspero
Oct 10, 2007·Proceedings of the National Academy of Sciences of the United States of America·Donald E NelsonJacqueline E Heard
Nov 27, 2007·The Plant Journal : for Cell and Molecular Biology·Antonio GonzalezAlan M Lloyd
Feb 5, 2008·Statistical Applications in Genetics and Molecular Biology·Sandra WaaijenborgAeilko H Zwinderman
Jul 23, 2008·The Plant Journal : for Cell and Molecular Biology·Jalean Joyanne PetrickaTimothy Mark Nelson
Jan 8, 2009·Plant Physiology·Kazuo NakashimaKazuko Yamaguchi-Shinozaki
Jan 30, 2009·The Plant Journal : for Cell and Molecular Biology·Bas RutjensMarcel Proveniers
Feb 19, 2009·Statistical Applications in Genetics and Molecular Biology·Elena ParkhomenkoJoseph Beyene
Apr 22, 2009·Proceedings of the National Academy of Sciences of the United States of America·Patrick G StephensonMatthew J Terry
Jul 22, 2009·The Plant Journal : for Cell and Molecular Biology·Rumi Tominaga-WadaTakuji Wada

Related Concepts

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