Functional analysis beyond enrichment: Non-redundant reciprocal linkage of genes and biological terms

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  Fontanillo, Celia ^a   Nogales Cadenas, Ruben ^a   Pascual Montano, Alberto ^a   de Las Rivas, Javier ^a  

^a CSIC   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

MULTIPROTEIN COMPLEX; NUCLEAR PROTEIN; PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

ALGORITHM; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; DIGITAL FILTERING; FUZZY SYSTEM; GENE IDENTIFICATION; GENETERM LINKER; GENETIC ANALYSIS; INFORMATION PROCESSING; INTERMETHOD COMPARISON; INTERNET; MATHEMATICAL COMPUTING; BIOLOGY; CLASSIFICATION; CLUSTER ANALYSIS; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETIC PREDISPOSITION; GENETICS; HUMAN; METHODOLOGY; PHYSIOLOGY; REPRODUCIBILITY; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE REGULATORY NETWORKS; GENETIC PREDISPOSITION TO DISEASE; HUMANS; INTERNET; NUCLEAR PROTEINS; PROTEINS; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION;

EID: 80052831114     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0024289     Document Type: Article

References (24)

1. Huang DW, Sherman BT, Lempicki RA, (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: 1-13.
2. Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM, Pascual-Montano A, (2007) GeneCodis: a web-based tool for finding significant concurrent annotations in gene lists. Genome Biol 8: R3.
3. Nogales-Cadenas R, Carmona-Saez P, Vazquez M, Vicente C, Yang X, et al. (2009) GeneCodis: interpreting gene lists through enrichment analysis and integration of diverse biological information. Nucleic Acids Res 37: W317-322.
4. Huang DW, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
5. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102: 15545-15550.
6. Gene Ontology Consortium (2010) The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res 38: D331-335.
7. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M, (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38: D355-360.
8. Apweiler R, Martin MJ, O'Donovan C, Magrane M, Alam-Faruque Y, et al. (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 38: D142-148.
9. Alves R, Rodriguez-Baena DS, Aguilar-Ruiz JS, (2010) Gene association analysis: a survey of frequent pattern mining from gene expression data. Brief Bioinform 11: 210-224.
10. Gupta T, Seifoddini H, (1990) Production data based similarity coefficient for machine-component grouping decisions in the design of a cellular manufacturing system. International Journal of Production Research 28: 1247-1269.
11. Toivonen H, Klemettinen M, Ronkainen P, Hatonen K, Mannila H, (1995) Pruning and grouping discovered association rules. MLnet Workshop on Statistics, Machine Learning, and Discovery in Databases pp. 47-52 Crete, Greece.
12. Draghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA, (2003) Global functional profiling of gene expression. Genomics 81: 98-104.
13. Benjamini Y, Hochberg Y, (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J Roy Stat Soc (Ser B) 57: 289-300.
14. Rousseeuw PJ, (1987) Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. Journal of Computational and Applied Mathematics 20: 53-65.
15. Bader GD, Hogue CW, (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4: 2.
16. Prieto C, De Las Rivas J, (2006) APID: Agile Protein Interaction DataAnalyzer. Nucleic Acids Res 34: W298-302.
17. Hernandez-Toro J, Prieto C, De Las Rivas J, (2007) APID2NET: unified interactome graphic analyzer. Bioinformatics 23: 2495-2497.
18. Dalton L, Ballarin V, Brun M, (2009) Clustering algorithms: on learning, validation, performance, and applications to genomics. Curr Genomics 10: 430-445.
19. Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, et al. (2010) CORUM: the comprehensive resource of mammalian protein complexes- 2009. Nucleic Acids Res 38: D497-501.
20. Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, et al. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res 38: D433-436.
21. Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA, (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33: D514-517.
22. Medrano-Soto A, Pal D, Eisenberg D, (2008) Inferring molecular function: contributions from functional linkages. Trends Genet 24: 587-590.
23. Llewellyn R, Eisenberg DS, (2008) Annotating proteins with generalized functional linkages. Proc Natl Acad Sci U S A 105: 17700-17705.
24. Merico D, Isserlin R, Stueker O, Emili A, Bader GD, (2010) Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One 5 (11): e13984.