Discovering modulators of gene expression.
Proteins that modulate the activity of transcription factors, often called modulators, play a critical role in creating tissue- and context-specific gene expression responses to the signals cells receive. GEM (Gene Expression Modulation) is a probabilistic framework that predicts modulators, their affected targets and mode of action by combining gene expression profiles, protein-protein interactions and transcription factor-target relationships. Using GEM, we correctly predicted a significant number of androgen receptor modulators and observed that most modulators can both act as co-activators and co-repressors for different target genes.
Babur
Ozgün
O
Center for Bioinformatics and Computer Engineering Department, Bilkent University, Ankara 06800, Turkey.
Demir
Emek
E
Gönen
Mithat
M
Sander
Chris
C
Dogrusoz
Ugur
U
D000465:Algorithms; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D008957:Models, Genetic; D011336:Probability; D025941:Protein Interaction Mapping; D011944:Receptors, Androgen / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
D011944:Receptors, Androgen; D014157:Transcription Factors
Int J Biochem Cell Biol. 2009 Mar;41(3):603-14
18692155
Nature. 2007 Jun 14;447(7146):799-816
17571346
Biochem J. 1996 Mar 1;314 ( Pt 2):439-43
8670054
Cell. 2002 Feb 22;108(4):465-74
11909518
Mol Cell Endocrinol. 2002 Apr 25;190(1-2):39-49
11997177
Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72
18988627
Int J Cancer. 2009 Oct 1;125(7):1514-22
19521982
Nature. 2009 Nov 5;462(7269):65-70
19890324
Ann N Y Acad Sci. 2007 Dec;1115:51-72
17925348
Nat Biotechnol. 2009 Sep;27(9):829-39
19741643
J Biol Chem. 1998 Apr 10;273(15):9158-67
9535906
Nat Struct Mol Biol. 2004 Sep;11(9):812-5
15332082
Mol Biol Cell. 1998 Sep;9(9):2527-43
9725910
Science. 2008 May 30;320(5880):1224-9
18511691
Nucleic Acids Res. 2007 Jan;35(Database issue):D137-40
17202159
Cell. 2009 Sep 4;138(5):1019-31
19698979
Thyroid. 2009 Sep;19(9):987-99
19678741
Endocr Rev. 2007 Dec;28(7):778-808
17940184
J Biol Chem. 2002 Nov 8;277(45):42852-8
12218053
Cell. 2010 Mar 5;140(5):744-52
20211142
Genome Biol. 2003;4(9):117
12952525
Nucleic Acids Res. 2003 Jan 1;31(1):374-8
12520026
J Biol Chem. 2001 Apr 20;276(16):13442-51
11278309
Genome Biol. 2002;3(1):RESEARCH0005
11806828
J Cell Sci. 2009 Nov 15;122(Pt 22):4027-34
19910494
J Biol Chem. 1999 Oct 22;274(43):30624-30
10521447