title: Insights from Chromosome-Centric Mapping of Disease-Associated Genes: Chromosome 12 Perspective.
abstract: In line with the aims of the Chromosome-based Human Proteome Project and the Biology/Disease-based Human Proteome Project, we have been studying differentially expressed transcripts and proteins in gliomas—the most prevalent primary brain tumors. Here, we present a perspective on important insights from this analysis in terms of their co-expression, co-regulation/de-regulation, and co-localization on chromosome 12 (Chr. 12). We observe the following: (1) Over-expression of genes mapping onto amplicon regions of chromosomes may be considered as a biological validation of mass spectrometry data. (2) Their co-localization further suggests common determinants of co-expression and co-regulation of these clusters. (3) Co-localization of "missing" protein genes of Chr. 12 in close proximity to functionally related genes may help in predicting their functions. (4) Further, integrating differentially expressed gene-protein sets and their ontologies with medical terms associated with clinical phenotypes in a chromosome-centric manner reveals a network of genes, diseases, and pathways—a diseasome network. Thus, chromosomal mapping of disease data sets can help uncover important regulatory and functional links that may offer new insights for biomarker development.
authors.affiliation: Institute of Bioinformatics , International Tech Park, Bangalore-560066, India.|Manipal University , Madhav Nagar, Manipal-576104, India.
authors.forename: Savita
authors.initials: S
authors.lastname: Jayaram
authors.affiliation: Institute of Bioinformatics , International Tech Park, Bangalore-560066, India.|Manipal University , Madhav Nagar, Manipal-576104, India.
authors.forename: Manoj Kumar
authors.initials: MK
authors.lastname: Gupta
authors.affiliation: Mazumdar Shaw Centre for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health , Bangalore-560099, India.
authors.forename: Bhadravathi Marigowda
authors.initials: BM
authors.lastname: Shivakumar
authors.affiliation: Manipal University , Madhav Nagar, Manipal-576104, India.|Thrombosis Research Institute, Narayana Health , Bangalore-560099, India.
authors.forename: Madankumar
authors.initials: M
authors.lastname: Ghatge
authors.affiliation: Manipal University , Madhav Nagar, Manipal-576104, India.|Thrombosis Research Institute, Narayana Health , Bangalore-560099, India.
authors.forename: Ankit
authors.initials: A
authors.lastname: Sharma
authors.affiliation: Thrombosis Research Institute, Narayana Health , Bangalore-560099, India.
authors.forename: Rajani Kanth
authors.initials: RK
authors.lastname: Vangala
authors.affiliation: Institute of Bioinformatics , International Tech Park, Bangalore-560066, India.|Mazumdar Shaw Centre for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health , Bangalore-560099, India.
authors.forename: Ravi
authors.initials: R
authors.lastname: Sirdeshmukh
mesh_terms: D001932:Brain Neoplasms / Q000235:genetics; D002874:Chromosome Mapping; D002881:Chromosomes, Human, Pair 12; D020022:Genetic Predisposition to Disease; D005910:Glioma / Q000235:genetics; D006801:Humans; D009363:Neoplasm Proteins / Q000235:genetics
chemical_list: D009363:Neoplasm Proteins
keywords: B/D-HPP; CHPP; amplicons; chromosome 12; diseasome; functional prediction; glioma; proteomics