A search engine to identify pathway genes from expression data on multiple organisms

BMC Systems Biology

Volumn 1, Issue , 2007, Pages

  Chen, Chunnuan ^a   Weirauch, Matthew T ^a   Powell, Corey C ^a   Zambon, Alexander C ^b   Stuart, Joshua M ^a  

^a University of California Santa Cruz   (United States)

^b GLADSTONE INSTITUTE OF CARDIOVASCULAR DISEASE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; HELICOBACTER PYLORI; HOMO SAPIENS; SACCHAROMYCES CEREVISIAE;

COLLAGEN;

ANIMAL; ARTICLE; CALCIUM SIGNALING; CELL ADHESION; COMPUTER PROGRAM; GENE EXPRESSION; GENETIC DATABASE; GENETIC TRANSCRIPTION; GENETICS; HUMAN; METABOLISM;

ANIMALS; CALCIUM SIGNALING; CELL ADHESION; COLLAGEN; DATABASES, GENETIC; GENE EXPRESSION; HUMANS; METABOLIC NETWORKS AND PATHWAYS; SOFTWARE; TRANSCRIPTION, GENETIC;

EID: 38149041693     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-1-20     Document Type: Article

References (47)

1. Schena M Shalon D Davis RW Brown PO Quantitative monitoring of gene expression patterns with a complementary DNA microarray Science 1995, 270(5235):467-470. 10.1126/science.270.5235.467 7569999
2. Eisen MB Spellman PT Brown PO Botstein D Cluster analysis and display of genome-wide expression patterns Proc Natl Acad Sci USA 1998, 95(25):14863-14868. 24541 9843981 10.1073/pnas.95.25.14863
3. Kim SK Lund J Kiraly M Duke K Jiang M Stuart JM Eizinger A Wylie BN Davidson GS A gene expression map for Caenorhabditis elegans Science 2001, 293(5537):2087-2092. 10.1126/science.1061603 11557892
4. Sheng Q Moreau Y De Moor B Biclustering microarray data by Gibbs sampling Bioinformatics 2003, 19:196-205. 10.1093/bioinformatics/btg1078
5. Tamayo P Slonim D Mesirov J Zhu Q Kitareewan S Dmitrovsky E Lander ES Golub TR Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation Proc Natl Acad Sci USA 1999, 96(6):2907-2912. 15868 10077610 10.1073/pnas.96.6.2907
6. Ihmels J Friedlander G Bergmann S Sarig O Ziv Y Barkai N Revealing modular organization in the yeast transcriptional network Nat Genet 2002, 31(4):370-377. 12134151
7. Owen AB Stuart J Mach K Villeneuve AM Kim S A gene recommender algorithm to identify coexpressed genes in C. elegans Genome Res 2003, 13(8):1828-1837. 403774 12902378
8. Lazzeroni LC Owen AB Plaid models for gene expression data Statistica Sinica 2002, 12:61-86.
9. Cheng Y Church GM Biclustering of expression data Proc Int Conf Intell Syst Mol Biol 2000, 8:93-103. 10977070
10. Kluger Y Basri R Chang JT Gerstein M Spectral biclustering of microarray data: Coclustering genes and conditions Genome Res 2003, 13(4):703-716. 430175 12671006 10.1101/gr.648603
11. Tanay A Sharan R Shamir R Discovering statistically significant biclusters in gene expression data Bioinformatics 2002, 18(Suppl 1):S136-144. 12169541
12. Dahlquist KD Salomonis N Vranizan K Lawlor SC Conklin BR GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways Nat Genet 2002, 31(1):19-20. 10.1038/ng0502-19 11984561
13. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nat Genet 2000, 25(1):25-29. 10.1038/75556 10802651
14. Ogata H Goto S Sato K Fujibuchi W Bono H Kanehisa M KEGG: Kyoto Encyclopedia of Genes and Genomes Nucleic Acids Res 1999, 27(1):29-34. 148090 9847135 10.1093/nar/27.1.29
15. van der Rest M Garrone R Collagen family of proteins Faseb J 1991, 5(13):2814-2823. 1916105
16. Collin T Marty A Llano I Presynaptic calcium stores and synaptic transmission Curr Opin Neurobiol 2005, 15(3):275-281. 10.1016/ j.conb.2005.05.003 15919193
17. D'Andrea A Pellman D Deubiquitinating enzymes: A new class of biological regulators Crit Rev Biochem Mol Biol 1998, 33(5):337-352. 10.1080/ 10409239891204251 9827704
18. Zhou R Silverman N Hong M Liao DS Chung Y Chen ZJ Maniatis T The role of ubiquitnation in Drosophila innate immunity J Biol Chem 2005.
19. Aruga J The role of Zic genes in neural development Mol Cell Neurosci 2004, 26(2):205-221. 10.1016/j.mcn.2004.01.004 15207846
20. Bataller L Wade DF Graus F Rosenfeld MR Dalmau J The MAZ protein is an autoantigen of Hodgkin's disease and paraneoplastic cerebellar dysfunction Ann Neurol 2003, 53(1):123-127. 10.1002/ana.10434 12509857
21. Fujii H Hamada H A CNS-specific POU transcription factor, Brn-2, is required for establishing mammalian neural cell lineages Neuron 1993, 11(6):1197-1206. 10.1016/0896-6273(93)90231-F 8274283
22. Hagino-Yamagishi K Minamikawa-Tachino R Ichikawa M Yazaki K Expression of brain-2 in the developing olfactory bulb Brain Res Dev Brain Res 1999, 113(1-2):133-137. 10.1016/S0165-3806(98)00192-8 10064882
