Categorizer: A tool to categorize genes into user-defined biological groups based on semantic similarity

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Na, Dokyun ^a,b   Son, Hyungbin ^b   Gsponer, Jörg ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b Chung Ang University   (South Korea)

Author keywords

Categorization; Enrichment analysis; Gene ontology; Neurodegenerative diseases; Semantic similarity

Indexed keywords

ACCURACY; ARTICLE; CLASSIFICATION; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; DNA MODIFICATION; GENE; GENOMICS; HUNTINGTON CHOREA; MATHEMATICAL COMPUTING; MOLECULAR BIOLOGY; PROTEOMICS; SEMANTICS; BIOLOGY; COMPUTER INTERFACE; GENETIC DATABASE; GENETICS; HUMAN; MOLECULAR GENETICS; PATHOLOGY; SOFTWARE;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; HUMANS; HUNTINGTON DISEASE; MOLECULAR SEQUENCE ANNOTATION; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84924331984     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-1091     Document Type: Article

References (46)

1. Gene Ontology. [ http://geneontology.org ]
2. Huang DW, Sherman BT, Lempicki RA: Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009, 37:1-13. 10.1093/nar/gkn923
3. Huang DW, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2008, 4:44-57. 10.1038/nprot.2008.211
4. Maere S, Heymans K, Kuiper M: BiNGO: a cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005, 21:3448-3449. 10.1093/bioinformatics/bti551
5. Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP: Next generation software for functional trend analysis. Bioinformatics 2009, 25:3043-3044. 10.1093/bioinformatics/btp498
6. Zhang S, Binari R, Zhou R, Perrimon N: A genomewide RNA interference screen for modifiers of aggregates formation by mutant Huntingtin in Drosophila . Genetics 2010, 184:1165-1179. 10.1534/genetics.109.112516
7. Doumanis J, Wada K, Kino Y, Moore AW, Nukina N: RNAi screening in Drosophila cells identifies new modifiers of mutant huntingtin aggregation. PLoS ONE 2009, 4:e7275. 10.1371/journal.pone.0007275
8. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, et al.: The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004, 32:D258-D261. 10.1093/nar/gkh036
9. GO Slims. [ http://www.geneontology.org/GO.slims.shtml ]
10. Pesquita C, Faria D, Falcão AO, Lord P, Couto FM: Semantic similarity in biomedical ontologies. PLoS Comput Biol 2009, 5:e1000443. 10.1371/journal.pcbi.1000443
11. Mazandu GK, Mulder NJ: Information content-based gene ontology semantic similarity approaches: toward a unified framework theory. Biomed Res Int 2013, 2013:Article ID 292063.
12. Resnik P: Using information content to evaluate semantic similarity in a taxonomy. Proceedings of the 14th International Joint Conference on Artificial Intelligence. Volume 1 1995, 448-453.
13. Lin D: An information - theoretic definition of similarity. Proceedings of the 15th Conference on Machine Learning 1998, 296-304.
14. Jiang JJ, Conrath DW: Semantic similarity based on corpus statistics and lexical taxonomy. Proceedings of the 15th International Conference on Research in Computational Linguistics 1997, 19-33.
15. Mazandu GK, Mulder NJ: DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures. BMC Bioinformatics 2013, 14:284.
16. Xu Y, Guo M, Shi W, Liu X, Wang C: A novel insight into Gene Ontology semantic similarity. Genomics 2013, 101:368-375. 10.1016/j.ygeno.2013.04.010
17. Couto FM, Silva MJ: Disjunctive shared information between ontology concepts: application to Gene Ontology. J Biomed Sem 2011, 2:5. 10.1186/2041-1480-2-5
18. Speer N, Spieth C, Zell A: A memetic clustering algorithm for the functional partition of genes based on the gene ontology. Proceedings of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2004) 2004, 252-259.
19. Schlicker A, Rahnenführer J, Albrecht M, Lengauer T, Domingues FS: GOTax: investigating biological processes and biochemical activities along the taxonomic tree. Genome Biol 2007, 8:R33. 10.1186/gb-2007-8-3-r33
20. Du Z, Li L, Chen C-F, Yu PS, Wang JZ: G-SESAME: web tools for GO-term-based gene similarity analysis and knowledge discovery. Nucleic Acids Res 2009, 37:W345-W349. 10.1093/nar/gkp463
21. del Pozo A, Pazos F, Valencia A: Defining functional distances over gene ontology. BMC Bioinformatics 2008, 9:50. 10.1186/1471-2105-9-50
22. Schlicker A, Lengauer T, Albrecht M: Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. Bioinformatics 2010, 26:i561-i567. 10.1093/bioinformatics/btq384
23. Yilmaz S, Jonveaux P, Bicep C, Pierron L, Smaïl-Tabbone M, Devignes MD: Gene-disease relationship discovery based on model-driven data integration and database view definition. Bioinformatics 2009, 25:230-236. 10.1093/bioinformatics/btn612
