RESUMO
The Human Proteome Project is moving into the next phase of creating and/or reconsidering the functional annotations of proteins using the chromosome-centric paradigm. This challenge cannot be solved exclusively using automated means, but rather requires human intelligence for interpreting the combined data. To foster the integration between human cognition and post-genome array a number of specific tools were recently developed, among them CAPER, GenomewidePDB, and The Proteome Browser (TPB). For the purpose of tackling the task of protein functional annotating the Gene-Centric Content Management System (GenoCMS) was expanded with new features. The goal was to enable bioinformaticans to develop self-made applications and to position these applets within the generalized informational canvas supported by GenoCMS. We report the results of GenoCMS-enabled integration of the concordant informational flows in the chromosome-centric framework of the human chromosome 18 project. The workflow described in the article can be scaled to other human chromosomes, and also supplemented with new tracks created by the user. The GenoCMS is an example of a project-oriented informational system, which are important for public data sharing.
RESUMO
The Chromosome-centric Human Proteome Project (C-HPP) is aimed to identify the variety of protein products and transcripts of the number of chromosomes. The Russian part of C-HPP is devoted to the study of the human chromosome 18. Using widely accepted Tophat and SpliceGrapher, a tool for accurate splice sites and alternative mRNA isoforms prediction, we performed the extensive mining of the splice variants of chromosome 18 transcripts and encoded protein products in liver, brain, lung, kidney, blood, testis, derma, and skeletal muscles. About 6.1 billion of the reads represented by 450 billion of the bases have been analyzed. The relative frequencies of splice events as well as gene expression profiles in normal tissues are evaluated. Using ExPASy PROSITE, the novel features and possible functional sites of previously unknown splice variants were highlighted. A set of unique proteotypic peptides enabling the identification of novel alternative protein species using mass-spectrometry is constructed. The revealed data will be integrated into the gene-centric knowledgebase of the Russian part of C-HPP available at http://kb18.ru and http://www.splicing.zz.mu/.
