ProbCD: Enrichment analysis accounting for categorization uncertainty

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Vêncio, Ricardo Z N ^a   Shmulevich, Ilya ^a  

^a INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS FRAMEWORKS; CATEGORICAL DATA; CONTINGENCY TABLE; EXPERIMENTAL TECHNIQUES; FISHER EXACT TEST; ONLINE INTERFACE; PROBABILISTIC INFORMATION; STOCHASTIC NATURE;

RANDOM PROCESSES;

UNCERTAINTY ANALYSIS;

ACCESS TO INFORMATION; ACCURACY; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTINGENCY TABLE; DATA ANALYSIS; FISHER EXACT TEST; GENETIC ANALYSIS; HIGH THROUGHPUT SCREENING; INTERNET; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; ONLINE SYSTEM; PROBABILITY; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; SYSTEMS BIOLOGY; UNCERTAINTY; ALGORITHM; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; METHODOLOGY; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; STATISTICAL MODEL;

ALGORITHMS; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION PROFILING; MODELS, BIOLOGICAL; MODELS, STATISTICAL; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 37549065883     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-383     Document Type: Article

References (29)

1. Dopazo J Functional Interpretation of Microarray Experiments OMICS: A Journal of Integrative Biology 2006, 10(3):. 17069516
2. Rivals I Personnaz L Taing L Potier M Enrichment or depletion of a GO category within a class of genes: Which test? Bioinformatics 2007, 23(4):401-407. 17182697
3. 2 from Contingency Tables, and the Calculation of P Journal of the Royal Statistical Society 1922, 85:87-94.
4. Goodman L Kruskal W Measures of Association for Cross Classifications Journal of the American Statistical Association 1954, 49(268):732-764.
5. Vencio R Koide T Gomes S Pereira C BayGO: Bayesian analysis of ontology term enrichment in microarray data BMC Bioinformatics 2006, 7:86. 1440873 16504085
6. Jiang Z Gentleman R Extensions to gene set enrichment Bioinformatics 2007, 23(3):306. 17127676
7. Goeman J Buhlmann P Analyzing gene expression data in terms of gene sets: Methodological issues Bioinformatics 2007, 23(8):980. 17303618
8. Joshi T Chen Y Becker J Alexandrov N Xu D Genome-Scale Gene Function Prediction Using Multiple Sources of High-Throughput Data in Yeast Saccharomyces cerevisiae Omics A Journal of Integrative Biology 2004, 8(4):322-333. 15703479
9. Levy E Ouzounis C Gilks W Audit B Probabilistic annotation of protein sequences based on functional classifications BMC Bioinformatics 2005, 6:302. 1361783 16354297
10. Engelhardt B Jordan M Muratore K Brenner S Protein molecular function prediction by Bayesian phylogenomics PLoS Comput Biol 2005, 1(5):. 1246806 16217548
11. Martin D Berriman M Barton G GOtcha: A new method for prediction of protein function assessed by the annotation of seven genomes BMC Bioinformatics 2004, 5:178. 535938 15550167
12. Engelhardt B Jordan M Brenner S A graphical model for predicting protein molecular function Proceedings of the 23rd international conference on Machine learning 2006, 297-304.
13. Carroll S Pavlovic V Protein classification using probabilistic chain graphs and the Gene Ontology structure Bioinformatics 2006, 22(15):1871. 16705013
14. Vinayagam A del Val C Schubert F Eils R Glatting K Suhai S König R GOPET: A tool for automated predictions of Gene Ontology terms BMC Bioinformatics 2006, 7:161. 1434778 16549020
15. Jones C Brown A Baumann U Estimating the annotation error rate of curated GO database sequence annotations BMC Bioinformatics 2007, 8:170. 1892569 17519041
16. Zhang W Shmulevich I Computational and Statistical Approaches to Genomics New York, NY, USA: Springer 2 2006
17. Zhang W Shmulevich I Astola J Microarray Quality Control Wiley-Liss 2004
18. The R Project for Statistical Computing http://www.r-project.org
19. Shannon P Reiss D Bonneau R Baliga N Gaggle: An open-source software system for integrating bioinformatics software and data sources BMC Bioinformatics 2006, 7:176. 1464137 16569235
20. ProbCD Home Page http://xerad.systemsbiology.net/ProbCD
21. Bernoulli scheme - Wikipedia, The Free Encyclopedia http://en.wikipedia.org/w/index.php?title=Bernoullischeme&o%ldid= 64557593
22. Andersson C Isaksson A Gustafsson M Bayesian detection of periodic mRNA time profiles without use of training examples BMC Bioinformatics 2006, 7:63. 1413563 16469110
23. Gene Ontology Current Annotations http://www.geneontology.org/ GO.current.annotations.shtml
24. The Gene Ontology Consortium http://www.geneontology.org
25. Guide to GO Evidence Codes http://www.geneontology.org/GO.evidence.shtml
26. Aubry M Monnier A Chicault C de Tayrac M Galibert M Burgun A Mosser J Combining evidence, biomedical literature and statistical dependence: new insights for functional annotation of gene sets BMC Bioinformatics 2006, 7:241. 1482722 16674810
27. Lewin A Grieve I Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data BMC Bioinformatics 2006, 7:426. 1622761 17018143
28. 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. 15972284
29. Sealfon R Hibbs M Huttenhower C Myers C Troyanskaya O GOLEM: An interactive graph-based gene-ontology navigation and analysis tool BMC Bioinformatics 2006, 7:443. 1618863 17032457