24. UniProtKB. [ http://www.uniprot.org ]
25. Lord PW, Stevens RD, Brass A, Goble CA: Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics 2003, 19:1275-1283. 10.1093/bioinformatics/btg153
26. Wu X, Pang E, Lin K, Pei Z-M: Improving the measurement of semantic similarity between gene ontology terms and gene products: insights from an edge- and IC-based hybrid method. PLoS ONE 2013, 8:e66745. 10.1371/journal.pone.0066745
27. Glass K, Glass K, Girvan M, Girvan M: Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets. Sci Rep 2014, 4:4191.
28. Na D, Rouf M, O' Kane CJ, Rubinsztein DC, Gsponer J: NeuroGeM, a knowledgebase of genetic modifiers in neurodegenerative diseases. BMC Med Genomics 2013, 6:52. 10.1186/1755-8794-6-52
29. NeuroGeM. [ http://chibi.ubc.ca/neurogem ]
30. Lu B, Vogel H: Drosophila models of neurodegenerative diseases. Annu Rev Pathol Mech Dis 2009, 4:315-342. 10.1146/annurev.pathol.3.121806.151529
31. Shorter J: Hsp104: a weapon to combat diverse neurodegenerative disorders. Neurosignals 2008, 16:63-74. 10.1159/000109760
32. Li S-H, Li X-J: Huntingtin-protein interactions and the pathogenesis of Huntington's disease. Trends Genet 2004, 20:146-154. 10.1016/j.tig.2004.01.008
33. Nucifora FC, Sasaki M, Peters MF, Huang H, Cooper JK, Yamada M, Takahashi H, Tsuji S, Troncoso J, Dawson VL, Dawson TM, Ross CA: Interference by huntingtin and atrophin-1 with cbp-mediated transcription leading to cellular toxicity. Science 2001, 291:2423-2428. 10.1126/science.1056784
34. Huang CC, Faber PW, Persichetti F, Mittal V, Vonsattel J-P, MacDonald ME, Gusella JF: Amyloid formation by mutant Huntingtin: threshold, progressivity and recruitment of normal polyglutamine proteins. Somat Cell Mol Genet 1988, 24:217-233.
35. Li SH, Cheng AL, Zhou H, Lam S, Rao M, Li H, Li XJ: Interaction of Huntington disease protein with transcriptional activator Sp1. Mol Cell Biol 2002, 22:1277-1287. 10.1128/MCB.22.5.1277-1287.2002
36. Takano H, Gusella JF: The predominantly HEAT-like motif structure of huntingtin and its association and coincident nuclear entry with dorsal, an NF-kB/Rel/dorsal family transcription factor. BMC Neurosci 2002, 3:15. 10.1186/1471-2202-3-15
37. Steffan JS, Kazantsev A, Spasic-Boskovic O, Greenwald M, Zhu YZ, Gohler H, Wanker EE, Bates GP, Housman DE, Thompson LM: The Huntington's disease protein interacts with p53 and CREB-binding protein and represses transcription. Proc Natl Acad Sci 2000, 97:6763-6768. 10.1073/pnas.100110097
38. Culver BP, Savas JN, Park SK, Choi JH, Zheng S, Zeitlin SO, Yates JR, Tanese N: Proteomic analysis of wild-type and mutant Huntingtin-associated proteins in mouse brains identifies unique interactions and involvement in protein synthesis. J Biol Chem 2012, 287:21599-21614. 10.1074/jbc.M112.359307
39. Mills JD, Janitz M: Alternative splicing of mRNA in the molecular pathology of neurodegenerative diseases. Neurobiol Aging 2012, 33:1012.e11-1012.e24. 10.1016/j.neurobiolaging.2011.10.030
40. Branco J, Al-Ramahi I, Ukani L, Pérez AM, Fernandez-Funez P, Rincón-Limas D, Botas J: Comparative analysis of genetic modifiers in Drosophila points to common and distinct mechanisms of pathogenesis among polyglutamine diseases. Hum Mol Genet 2007, 17:376-390. 10.1093/hmg/ddm315
41. Pallos J, Bodai L, Lukacsovich T, Purcell JM, Steffan JS, Thompson LM, Marsh JL: Inhibition of specific HDACs and sirtuins suppresses pathogenesis in a Drosophila model of Huntington's disease. Hum Mol Genet 2008, 17:3767-3775. 10.1093/hmg/ddn273
42. Fujikake N, Nagai Y, Popiel HA, Okamoto Y, Yamaguchi M, Toda T: Heat shock transcription factor 1-activating compounds suppress polyglutamine-induced neurodegeneration through induction of multiple molecular chaperones. J Biol Chem 2008, 283:26188-26197. 10.1074/jbc.M710521200
43. Mazandu GK, Mulder NJ: A topology-based metric for measuring term similarity in the gene ontology. Adv Bioinformatics 2012, 2012:975783.
44. Wang JZ, Du Z, Payattakool R, Yu PS, Chen C-F: A new method to measure the semantic similarity of GO terms. Bioinformatics 2007, 23:1274-1281. 10.1093/bioinformatics/btm087
45. Zhang P, Zhang J, Sheng H, Russo JJ, Osborne B, Buetow K: Gene functional similarity search tool (GFSST). BMC Bioinformatics 2006, 7:135. 10.1186/1471-2105-7-135
46. Guo X, Liu R, Shriver CD, Hu H, Liebman MN: Assessing semantic similarity measures for the characterization of human regulatory pathways. Bioinformatics 2006, 22:967-973. 10.1093/bioinformatics/btl042