GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining
Bioengineering Department, Politecnico di Milano, I-20133 Milano, Italy
* To whom correspondence should be addressed. Tel: + 39 02 2399 3336/03; Fax: + 39 02 2399 3360; Email: masseroli{at}biomed.polimi.it
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
Received February 15, 2004; Revised and Accepted April 8, 2004
Statistical and clustering analyses of gene expression results from high-density microarray experiments produce lists of hundreds of genes regulated differentially, or with particular expression profiles, in the conditions under study. Independent of the microarray platforms and analysis methods used, these lists must be biologically interpreted to gain a better knowledge of the patho-physiological phenomena involved. To this end, numerous biological annotations are available within heterogeneous and widely distributed databases. Although several tools have been developed for annotating lists of genes, most of them do not give methods for evaluating the relevance of the annotations provided, or for estimating the functional bias introduced by the gene set on the array used to identify the gene list considered. We developed Genome Functional INtegrated Discoverer (GFINDer), a web server able to automatically provide large-scale lists of user-classified genes with functional profiles biologically characterizing the different gene classes in the list. GFINDer automatically retrieves annotations of several functional categories from different sources, identifies the categories enriched in each class of a user-classified gene list and calculates statistical significance values for each category. Moreover, GFINDer enables the functional classification of genes according to mined functional categories and the statistical analysis is of the classifications obtained, aiding better interpretation of microarray experiment results. GFINDer is available online at http://www.medinfopoli.polimi.it/GFINDer/.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. V. Antonov, T. Schmidt, Y. Wang, and H. W. Mewes ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data Nucleic Acids Res., July 1, 2008; 36(suppl_2): W347 - W351. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Q. Zheng and X.-J. Wang GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis Nucleic Acids Res., July 1, 2008; 36(suppl_2): W358 - W363. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Al-Shahrour, J. Carbonell, P. Minguez, S. Goetz, A. Conesa, J. Tarraga, I. Medina, E. Alloza, D. Montaner, and J. Dopazo Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments Nucleic Acids Res., July 1, 2008; 36(suppl_2): W341 - W346. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 I. Rivals, L. Personnaz, L. Taing, and M.-C. Potier Enrichment or depletion of a GO category within a class of genes: which test? Bioinformatics, February 15, 2007; 23(4): 401 - 407. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Wu, X. Mao, T. Cai, J. Luo, and L. Wei KOBAS server: a web-based platform for automated annotation and pathway identification. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W720 - W724. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. V. Antonov, I. V. Tetko, and H. W. Mewes A systematic approach to infer biological relevance and biases of gene network structures Nucleic Acids Res., January 10, 2006; 34(1): e6 - e6. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Mao, T. Cai, J. G. Olyarchuk, and L. Wei Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary Bioinformatics, October 1, 2005; 21(19): 3787 - 3793. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Maere, K. Heymans, and M. Kuiper BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks Bioinformatics, August 15, 2005; 21(16): 3448 - 3449. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Masseroli, O. Galati, and F. Pinciroli GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists Nucleic Acids Res., July 1, 2005; 33(suppl_2): W717 - W723. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Zhang, S. Kirov, and J. Snoddy WebGestalt: an integrated system for exploring gene sets in various biological contexts Nucleic Acids Res., July 1, 2005; 33(suppl_2): W741 - W748. [Abstract] [Full Text] [PDF]
|
|