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Volumn 11, Issue 1, 2010, Pages

Genomics Portals: Integrative web-platform for mining genomics data

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING SITE; DATA ANALYSIS; DATA BASE; DATA MINING; GENE EXPRESSION; GENOMICS; KNOWLEDGE BASE; ANIMAL; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; HUMAN; INTERNET; METHODOLOGY; MOUSE; RAT;

EID: 77349095040     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-27     Document Type: Article
Times cited : (11)

References (46)
  • 3
    • 38049148026 scopus 로고    scopus 로고
    • DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis
    • 10.1186/1471-2105-8-426, 2186358, 17980028
    • Sherman B, Huang D, Tan Q, Guo Y, Bour S, Liu D, Stephens R, Baseler M, Lane HC, Lempicki R. DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics 2007, 8:426. 10.1186/1471-2105-8-426, 2186358, 17980028.
    • (2007) BMC Bioinformatics , vol.8 , pp. 426
    • Sherman, B.1    Huang, D.2    Tan, Q.3    Guo, Y.4    Bour, S.5    Liu, D.6    Stephens, R.7    Baseler, M.8    Lane, H.C.9    Lempicki, R.10
  • 5
    • 33645745361 scopus 로고    scopus 로고
    • Integrative biology of prostate cancer progression 2
    • 10.1146/annurev.pathol.1.110304.100047, 18039115
    • Tomlins SA, Rubin MA, Chinnaiyan AM. Integrative biology of prostate cancer progression 2. Annu Rev Pathol 2006, 1:243-271. 10.1146/annurev.pathol.1.110304.100047, 18039115.
    • (2006) Annu Rev Pathol , vol.1 , pp. 243-271
    • Tomlins, S.A.1    Rubin, M.A.2    Chinnaiyan, A.M.3
  • 6
    • 50649108994 scopus 로고    scopus 로고
    • An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs) 9
    • 10.1101/gr.077479.108, 2527707, 18577705
    • Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Graf S, Tomazou EM, Backdahl L, Johnson N, Herberth M, et al. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs) 9. Genome Res 2008, 18:1518-1529. 10.1101/gr.077479.108, 2527707, 18577705.
    • (2008) Genome Res , vol.18 , pp. 1518-1529
    • Rakyan, V.K.1    Down, T.A.2    Thorne, N.P.3    Flicek, P.4    Kulesha, E.5    Graf, S.6    Tomazou, E.M.7    Backdahl, L.8    Johnson, N.9    Herberth, M.10
  • 8
    • 38549134505 scopus 로고    scopus 로고
    • Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata
    • 10.1093/nar/gkm815, 2238822, 17932051
    • Faith JJ, Driscoll ME, Fusaro VA, Cosgrove EJ, Hayete B, Juhn FS, Schneider SJ, Gardner TS. Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucl Acids Res 2008, 36:D866-D870. 10.1093/nar/gkm815, 2238822, 17932051.
    • (2008) Nucl Acids Res , vol.36
    • Faith, J.J.1    Driscoll, M.E.2    Fusaro, V.A.3    Cosgrove, E.J.4    Hayete, B.5    Juhn, F.S.6    Schneider, S.J.7    Gardner, T.S.8
  • 11
    • 62349088493 scopus 로고    scopus 로고
    • GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed
    • 10.1186/1471-2105-9-548, 2629779, 19094235
    • Chen R, Mallelwar R, Thosar A, Venkatasubrahmanyam S, Butte A. GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed. BMC Bioinformatics 2008, 9:548. 10.1186/1471-2105-9-548, 2629779, 19094235.
    • (2008) BMC Bioinformatics , vol.9 , pp. 548
    • Chen, R.1    Mallelwar, R.2    Thosar, A.3    Venkatasubrahmanyam, S.4    Butte, A.5
  • 12
    • 54349101605 scopus 로고    scopus 로고
    • Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues
    • 10.1186/gb-2008-9-9-r139, 2592717, 18803840
    • Kilpinen S, Autio R, Ojala K, Iljin K, Bucher E, Sara H, Pisto T, Saarela M, Skotheim R, Bjorkman M, et al. Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. Genome Biology 2008, 9:R139. 10.1186/gb-2008-9-9-r139, 2592717, 18803840.
    • (2008) Genome Biology , vol.9
    • Kilpinen, S.1    Autio, R.2    Ojala, K.3    Iljin, K.4    Bucher, E.5    Sara, H.6    Pisto, T.7    Saarela, M.8    Skotheim, R.9    Bjorkman, M.10
  • 13
