Consistency, comprehensiveness, and compatibility of pathway databases

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Soh, Donny ^a,b,c   Dong, Difeng ^a   Guo, Yike ^b   Wong, Limsoon ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c INSTITUTE FOR INFOCOMM RESEARCH   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL DATABASE; BIOLOGICAL INFORMATION; DATA-SOURCES; INTERACTING GENES; LEVEL OF CONSISTENCIES; MICROARRAY EXPERIMENTS; PATHWAY DATABASE;

ACTIVE NETWORKS; GENES;

DATABASE SYSTEMS;

ARTICLE; BIOLOGY; DNA MICROARRAY; FACTUAL DATABASE; GENE EXPRESSION PROFILING; GENETIC DATABASE; METHODOLOGY;

COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; DATABASES, GENETIC; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 77956480115     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-449     Document Type: Article

References (34)

1. Soh D, Dong D, Guo Y, Wong L. Enabling more sophisciated gene expression analysis for understanding diseases and optimizing treatments. ACM SIGKDD Explorations 2007, 3-13.
2. Khatri P, Draghici S. Ontological analysis of gene expression data: Current tools, limitations, and open problems. Bioinformatics 2005, 21:3587-3595. 10.1093/bioinformatics/bti565, 2435250, 15994189.
3. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS 2005, 102(43):15545-15550. 10.1073/pnas.0506580102, 1239896, 16199517.
4. Goeman JJ, van de Geer SA, de Kort F, van Houwelingen HC. A global test for groups of genes: Testing association with a clinical outcome. Bioinformatics 2004, 20:93-99. 10.1093/bioinformatics/btg382, 14693814.
5. Pavlidis P, Qin J, Arango V, Mann JJ, Sibille E. Using the Gene Ontology for microarray data mining: A comparison of methods and application to age effects in human prefrontal cortex. Neurochemical Research 2004, 29(6):1213-1222. 10.1023/B:NERE.0000023608.29741.45, 15176478.
6. Lee HK, Braynen W, Keshav K, Pavlidis P. ErmineJ: Tool for functional analysis of gene expression data sets. BMC Bioinformatics 2005, 6:269. 10.1186/1471-2105-6-269, 1310606, 16280084.
7. Pathway Express. , http://vortex.cs.wayne.edu/ontoexpress/
8. NCBI Database. , http://www.ncbi.nlm.nih.gov/
9. Khatri P, Draghici S. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Research 2006, 34:354-357.
10. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 1999, 27:29-34. 10.1093/nar/27.1.29, 148090, 9847135.
11. KEGG Database. , http://www.genome.ad.jp/kegg/pathway.html
12. Ingenuity Database. , http://www.ingenuity.com/
13. Gene Ontology Database. , http://www.geneontology.org/
14. WikiPathways Database. , http://www.wikipathways.org/
15. Green MLKP. The outcomes of pathway database computations depend on pathway ontology. Nucleic Acids Res 2006, 34(13):3687-97. 10.1093/nar/gkl438, 1540720, 16893953.
16. BioPAX. , http://www.biopax.org
17. Nurseitov N, Paulson M, Reynolds R, Izurieta C. Comparison of JSON and XML Data Interchange Formats: A Case Study. CAINE 2009, 157-162.
18. JSON. , http://www.json.org
19. Sakr S. XML compression techniques: A survey and comparison. J Comput Syst Sci 2009, 75(5):303-322.
20. PathwayAPI. , http://www.PathwayAPI.com
21. GPMLFormat. , http://www.pathvisio.org/wiki/EverythingGpml
22. Efroni S, Schaefer CF, Buetow KH. Identification of key processes underlying cancer phenotypes using biologic pathway analysis. PLoS ONE 2007, 2. 10.1371/journal.pone.0000425, 1855990, 17487280.
23. Draghici S, Khatri P, Tarca AL, Amin K, Done A, Voichita C, Georgescu C, Romero R. A systems biology approach for pathway level analysis. Genome Research 2007, 17(10):1537-1545. 10.1101/gr.6202607, 1987343, 17785539.
24. Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ. Discovering statistically significant pathways in expression profiling studies. PNAS 2005, 102:13544-13549. 10.1073/pnas.0506577102, 1200092, 16174746.
25. Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, Lewis S, Birney E, Stein L. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 2005, (33 Database). 540026, 15608231.
26. Elliott B, Kirac M, Cakmak A, Yavas G, Mayes S, Cheng E, Wang Y, Gupta C, Ozsoyoglu G, Meral Ozsoyoglu Z. PathCase: pathways database system. Bioinformatics 2008, 24(21):2526-2533. 10.1093/bioinformatics/btn459, 18728044.
27. Krishnamurthy L, Nadeau J, Ozsoyoglu G, Ozsoyoglu M, Schaeffer G, Tasan M, Xu W. Pathways database system: an integrated system for biological pathways. Bioinformatics 2003, 19(8):930-937. 10.1093/bioinformatics/btg113, 12761054.
28. Doniger S, Salomonis N, Dahlquist K, Vranizan K, Lawlor S, Conklin B. MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biology 2003, 4:R7+. 10.1186/gb-2003-4-1-r7, 151291, 12540299.
29. Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart JM, Conklin BR, Pico AR. GenMAPP 2: New Features and Resources for Pathway Analysis. BMC Bioinformatics 2007, 8:217+. 10.1186/1471-2105-8-217, 1924866, 17588266.
30. Karp PD, Ouzounis CA, Moore-Kochlacs C, Goldovsky L, Kaipa P, Ahren D, Tsoka S, Darzentas N, Kunin V, Lopez-Bigas N. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Research 2005, 19:6083-89.
31. van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, Evelo C. Presenting and exploring biological pathways with PathVisio. BMC bioinformatics 2008, 9:399+. 10.1186/1471-2105-9-399, 2569944, 18817533.
32. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
33. PathwayCommons. , http://www.PathwayCommons.org
34. Karp PD, Lee TJ, Wagner V. BioWarehouse: Relational Integration of Eleven Bioinformatics Databases and Formats. DILS 2008, 5-7.