GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics.

Nucleic Acids Research
Daniel Tabas-MadridAlberto Pascual-Montano

Abstract

Since its first release in 2007, GeneCodis has become a valuable tool to functionally interpret results from experimental techniques in genomics. This web-based application integrates different sources of information to finding groups of genes with similar biological meaning. This process, known as enrichment analysis, is essential in the interpretation of high-throughput experiments. The frequent feedbacks and the natural evolution of genomics and bioinformatics have allowed the growth of the tool and the development of this third release. In this version, a special effort has been made to remove noisy and redundant output from the enrichment results with the inclusion of a recently reported algorithm that summarizes significantly enriched terms and generates functionally coherent modules of genes and terms. A new comparative analysis has been added to allow the differential analysis of gene sets. To expand the scope of the application, new sources of biological information have been included, such as genetic diseases, drugs-genes interactions and Pubmed information among others. Finally, the graphic section has been renewed with the inclusion of new interactive graphics and filtering options. The application is freely availab...Continue Reading

References

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Citations

Sep 10, 2013·Proceedings of the National Academy of Sciences of the United States of America·Omer GokcumenJan O Korbel
Jun 12, 2013·Nucleic Acids Research·Daniel D'AndreaAnna Tramontano
Oct 8, 2013·European Journal of Medical Research·Yong Jin, Wei Da
Apr 5, 2013·PloS One·Takeshi ChiyomaruRajvir Dahiya
Dec 21, 2013·Molecular Biology of the Cell·Giulia AntonialiGianluca Tell
Dec 18, 2013·Nature Structural & Molecular Biology·Emiliano P RicciMelissa J Moore
Jan 31, 2014·Proceedings of the National Academy of Sciences of the United States of America·José M Franco-ZorrillaRoberto Solano
Mar 29, 2014·Chemical Communications : Chem Comm·Smita NaharSouvik Maiti
Apr 10, 2014·Journal of Bioinformatics and Computational Biology·Nermin Pinar KarabulutMurat Cokol
Nov 30, 2013·Human Molecular Genetics·Martine Chevillard-BrietFabrice Escaffit
Dec 11, 2013·Proceedings of the National Academy of Sciences of the United States of America·Xiaohui NiJie Wang
Sep 28, 2014·Nucleic Acids Research·Cornelia VeselyMichael F Jantsch
Jul 27, 2014·The Journal of Antimicrobial Chemotherapy·Nicola SquillaceAndrea Gori
May 6, 2015·Molecular Medicine Reports·Guoqiang ChenMeng Yu
Nov 27, 2015·Journal of Neuroimmune Pharmacology : the Official Journal of the Society on NeuroImmune Pharmacology·Liz SimonPatricia Molina
Feb 4, 2016·Journal of Neuroinflammation·Shalini SwaroopAnirban Basu
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Feb 13, 2015·Proceedings of the National Academy of Sciences of the United States of America·James R BayrerRobert J Fletterick
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Dec 19, 2015·BMC Evolutionary Biology·Eva M StruckenCedric Gondro

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Software Mentioned

Ruby
OMIM
GO
GeneCodis3
GeneTerm Linker or
Mapper
DAVID
ProfCom
Onto
GeneCodis

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