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J Proteome Res. 2015 Sep 4;14(9):3432-40. doi: 10.1021/acs.jproteome.5b00488. Epub 2015 Jul 15.

Insights from Chromosome-Centric Mapping of Disease-Associated Genes: Chromosome 12 Perspective.

Author information

1
Institute of Bioinformatics , International Tech Park, Bangalore-560066, India.
2
Manipal University , Madhav Nagar, Manipal-576104, India.
3
Mazumdar Shaw Centre for Translational Research, Mazumdar Shaw Medical Foundation, Narayana Health , Bangalore-560099, India.
4
Thrombosis Research Institute, Narayana Health , Bangalore-560099, India.

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.

KEYWORDS:

B/D-HPP; CHPP; amplicons; chromosome 12; diseasome; functional prediction; glioma; proteomics

PMID:
26143930
DOI:
10.1021/acs.jproteome.5b00488
[Indexed for MEDLINE]

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