23. Hagino-Yamagishi K Saijoh Y Ikeda M Ichikawa M Minamikawa-Tachino R Hamada H Predominant expression of Brn-2 in the postmitotic neurons of the developing mouse neocortex Brain Res 1997, 752(1-2):261-268. 10.1016/ S0006-8993(96)01472-2 9106466
24. Roberts GM Davies EV Hallett MB Slow Ca2+ waves in large myeloid cells as a result of a diffusible cytosolic factor J Leukoc Biol 1995, 57(6):837-841. 7790765
25. Fomina AF Fanger CM Kozak JA Cahalan MD Single channel properties and regulated expression of Ca(2+) release-activated Ca(2+) (CRAC) channels in human T cells J Cell Biol 2000, 150(6):1435-1444. 10.1083/ jcb.150.6.1435 10995447
26. Bignone PA Baines AJ Spectrin alpha II and beta II isoforms interact with high affinity at the tetramerization site Biochem J 2003, 374(Pt 3):613-624. 1223645 12820899 10.1042/BJ20030507
27. Link CD Taft A Kapulkin V Duke K Kim S Fei Q Wood DE Sahagan BG Gene expression analysis in a transgenic Caenorhabditis elegans Alzheimer's disease model Neurobiol Aging 2003, 24(3):397-413. 10.1016/ S0197-4580(02)00224-5 12600716
28. Selcen D Engel AG Myofibrillar myopathy caused by novel dominant negative alpha B-crystallin mutations Ann Neurol 2003, 54(6):804-810. 10.1002/ana.10767 14681890
29. Punyadeera C Zorenc AH Koopman R McAinch AJ Smit E Manders R Keizer HA Cameron-Smith D van Loon LJ The effects of exercise and adipose tissue lipolysis on plasma adiponectin concentration and adiponectin receptor expression in human skeletal muscle Eur J Endocrinol 2005, 152(3):427-436. 10.1530/eje.1.01872 15757860
30. Ralser M Nonhoff U Albrecht M Lengauer T Wanker EE Lehrach H Krobitsch S Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways Hum Mol Genet 2005, 14(19):2893-2909. 10.1093/hmg/ddi321 16115810
31. Nakazawa T Nakajima A Seki N Okawa A Kato M Moriya H Amizuka N Einhorn TA Yamazaki M Gene expression of periostin in the early stage of fracture healing detected by cDNA microarray analysis J Orthop Res 2004, 22(3):520-525. 10.1016/j.orthres.2003.10.007 15099630
32. Alexander D Judex M Meyringer R Weis-Klemm M Gay S Muller-Ladner U Aicher WK Transcription factor Egr-1 activates collagen expression in immortalized fibroblasts or fibrosarcoma cells Biol Chem 2002, 383(12):1845-1853. 10.1515/BC.2002.208 12553721
33. Siepel A Bejerano G Pedersen JS Hinrichs AS Hou M Rosenbloom K Clawson H Spieth J Hillier LW Richards S Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes Genome Res 2005, 15(8):1034-1050. 1182216 16024819 10.1101/gr.3715005
34. http://www.biocarta.com/
35. Walhout AJ Vidal M Protein interaction maps for model organisms Nat Rev Mol Cell Biol 2001, 2(1):55-62. 10.1038/35048107 11413466
36. Kamath RS Ahringer J Genome-wide RNAi screening in Caenorhabditis elegans Methods 2003, 30(4):313-321. 10.1016/S1046-2023(03)00050-1 12828945
37. Remm M Storm CE Sonnhammer EL Automatic clustering of orthologs and in-paralogs from pairwise species comparisons J Mol Biol 2001, 314(5):1041-1052. 10.1006/jmbi.2000.5197 11743721
38. Li L Stoeckert CJ Jr Roos DS OrthoMCL: Identification of ortholog groups for eukaryotic genomes Genome Res 2003, 13(9):2178-2189. 403725 12952885 10.1101/gr.1224503
39. http://sysbio.cse.ucsc.edu/msgr
40. Stuart JM Segal E Koller D Kim SK A gene-coexpression network for global discovery of conserved genetic modules Science 2003, 302(5643):249-255. 10.1126/science.1087447 12934013
41. Maglott D Ostell J Pruitt KD Tatusova T Entrez Gene: Gene-centered information at NCBI Nucleic Acids Res 2005, 33(Database):D54-58. 539985 15608257 10.1093/nar/gki031
42. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215(3):403-410. 2231712
43. Wingender E Dietze P Karas H Knuppel R TRANSFAC: A database on transcription factors and their DNA binding sites Nucleic Acids Res 1996, 24(1):238-241. 145586 8594589 10.1093/nar/24.1.238
44. Karolchik D Baertsch R Diekhans M Furey TS Hinrichs A Lu YT Roskin KM Schwartz M Sugnet CW Thomas DJ The UCSC Genome Browser Database Nucleic Acids Res 2003, 31(1):51-54. 165576 12519945 10.1093/nar/gkg129
45. Lander ES Linton LM Birren B Nusbaum C Zody MC Baldwin J Devon K Dewar K Doyle M FitzHugh W Initial sequencing and analysis of the human genome Nature 2001, 409(6822):860-921. 10.1038/35057062 11237011
46. Schwartz S Elnitski L Li M Weirauch M Riemer C Smit A Green ED Hardison RC Miller W MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences Nucleic Acids Res 2003, 31(13):3518-3524. 168985 12824357 10.1093/nar/gkg579
47. Consortium TE The ENCODE (ENCyclopedia Of DNA Elements) Project Science 2004, 306(5696):636-640. 10.1126/science.1105136 15499007