title: IDPT: Insights into potential intrinsically disordered proteins through transcriptomic analysis of genes for prostate carcinoma epigenetic data.
abstract: Involvement of intrinsically disordered proteins (IDPs) with various dreadful diseases like cancer is an interesting research topic. In order to gain novel insights into the regulation of IDPs, in this article, we perform a transcriptomic analysis of mRNAs (genes) for transcripts encoding IDPs on a human multi-omics prostate carcinoma dataset having both gene expression and methylation data. In this regard, firstly the genes that consist of both the expression and methylation data, and that are corresponding to the cancer-related prostate-tissue-specific disordered proteins of MobiDb database, are selected. We apply standard t-test for determining differentially expressed genes as well as differentially methylated genes. A network having these genes and their targeter miRNAs from Diana Tarbase v7.0 database and corresponding Transcription Factors from TRANSFAC and ITFP databases, is then built. Thereafter, we perform literature search, and KEGG pathway and Gene Ontology analyses using DAVID database. Finally, we report several significant potential gene-markers (with the corresponding IDPs) that have inverse relationship between differential expression and methylation patterns, and that are hub genes of the TF-miRNA-gene network.
authors.affiliation: Machine Intelligence Unit, Indian Statistical Institute, Kolkata-700108, India. Electronic address: sauravmtech2@gmail.com.
authors.forename: Saurav
authors.initials: S
authors.lastname: Mallik
authors.affiliation: Department of Computer Science and Engineering, Jadavpur University, Kolkata-700032, India. Electronic address: sagnik.sen2008@gmail.com.
authors.forename: Sagnik
authors.initials: S
authors.lastname: Sen
authors.affiliation: Department of Computer Science and Engineering, Jadavpur University, Kolkata-700032, India. Electronic address: umaulik@cse.jdvu.ac.in.
authors.forename: Ujjwal
authors.initials: U
authors.lastname: Maulik
mesh_terms: D002277:Carcinoma / Q000235:genetics* / Q000378:metabolism; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D064267:Intrinsically Disordered Proteins / Q000378:metabolism*; D008297:Male; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000378:metabolism; D012196:Review Literature as Topic; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D064267:Intrinsically Disordered Proteins; D014157:Transcription Factors
keywords: Epigenetic genemarkers; Hub genes; Intrinsically disordered proteins; Multi-omics prostate carcinoma epigenetic dataset; TF-miRNA-gene network; Transcriptomic analysis of genes; t-test