PuTmiR: a database for extracting neighboring transcription factors of human microRNAs.
BACKGROUND
Some of the recent investigations in systems biology have revealed the existence of a complex regulatory network between genes, microRNAs (miRNAs) and transcription factors (TFs). In this paper, we focus on TF to miRNA regulation and provide a novel interface for extracting the list of putative TFs for human miRNAs. A putative TF of an miRNA is considered here as those binding within the close genomic locality of that miRNA with respect to its starting or ending base pair on the chromosome. Recent studies suggest that these putative TFs are possible regulators of those miRNAs.


METHODS
The interface is built around two datasets that consist of the exhaustive lists of putative TFs binding respectively in the 10 kb upstream region (USR) and downstream region (DSR) of human miRNAs. A web server, named as PuTmiR, is designed. It provides an option for extracting the putative TFs for human miRNAs, as per the requirement of a user, based on genomic locality, i.e., any upstream or downstream region of interest less than 10 kb. The degree distributions of the number of putative TFs and miRNAs against each other for the 10 kb USR and DSR are analyzed from the data and they explore some interesting results. We also report about the finding of a significant regulatory activity of the YY1 protein over a set of oncomiRNAs related to the colon cancer.


CONCLUSIONS
The interface provided by the PuTmiR web server provides an important resource for analyzing the direct and indirect regulation of human miRNAs. While it is already an established fact that miRNAs are regulated by TFs binding to their USR, this database might possibly help to study whether an miRNA can also be regulated by the TFs binding to their DSR.
Bandyopadhyay
Sanghamitra
S
Machine Intelligence Unit, Indian Statistical Institute, 203 B, T Road, Kolkata-700108, India.
Bhattacharyya
Malay
M
D001665:Binding Sites; D030541:Databases, Genetic; D053263:Gene Regulatory Networks; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D017423:Sequence Analysis, RNA; D012984:Software; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*
D035683:MicroRNAs; D014157:Transcription Factors
Cell. 2007 May 4;129(3):617-31
17482553
Genes Dev. 2008 Dec 1;22(23):3242-54
19015276
Proteomics. 2008 May;8(10):1975-9
18491312
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6
14681465
Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8
17991681
Mol Syst Biol. 2006;2:46
16969338
Nature. 2005 Jun 9;435(7043):834-8
15944708
PLoS Comput Biol. 2007 Jul;3(7):e131
17630826
Cancer Cell. 2008 Nov 4;14(5):369-81
18977326
Science. 2005 Dec 16;310(5755):1817-21
16308420
Mol Syst Biol. 2007;3:152
18091723
BMC Bioinformatics. 2009 May 28;10:163
19476620
Mol Cell Biol. 2007 Oct;27(19):6889-902
17636019
Genome Biol. 2007;8(2):R27
17326821
Cancer Res. 2008 Dec 15;68(24):10094-104
19074875
Bioinformatics. 2008 Feb 1;24(3):303-8
18055479
Nature. 2010 Feb 4;463(7281):616
20130638
Silence. 2010 Feb 02;1(1):6
20226080
BMC Genomics. 2008 Nov 27;9:564
19038026
Nucleic Acids Res. 2003 Jan 1;31(1):374-8
12520026
Proc Natl Acad Sci U S A. 2002 Nov 26;99(24):15524-9
12434020
Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17719-24
17965236
Nucleic Acids Res. 2010 Jan;38(Database issue):D119-22
19786497
Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):381-2
11209037
Cell. 2004 Jan 23;116(2):281-97
14744438
Nature. 2005 Mar 17;434(7031):338-45
15735639