GOTree Machine (GOTM): A web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies

BMC Bioinformatics

Volumn 5, Issue , 2004, Pages

  Zhang, Bing ^a   Schmoyer, Denise ^a   Kirov, Stefan ^a   Snoddy, Jay ^a  

^a OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS TOOLS; DIRECTED ACYCLIC GRAPH (DAG); FUNCTIONAL GENOMICS; FUNCTIONAL INFORMATION; HIGH-THROUGHPUT ANALYSIS; HIGH-THROUGHPUT METHOD; HIGH-THROUGHPUT TECHNOLOGIES; TREE-LIKE STRUCTURES;

BIOINFORMATICS; DATA VISUALIZATION; TOOLS;

GENES;

DNA;

ANALYTIC METHOD; ARTICLE; COMPUTER PROGRAM; DATA ANALYSIS; DNA MICROARRAY; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC REGULATION; GENOMICS; HUMAN COMPUTER INTERACTION; INTERNET; MEDICAL INFORMATION SYSTEM; MOLECULAR BIOLOGY; ONLINE SYSTEM; PROTEOMICS; STATISTICAL ANALYSIS; ANIMAL; BIOLOGY; CLUSTER ANALYSIS; COMPUTER GRAPHICS; COMPUTER INTERFACE; DIPTERA; GENE; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETICS; GENOME; HUMAN; HUMAN GENOME; MOUSE; PHYSIOLOGY; RAT; STATISTICS AND NUMERICAL DATA;

ANIMALS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COMPUTER GRAPHICS; DATA INTERPRETATION, STATISTICAL; DATABASES, GENETIC; DIPTERA; GENE EXPRESSION PROFILING; GENES; GENES, INSECT; GENOME; GENOME, HUMAN; HUMANS; INTERNET; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RATS; SOFTWARE; SOFTWARE DESIGN; USER-COMPUTER INTERFACE;

EID: 2942550697     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-16     Document Type: Article

References (29)

1. Wain HM, Bruford EA, Lovering RC, Lush MJ, Wright MW, Povey S: Guidelines for Human Gene Nomenclature. Genomics 2002, 79:464-470.
2. The Gene Ontology Consortium: Creating the Gene Ontology resource: design and implementation. Genome Res 2001, 11:1425-1433.
3. Jenssen T-K, Legreid A, Komorowski J, Hovig E: A literature network of human genes for high-throughput analysis of gene expression. Nat Genet 2001, 28:21-28.
4. Masys DR, Welsh JB, Fink JL, Gribskov M, Klacansky I, Corbeil J: Use of keyword hierarchies to interpret gene expression patterns. Bioinformatics 2001, 17:319-326.
5. Chaussabel D, Sher A: Mining microarray expression data by literature profiling. Genome Biol 2002, 3:R55.
6. The Gene Ontology Consortium: Gene Ontology: tool for the unification of biology. Nat Genet 2000, 25:25-29.
7. Herrero J, Al-Shahrour F, Diaz-Uriarte R, Mateos A, Vaquerizas JM, Santoyo J, Dopazo J: GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Res 2003, 31:3461-3467.
8. Draghici S, Khatri P, Martins RP, Oscategoryeier GC, Krawetz SA: Global functional profiling of gene expression. Genomics 2003, 81:98-104.
9. Khatri P, Draghici S, Ostermeier GC, Krawetz SA: Profiling gene expression using Onto-Express. Genomics 2002, 79:266-270.
10. Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, Bussey KJ, Riss J, Barrett JC, Weinstein JN: GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 2003, 4:R28.
11. Doniger SW, Salomonis N, Dahlquist KD, Vranizan K, Lawlor SC, Conklin BR: MAPPFinder: using Gene Ontology and Gen-MAPP to create a global gene-expression profile from microarray data. Genome Biol 2003, 4:R7.
12. GoSurfer [http://biosun1.harvard.edu/complab/gosurfer/]
13. PHP Layers Menu System [http://phplayersmenu.sourceforge.net/]
14. ChartDirector [http://www.advsofteng.com/index.html]
15. Graphviz [http://www.research.att.com/sw/tools/graphviz/]
16. NCBI LocusLink database [http://www.ncbi.nlm.nih.gov/LocusLink/]
17. Gene Ontolgy consortium [http://www.geneontology.org]
18. Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A, Patapoutian A, Hampton GM, Schultz PG, Hogenesch JB: Large-scale analysis of the human and mouse transcriptomes. Proc Natl Acad Sci USA 2002, 99:4465-4470.
19. Eddy EM: Male germ cell gene expression. Recent Prog Horm Res 2002, 57:103-28.
20. Urner F, Sakkas D: Protein phosphorylation in mammalian spermatozoa. Reproduction 2003, 125:17-26.
21. Nolan JP, Hammerstedt RH: Regulation of membrane stability and the acrosome reaction in mammalian sperm. FASEB J 1997, 11:670-682.
22. Reisse S, Rothardt G, Völkl A, Beier K: Peroxisomes and ether lipid biosynthesis in rat testis and epididymis. Biol Reprod 2001, 64:1689-1694.
23. Kmiec Z: Cooperation of liver cells in health and disease. Adv Anat Embryol Cell Biol 2001, 161:1-151.
24. AmiGO [http://www.godatabase.org/cgi-bin/go.cgi/]
25. Blaschke C, Valencia A: Automatic classification of protein functions from the literature. Compar Funct Genom 2003, 4:75-79.
26. Raychaudhuri S, Chang JT, Sutphin PD, Altman RB: Associating genes with gene ontology codes using a maximum entropy analysis of biomedical literature. Genome Res 2002, 12:203-214.
27. Lagreid A, Hvidsten TR, Midelfart H, Komorowski J, Sandvik AK: Predicting Gene Ontology biological process from temporal gene expression patterns. Genome Res 2003, 13:965-979.
28. Hvidsten TR, Komorowski J, Sandvik AK, Laegreid A: Predicting gene function from gene expressions and ontologies. Pac Symp Biocomput 2001:299-310.
29. Schug J, Diskin S, Mazzarelli J, Brunk BP, Stoeckert CJ: Predicting Gene Ontology functions from ProDom and CDD protein domains. Genome Res 2002, 2:648-655.