Colorectal cancer atlas: An integrative resource for genomic and proteomic annotations from colorectal cancer cell lines and tissues

David Chisanga, Shivakumar Keerthikumar, Mohashin Pathan, Dinuka Ariyaratne, Hina Kalra, Stephanie Boukouris, Nidhi Abraham Mathew, Haidar Al Saffar, Lahiru Gangoda, Ching-Seng Ang, Oliver M Sieber, John M Mariadason, Ramanuj Dasgupta, Naveen Chilamkurti, Suresh Mathivanan, David Chisanga, Shivakumar Keerthikumar, Mohashin Pathan, Dinuka Ariyaratne, Hina Kalra, Stephanie Boukouris, Nidhi Abraham Mathew, Haidar Al Saffar, Lahiru Gangoda, Ching-Seng Ang, Oliver M Sieber, John M Mariadason, Ramanuj Dasgupta, Naveen Chilamkurti, Suresh Mathivanan

Abstract

In order to advance our understanding of colorectal cancer (CRC) development and progression, biomedical researchers have generated large amounts of OMICS data from CRC patient samples and representative cell lines. However, these data are deposited in various repositories or in supplementary tables. A database which integrates data from heterogeneous resources and enables analysis of the multidimensional data sets, specifically pertaining to CRC is currently lacking. Here, we have developed Colorectal Cancer Atlas (http://www.colonatlas.org), an integrated web-based resource that catalogues the genomic and proteomic annotations identified in CRC tissues and cell lines. The data catalogued to-date include sequence variations as well as quantitative and non-quantitative protein expression data. The database enables the analysis of these data in the context of signaling pathways, protein-protein interactions, Gene Ontology terms, protein domains and post-translational modifications. Currently, Colorectal Cancer Atlas contains data for >13 711 CRC tissues, >165 CRC cell lines, 62 251 protein identifications, >8.3 million MS/MS spectra, >18 410 genes with sequence variations (404 278 entries) and 351 pathways with sequence variants. Overall, Colorectal Cancer Atlas has been designed to serve as a central resource to facilitate research in CRC.

© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Figures

Figure 1.
Figure 1.
Snapshot of Colorectal Cancer Atlas features. An overview of proteomic and genomic data features for APC gene is displayed. A user can query the database using a gene symbol or a protein name. A gene information page will provide the users with details pertaining to protein domains, post-translational modifications (PTM), reported mutations in cell lines/tissues, quantitative protein expression, pathway, protein–protein interaction (PPI) and cell line drug sensitivity.
Figure 2.
Figure 2.
PTMs and domains in β-catenin are affected due to mutation. Snapshot of β-catenin molecular page is displayed. The PTMs affected by mutations can be viewed in the tab PTMs. Mutations in β-catenin at positions important for phosphorylation (S33, S37, T41 and S45) allows for the stabilization of β-catenin and constitutive activation of the Wnt signaling pathway. The upstream kinases responsible for the phosphorylation is also provided along with the literature reference. Likewise, mutations in the armadillo domain can be viewed by correlating the sequence variants and the domain span regions. For example, mutations in the armadillo domain (p.R582) in β-catenin have been described which have been reported to alter the binding of β-catenin to TCF4 (24).

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Source: PubMed

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