GO-based Functional Dissimilarity of Gene Sets

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Díaz Díaz, Norberto ^a   Aguilar Ruiz, Jesús S ^a  

^a UNIVERSIDAD PABLO DE OLAVIDE   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

FUNCTION EVALUATION; PROTEINS;

BIOLOGICAL PROCESS; COMPARATIVE ANALYSIS; DISSIMILARITY MEASURES; FUNCTIONAL SIMILARITY; GENE FUNCTION; GENE ONTOLOGY; NUMERICAL VALUES; PAIRWISE DISTANCES;

GENES;

PROTEIN;

ALGORITHM; ARTICLE; GENE; GENETIC DATABASE; GENETICS; HUMAN; LINGUISTICS; MEDICAL INFORMATION SYSTEM; RECEIVER OPERATING CHARACTERISTIC; SACCHAROMYCES CEREVISIAE; SEMANTICS;

ALGORITHMS; DATABASES, GENETIC; GENES; HUMANS; PROTEINS; ROC CURVE; SACCHAROMYCES CEREVISIAE; SEMANTICS; UNIFIED MEDICAL LANGUAGE SYSTEM; VOCABULARY, CONTROLLED;

EID: 80052151544     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-360     Document Type: Article

References (44)

1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
2. Yu U, Choi Y, Choi J, Kim S. TO-GO: a Java-based Gene Ontology navigation environment. Bioinformatics 2005, 21(17):3580-3581. 10.1093/bioinformatics/bti560, 15994194.
3. Khatri P, Drǎghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 2005, 21(18):3587-3595. 10.1093/bioinformatics/bti565, 2435250, 15994189.
4. Beisvag V, Junge FK, Bergum H, Jolsum L, Lydersen S, Gunther CC, Ramampiaro H, Langaas M, Sandvik AK, Laegreid A. GeneTools- application for functional annotation and statistical hypothesis testing. BMC Bioinformatics 2006, 7:470. 10.1186/1471-2105-7-470, 1630634, 17062145.
5. Pontius J, Wagner L, Schuler G. UniGene: a unified view of the transcriptome. The NCBI Handbook. Bethesda (MD): National Center for Biotechnology Information 2003,
6. Maglott D, Ostell J, Pruitt K, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Research 2005, (33 Database):D54-D58.
7. Bairoch A, Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Research 2000, 28:45-48. 10.1093/nar/28.1.45, 102476, 10592178.
8. Sealfon RS, Hibbs MA, Huttenhower C, Myers CL, Troyanskaya OG. GOLEM: an interactive graph-based gene-ontology navigation and analysis tool. BMC Bioinformatics 2006, 7:443. 10.1186/1471-2105-7-443, 1618863, 17032457.
9. Berriz G, King O, Bryan B, Sander C, Roth F. Characterizing gene sets with FuncAssociate. Bioinformatics 2003, 19:2502-2504. 10.1093/bioinformatics/btg363, 14668247., http://llama.med.harvard.edu/Software.html
10. Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinformatics 2005, 21(16):3448-3449. 10.1093/bioinformatics/bti551, 15972284., http://dx.doi.org/10.1093/bioinformatics/bti551
11. Huang D, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler MW, Lane HC, Lempicki RA. DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic acids research 2007, (35 Web Server):gkm415+., http://dx.doi.org/10.1093/nar/gkm415
12. Couto F, Silva M, Coutinho P. Implementation of a Functional Semantic Similarity Measure between Gene-Products. DI/FCUL TR 03-29, Department of Informatics, University of Lisbon 2003, http://docs.di.fc.ul.pt/jspui/handle/10455/2935
13. Kriventseva E, Fleischmann W, Apweiler R. CluSTr: a database of Clusters of SWISS-PROT+TrEMBL proteins. Nucelic Acids Res 2001, 29:33-36.
14. Lee SG, Hur JU, Kim YS. A graph-theoretic modeling on GO space for biological interpretation of gene clusters. Bioinformatics 2004, 20(3):381-388. 10.1093/bioinformatics/btg420, 14960465.
15. Jiang JJ, Conrath DW. Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy. International Conference Research on Computational Linguistics 1997, 19-33.
16. Lin D. An Information-Theoretic Definition of Similarity. Proceedings of the 15th International Conference on Machine Learning, Morgan Kaufmann, San Francisco, CA 1998, 296-304.
17. Resnik P. Semantic Similarity in a Taxonomy: An Information-Based Measure and its Application to Problems of Ambiguity in Natural Language. Journal of Artificial Intelligence Research 1999, 11:95-130.
18. Guo X, Liu R, Shriver CD, Hu H, Liebman MN. Assessing semantic similarity measures for the characterization of human regulatory pathways. Bioinformatics 2006, 22(8):967-973. 10.1093/bioinformatics/btl042, 16492685.
19. Sevilla JL, Segura V, Podhorski A, Guruceaga E, Mato JM, Martinez-Cruz LA, Corrales FJ, Rubio A. Correlation between Gene Expression and GO Semantic Similarity. IEEE/ACM Trans Comput Biol Bioinformatics 2005, 2(4):330-338.
20. Wang H, Azuaje F, Bodenreider O, Dopazo J. Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships. Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'2004) 2004, 25-31.
21. Pozo AD, Pazos F, Valencia A. Defining functional distances over Gene Ontology. BMC Bioinformatics 2008, 9:50-65. 10.1186/1471-2105-9-50, 2375122, 18221506.
22. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJA, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucl Acids Res 2009, 37(suppl 1):D211-215. 2686546, 18940856.
23. Wang JZZ, Du Z, Payattakool R, Yu PSS, Chen CFF. A New Method to Measure the Semantic Similarity of GO Terms. Bioinformatics 2007, 23(10):1274-1281. 10.1093/bioinformatics/btm087, 17344234.
24. Lord PW, Stevens RD, Brass A, Goble CA. Semantic similarity measures as tools for exploring the gene ontology. Pac Symp Biocomput 2003, 601-612., http://view.ncbi.nlm.nih.gov/pubmed/12603061
25. Liu H, Hu ZZ, Wu CH. DynGO: a tool for visualizing and mining of Gene Ontology and its associations. BMC bioinformatics 2005, 6., http://dx.doi.org/10.1186/1471-2105-6-201
26. Azuaje F, Al-Shahrour F, Dopazo J. Ontology-Driven Approaches to Analyzing Data in Functional Genomics. Methods in Molecular Biology 2005, 316:67-86.
27. Chagoyen M, Carazo J, Montano AP. Assessment of protein set coherence using functional annotations. BMC Bioinformatics 2008, 9:444+. 10.1186/1471-2105-9-444, 2588600, 18937846., http://dx.doi.org/10.1186/1471-2105-9-444
28. Guo X. Gene Ontology-based Semantic Similarity Measures. World Wide Web electronic publication 2008, http://www.bioconductor.org/packages/2.2/bioc/vignettes/SemSim/inst/doc/SemSim.pdf
29. Brameier M, Wiuf C. Co-clustering and visualization of gene expression data and gene ontology terms for Saccharomyces cerevisiae using self-organizing maps. J of Biomedical Informatics 2007, 40:160-173., http://portal.acm.org/citation.cfm?id=1230523
30. Wu H, Su Z, Mao F, Olman V, Xu Y. Prediction of functional modules based on comparative genome analysis and Gene Ontology application. Nucleic Acids Research 2005, 33(9):2822-2837. 10.1093/nar/gki573, 1130488, 15901854., http://dx.doi.org/10.1093/nar/gki573
31. Tao Y, Sam L, Li J, Friedman C, Lussier YA. Information theory applied to the sparse gene ontology annotation network to predict novel gene function. Bioinformatics 2007, 23(13):i529-538. 10.1093/bioinformatics/btm195, 2882681, 17646340., http://dx.doi.org/10.1093/bioinformatics/btm195
32. Xu T, Du L, Zhou Y. Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data. BMC Bioinformatics 2008, 9:472+. 10.1186/1471-2105-9-472, 2612010, 18986551., http://dx.doi.org/10.1186/1471-2105-9-472
33. Lerman G, Shakhnovich BE. Defining functional distance using manifold embeddings of gene ontology annotations. Proceedings of the National Academy of Sciences of the United States of America 2007, 104(27):11334-11339. 10.1073/pnas.0702965104, 2040899, 17595300.
34. Schlicker A, Domingues FS, Rahnenfuhrer J, Lengauer T. A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics 2006, 7:302+. 10.1186/1471-2105-7-302, 1559652, 16776819.
35. Schlicker A, Albrecht M. FunSimMat: a comprehensive functional similarity database. Nucl Acids Res 2008, (36 Database):D434-D439.
36. Bastos H, Faria D, Pesquita C, Falcão AO. Using GO terms to evaluate protein clustering. BioOntologies SIG at ISMB/ECCB - 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) 2007, http://hdl.handle.net/10455/6214
37. Zheng B, Lu X. Novel metrics for evaluating the functional coherence of protein groups via protein semantic network. Genome Biology 2007, 8(7):R153+. 2323239, 17672896., http://dx.doi.org/10.1186/gb-2007-8-7-r153
38. Ruths T, Ruths D, Nakhleh L. GS2: an efficiently computable measure of GO-based similarity of gene sets. Bioinformatics 2009, 25(9):1178-1184. 10.1093/bioinformatics/btp128, 2672633, 19289444.
39. Richards AJ, Muller B, Shotwell M, Cowart LA, Rohrer B, Lu X. Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph. Bioinformatics 2010, 26(12):i79-i87. 10.1093/bioinformatics/btq203, 2881388, 20529941., http://dx.doi.org/10.1093/bioinformatics/btq203
40. Pesquita C, Faria D, Falcão AO, Lord P, Couto FM. Semantic Similarity in Biomedical Ontologies. PLoS Comput Biol 2009, 5(7):e1000443+. 2712090, 19649320.
41. Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. The GOA database in 2009-an integrated Gene Ontology Annotation resource. Nucleic acids research 2009, (37 Database):D396-403., http://dx.doi.org/10.1093/nar/gkn803
42. Yu G, Li F, Qin Y, Bo X, Wu Y, Wang S. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 2010, 26(7):976-978. 10.1093/bioinformatics/btq064, 20179076., http://dx.doi.org/10.1093/bioinformatics/btq064
43. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic acids research 2010, (38 Database):D355-360.
44. Aurenhammer F, Klein R. Voronoi Diagrams 1999, Amsterdan: Handbook of Computational Geometry. Elsevier Science Publishers B.V, Sack J-R, Urrutia J.