Literature DB >> 19274049

A census of human transcription factors: function, expression and evolution.

Juan M Vaquerizas1, Sarah K Kummerfeld, Sarah A Teichmann, Nicholas M Luscombe.   

Abstract

Transcription factors are key cellular components that control gene expression: their activities determine how cells function and respond to the environment. Currently, there is great interest in research into human transcriptional regulation. However, surprisingly little is known about these regulators themselves. For example, how many transcription factors does the human genome contain? How are they expressed in different tissues? Are they evolutionarily conserved? Here, we present an analysis of 1,391 manually curated sequence-specific DNA-binding transcription factors, their functions, genomic organization and evolutionary conservation. Much remains to be explored, but this study provides a solid foundation for future investigations to elucidate regulatory mechanisms underlying diverse mammalian biological processes.

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Year:  2009        PMID: 19274049     DOI: 10.1038/nrg2538

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  117 in total

1.  Serial regulation of transcriptional regulators in the yeast cell cycle.

Authors:  I Simon; J Barnett; N Hannett; C T Harbison; N J Rinaldi; T L Volkert; J J Wyrick; J Zeitlinger; D K Gifford; T S Jaakkola; R A Young
Journal:  Cell       Date:  2001-09-21       Impact factor: 41.582

2.  FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster.

Authors:  Boris Adryan; Sarah A Teichmann
Journal:  Bioinformatics       Date:  2006-04-13       Impact factor: 6.937

3.  p67SRF is a constitutive nuclear protein implicated in the modulation of genes required throughout the G1 period.

Authors:  C Gauthier-Rouvière; J C Cavadore; J M Blanchard; N J Lamb; A Fernandez
Journal:  Cell Regul       Date:  1991-07

Review 4.  The evolution of cell types in animals: emerging principles from molecular studies.

Authors:  Detlev Arendt
Journal:  Nat Rev Genet       Date:  2008-11       Impact factor: 53.242

Review 5.  Online Mendelian Inheritance in Man (OMIM) as a knowledgebase for human developmental disorders.

Authors:  S A Boyadjiev; E W Jabs
Journal:  Clin Genet       Date:  2000-04       Impact factor: 4.438

6.  A forkhead-domain gene is mutated in a severe speech and language disorder.

Authors:  C S Lai; S E Fisher; J A Hurst; F Vargha-Khadem; A P Monaco
Journal:  Nature       Date:  2001-10-04       Impact factor: 49.962

7.  Genome-wide analysis of Foxp3 target genes in developing and mature regulatory T cells.

Authors:  Ye Zheng; Steven Z Josefowicz; Arnold Kas; Tin-Tin Chu; Marc A Gavin; Alexander Y Rudensky
Journal:  Nature       Date:  2007-01-21       Impact factor: 49.962

8.  Evolvability and hierarchy in rewired bacterial gene networks.

Authors:  Mark Isalan; Caroline Lemerle; Konstantinos Michalodimitrakis; Carsten Horn; Pedro Beltrao; Emanuele Raineri; Mireia Garriga-Canut; Luis Serrano
Journal:  Nature       Date:  2008-04-17       Impact factor: 49.962

Review 9.  RNA-Seq: a revolutionary tool for transcriptomics.

Authors:  Zhong Wang; Mark Gerstein; Michael Snyder
Journal:  Nat Rev Genet       Date:  2009-01       Impact factor: 53.242

10.  A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks.

Authors:  John S Reece-Hoyes; Bart Deplancke; Jane Shingles; Christian A Grove; Ian A Hope; Albertha J M Walhout
Journal:  Genome Biol       Date:  2005-12-30       Impact factor: 13.583

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  700 in total

1.  Research resource: interactome of human embryo implantation: identification of gene expression pathways, regulation, and integrated regulatory networks.

Authors:  Signe Altmäe; Jüri Reimand; Outi Hovatta; Pu Zhang; Juha Kere; Triin Laisk; Merli Saare; Maire Peters; Jaak Vilo; Anneli Stavreus-Evers; Andres Salumets
Journal:  Mol Endocrinol       Date:  2011-11-10

2.  Proteomic methodologies to study transcription factor function.

Authors:  Harry W Jarrett
Journal:  Methods Mol Biol       Date:  2012

Review 3.  Enhancers: multi-dimensional signal integrators.

Authors:  Fulai Jin; Yan Li; Bing Ren; Rama Natarajan
Journal:  Transcription       Date:  2011 Sep-Oct

4.  Glucocorticoid-dependent phosphorylation of the transcriptional coregulator GRIP1.

Authors:  Jana Dobrovolna; Yurii Chinenov; Megan A Kennedy; Bill Liu; Inez Rogatsky
Journal:  Mol Cell Biol       Date:  2011-12-12       Impact factor: 4.272

5.  Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention.

Authors:  Karen Yap; Zhao Qin Lim; Piyush Khandelia; Brad Friedman; Eugene V Makeyev
Journal:  Genes Dev       Date:  2012-06-01       Impact factor: 11.361

6.  Integrating one-dimensional and three-dimensional maps of genomes.

Authors:  Natalia Naumova; Job Dekker
Journal:  J Cell Sci       Date:  2010-06-15       Impact factor: 5.285

Review 7.  Annotating non-coding regions of the genome.

Authors:  Roger P Alexander; Gang Fang; Joel Rozowsky; Michael Snyder; Mark B Gerstein
Journal:  Nat Rev Genet       Date:  2010-07-13       Impact factor: 53.242

8.  Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data.

Authors:  Roger Pique-Regi; Jacob F Degner; Athma A Pai; Daniel J Gaffney; Yoav Gilad; Jonathan K Pritchard
Journal:  Genome Res       Date:  2010-11-24       Impact factor: 9.043

9.  High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.

Authors:  Alan P Boyle; Lingyun Song; Bum-Kyu Lee; Darin London; Damian Keefe; Ewan Birney; Vishwanath R Iyer; Gregory E Crawford; Terrence S Furey
Journal:  Genome Res       Date:  2010-11-24       Impact factor: 9.043

Review 10.  Determining causality and consequence of expression quantitative trait loci.

Authors:  A Battle; S B Montgomery
Journal:  Hum Genet       Date:  2014-04-26       Impact factor: 4.132

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