The Gene-Centric Content Management System and Its Application for Cognitive Proteomics

Proteomes
Ekaterina V PoverennayaAndrey V Lisitsa

Abstract

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.

References

Jul 30, 2005·Proteomics·Eric W DeutschRuedi Aebersold
Dec 9, 2010·Nature Biotechnology·Mathias UhlenFredrik Ponten
Jul 12, 2011·Molecular & Cellular Proteomics : MCP·Pierre LegrainGilbert S Omenn
Dec 4, 2012·Nucleic Acids Research·Juan Antonio VizcaínoHenning Hermjakob
Dec 5, 2012·Journal of Proteome Research·Pascale GaudetLydie Lane
Dec 12, 2012·Journal of Proteome Research·Robert J A GoodeA Ian Smith
Dec 22, 2012·Journal of Proteome Research·Feifei GuoFuchu He
Dec 22, 2012·Journal of Proteome Research·Victor G ZgodaAlexander I Archakov
Feb 28, 2013·Nature Methods·Lloyd M SmithUNKNOWN Consortium for Top Down Proteomics
Sep 3, 2013·Biochimica Et Biophysica Acta·Ekaterina V PoverennayaAlexander I Archakov
Jan 21, 2014·Expert Review of Proteomics·Andrey LisitsaAlexander Archakov
May 30, 2014·Nature·Min-Sik KimAkhilesh Pandey
May 30, 2014·Nature·Mathias WilhelmBernhard Kuster
Oct 29, 2014·Expert Review of Proteomics·Neil L KelleherRichard D LeDuc
Feb 24, 2015·Bioinformatics·David Fenyö, Ronald C Beavis
May 16, 2015·Biomedit︠s︡inskai︠a︡ khimii︠a︡·E A PonomarenkoA I Archakov
Jul 7, 2015·Journal of Proteome Research·George Sergeevich KrasnovElena Alexandrovna Ponomarenko
Apr 6, 2016·Molecular Systems Biology·Mathias UhlénJens Nielsen
Jun 15, 2016·International Journal of Analytical Chemistry·Elena A PonomarenkoAlexander I Archakov
Nov 5, 2016·Journal of Proteome Research·Yves VandenbrouckCharles Pineau
Nov 5, 2016·Journal of Proteome Research·Ekaterina V PoverennayaAlexander I Archakov
Aug 31, 2017·Journal of Proteome Research·Gilbert S OmennEric W Deutsch

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Citations

Feb 15, 2019·Reproductive Biology and Endocrinology : RB&E·Muzaffer A BhatDebabrata Ghosh

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Methods Mentioned

BETA
RNA-seq
affinity-purification
chemical modifications

Software Mentioned

Gene - Centric Content Management System ( GenoCMS )
HPP
SRM
GPMdb
GenomewidePDB
PRIDE
CAPER
GenoCMS
Proteome Browser ( TBP )
RESTful

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