title: Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes.
abstract: Transcription factors (TFs) bind at multiple sites in the genome and regulate expression of many genes. Regulating TF binding in a gene specific manner remains a formidable challenge in drug discovery because the same binding motif may be present at multiple locations in the genome. Here, we present Onco-Regulon (http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm), an integrated database of regulatory motifs of cancer genes clubbed with Unique Sequence-Predictor (USP) a software suite that identifies unique sequences for each of these regulatory DNA motifs at the specified position in the genome. USP works by extending a given DNA motif, in 5'→3', 3' →5' or both directions by adding one nucleotide at each step, and calculates the frequency of each extended motif in the genome by Frequency Counter programme. This step is iterated till the frequency of the extended motif becomes unity in the genome. Thus, for each given motif, we get three possible unique sequences. Closest Sequence Finder program predicts off-target drug binding in the genome. Inclusion of DNA-Protein structural information further makes Onco-Regulon a highly informative repository for gene specific drug development. We believe that Onco-Regulon will help researchers to design drugs which will bind to an exclusive site in the genome with no off-target effects, theoretically.Database URL: http://www.scfbio-iitd.res.in/software/onco/NavSite/index.htm.
authors: Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology-Delhi, New Delhi, India.
authors: Navneet
authors: N
authors: Tomar
authors: Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology-Delhi, New Delhi, India Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, Delhi, India.
authors: Akhilesh
authors: A
authors: Mishra
authors: Labaratory of Molecular Biology, South Asian University, New Delhi, India nmrinal@gmail.com.
authors: Nirotpal
authors: N
authors: Mrinal
authors: Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology-Delhi, New Delhi, India Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, Delhi, India Department of Chemistry, Indian Institute of Technology-Delhi, Delhi nmrinal@gmail.com.
authors: B
authors: B
authors: Jayaram
mesh_terms: D000818:Animals; D030561:Databases, Nucleic Acid; D052138:Genes, Neoplasm; D015894:Genome, Human; D006801:Humans; D009363:Neoplasm Proteins / Q000235:genetics*; D009369:Neoplasms / Q000235:genetics*; D059372:Nucleotide Motifs; D020218:Response Elements; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D009363:Neoplasm Proteins; D014157:Transcription Factors