Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data

BMC Bioinformatics

Volumn 10, Issue SUPPL. 11, 2009, Pages

  Van den Berg, Bart H J ^a,c   Thanthiriwatte, Chamali ^b,c   Manda, Prashanti ^b,c   Bridges, Susan M ^b,c  

^a MISSISSIPPI STATE UNIVERSITY   (United States)

^b MISSISSIPPI STATE UNIVERSITY   (United States)

^c MISSISSIPPI STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL TOOLS; FUNCTIONAL ANNOTATION; FUNCTIONAL GENOMICS; FUNCTIONAL MODEL; GENE EXPRESSION DATASETS; MICROARRAY TECHNOLOGIES; PERFORMANCE ANALYSIS; SUPPORT ANALYSIS;

AGRICULTURE; ANIMALS; COMPUTATIONAL METHODS; DATA PROCESSING; GENE EXPRESSION; STATISTICAL TESTS;

TOOLS;

ARTICLE; CHICKEN; COMPARATIVE STUDY; CONTROLLED STUDY; DATA BASE; DNA MICROARRAY; FUNCTIONAL GENOMICS; GENE EXPRESSION; MOLECULAR BIOLOGY; MOLECULAR PROBE; NONHUMAN; STANDARDIZATION; STATISTICAL ANALYSIS;

AGRICULTURE; ANIMALS; CHICKENS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 70449367105     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: None     Document Type: Article

References (28)

1. da Huang W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009, 37(1):1-13. 2615629, 19033363, 10.1093/nar/gkn923.
2. Khatri P, Draghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 2005, 21(18):3587-3595. 2435250, 15994189, 10.1093/bioinformatics/bti565.
3. Draghici S, Khatri P, Bhavsar P, Shah A, Krawetz SA, Tainsky MA. Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res 2003, 31(13):3775-3781. 169030, 12824416, 10.1093/nar/gkg624.
4. Zhou X, Su Z. EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species. BMC Genomics 2007, 8:246. 1940007, 17645808, 10.1186/1471-2164-8-246.
5. Beissbarth T, Speed TP. GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 2004, 20(9):1464-1465. 10.1093/bioinformatics/bth088, 14962934.
6. Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome biology 2003, 4(5):P3. 10.1186/gb-2003-4-5-p3, 12734009.
7. Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP. GenePattern 2.0. Nature genetics 2006, 38(5):500-501. 10.1038/ng0506-500, 16642009.
8. McCarthy FM, Bridges SM, Wang N, Magee GB, Williams WP, Luthe DS, Burgess SC. AgBase: a unified resource for functional analysis in agriculture. Nucleic Acids Res 2007, (35 Database):D599-603. 1751552, 17135208, 10.1093/nar/gkl936.
9. Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R. The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res 2004, (32 Database):D262-266. 308756, 14681408, 10.1093/nar/gkh021.
10. Galperin MY, Cochrane GR. Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009. Nucleic Acids Res 2009, (37 Database):D1-4. 2686608, 19033364, 10.1093/nar/gkn942.
11. UniGene website. , http://www.ncbi.nlm.nih.gov/./unigene/
12. Entrez website. , http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
13. UniProt/SwissProt Homepage. , http://www.uniprot.org/
14. Gene Ontology Annotaton (GOA) database. , http://www.ebi.ac.uk/GOA/
15. International Protein Index (IPI). , http://www.ebi.ac.uk/IPI/IPIhelp.html
16. Buza TJ, McCarthy FM, Wang N, Bridges SM, Burgess SC. Gene Ontology annotation quality analysis in model eukaryotes. Nucleic Acids Res 2008, 36(2):e12. 2241866, 18187504, 10.1093/nar/gkm1167.
17. McCarthy FM, Wang N, Magee GB, Nanduri B, Lawrence ML, Camon EB, Barrell DG, Hill DP, Dolan ME, Williams WP. AgBase: a functional genomics resource for agriculture. BMC Genomics 2006, 7:229. 1618847, 16961921, 10.1186/1471-2164-7-229.
18. Goeman JJ, Buhlmann P. Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 2007, 23(8):980-987. 10.1093/bioinformatics/btm051, 17303618.
19. Gold DL, Coombes KR, Wang J, Mallick B. Enrichment analysis in high-throughput genomics - accounting for dependency in the NULL. Brief Bioinform 2007, 8(2):71-77. 10.1093/bib/bbl019, 17077137.
20. Vencio RZ, Shmulevich I. ProbCD: enrichment analysis accounting for categorization uncertainty. BMC bioinformatics 2007, 8:383. 2169266, 17935624, 10.1186/1471-2105-8-383.
21. Benjamini Y, Hochberg Y. Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society B 1995, 57:289-300.
22. Yekutieli Y, Benjamini Y. The control of the false discovery rate in multiple testing under dependency. The Annals of Statistics 2001, 29:1165-1188.
23. Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ. Discovering statistically significant pathways in expression profiling studies. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(38):13544-13549. 1200092, 16174746, 10.1073/pnas.0506577102.
24. Lewin A, Grieve IC. Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data. BMC bioinformatics 2006, 7:426. 1622761, 17018143, 10.1186/1471-2105-7-426.
25. Al-Shahrour F, Minguez P, Tarraga J, Medina I, Alloza E, Montaner D, Dopazo J. FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res 2007, (35 Web Server):W91-96. 1933151, 17478504, 10.1093/nar/gkm260.
26. Burnside J, Neiman P, Tang J, Basom R, Talbot R, Aronszajn M, Burt D, Delrow J. Development of a cDNA array for chicken gene expression analysis. BMC Genomics 2005, 6(1):13. 549535, 15694003, 10.1186/1471-2164-6-13.
27. Nanduri B, Lawrence ML, Boyle CR, Ramkumar M, Burgess SC. Effects of subminimum inhibitory concentrations of antibiotics on the Pasteurella multocida proteome. J Proteome Res 2006, 5(3):572-580. 10.1021/pr050360r, 16512672.
28. Zhou H, Lamont SJ. Global gene expression profile after Salmonella enterica Serovar enteritidis challenge in two F8 advanced intercross chicken lines. Cytogenetic and genome research 2007, 117(1-4):131-138.