    • 43449088832 scopus 로고    scopus 로고
    • A modular approach for integrative analysis of large-scale gene-expression and drug-response data
    • 10.1038/nbt1397, 18464786
    • Kutalik Z, Beckmann JS, Bergmann S. A modular approach for integrative analysis of large-scale gene-expression and drug-response data. Nat Biotechnol 2008, 26:531-539. 10.1038/nbt1397, 18464786.
    • (2008) Nat Biotechnol , vol.26 , pp. 531-539
    • Kutalik, Z.1    Beckmann, J.S.2    Bergmann, S.3
  • 14
    • 58049194189 scopus 로고    scopus 로고
    • TranscriptomeBrowser: A Powerful and Flexible Toolbox to Explore Productively the Transcriptional Landscape of the Gene Expression Omnibus Database
    • 10.1371/journal.pone.0004001, 2602602, 19104654
    • Lopez F, Textoris J, Bergon A, Didier G, Remy E, Granjeaud S, Imbert J, Nguyen C, Puthier D. TranscriptomeBrowser: A Powerful and Flexible Toolbox to Explore Productively the Transcriptional Landscape of the Gene Expression Omnibus Database. PLoS ONE 2008, 3:e4001. 10.1371/journal.pone.0004001, 2602602, 19104654.
    • (2008) PLoS ONE , vol.3
    • Lopez, F.1    Textoris, J.2    Bergon, A.3    Didier, G.4    Remy, E.5    Granjeaud, S.6    Imbert, J.7    Nguyen, C.8    Puthier, D.9
  • 15
    • 6944244084 scopus 로고    scopus 로고
    • A module map showing conditional activity of expression modules in cancer
    • 10.1038/ng1434, 15448693
    • Segal E, Friedman N, Koller D, Regev A. A module map showing conditional activity of expression modules in cancer. Nat Genet 2004, 36:1090-1098. 10.1038/ng1434, 15448693.
    • (2004) Nat Genet , vol.36 , pp. 1090-1098
    • Segal, E.1    Friedman, N.2    Koller, D.3    Regev, A.4
  • 16
    • 67650930713 scopus 로고    scopus 로고
    • Genomewide Analysis of Aryl Hydrocarbon Receptor Binding Targets Reveals an Extensive Array of Gene Clusters that Control Morphogenic and Developmental Programs
    • 2717142, 19654925
    • Sartor MA, Schnekenburger M, Marlow JL, Reichard JF, Wang Y, Fan Y, Ma C, Karyala S, Halbleib D, Liu X, et al. Genomewide Analysis of Aryl Hydrocarbon Receptor Binding Targets Reveals an Extensive Array of Gene Clusters that Control Morphogenic and Developmental Programs. Environ Health Perspect 2009, 117:1139-1146. 2717142, 19654925.
    • (2009) Environ Health Perspect , vol.117 , pp. 1139-1146
    • Sartor, M.A.1    Schnekenburger, M.2    Marlow, J.L.3    Reichard, J.F.4    Wang, Y.5    Fan, Y.6    Ma, C.7    Karyala, S.8    Halbleib, D.9    Liu, X.10
  • 17
    • 52949087576 scopus 로고    scopus 로고
    • A Genomewide Functional Network for the Laboratory Mouse
    • 10.1371/journal.pcbi.1000165, 2527685, 18818725
    • Guan Y, Myers CL, Lu R, Lemischka IR, Bult CJ, Troyanskaya OG. A Genomewide Functional Network for the Laboratory Mouse. PLoS Comput Biol 2008, 4:e1000165. 10.1371/journal.pcbi.1000165, 2527685, 18818725.
    • (2008) PLoS Comput Biol , vol.4
    • Guan, Y.1    Myers, C.L.2    Lu, R.3    Lemischka, I.R.4    Bult, C.J.5    Troyanskaya, O.G.6
  • 18
    • 47549116997 scopus 로고    scopus 로고
    • A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
    • 10.1186/gb-2008-9-s1-s2, 2447536, 18613946
    • Pena-Castillo L, Tasan M, Myers C, Lee H, Joshi T, Zhang C, Guan Y, Leone M, Pagnani A, Kim W, et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biology 2008, 9:S2. 10.1186/gb-2008-9-s1-s2, 2447536, 18613946.
    • (2008) Genome Biology , vol.9
    • Pena-Castillo, L.1    Tasan, M.2    Myers, C.3    Lee, H.4    Joshi, T.5    Zhang, C.6    Guan, Y.7    Leone, M.8    Pagnani, A.9    Kim, W.10
  • 19
    • 47549116753 scopus 로고    scopus 로고
    • An en masse phenotype and function prediction system for Mus musculus
    • 10.1186/gb-2008-9-s1-s8, 2447542, 18613952
    • Tasan M, Tian W, Hill D, Gibbons F, Blake J, Roth F. An en masse phenotype and function prediction system for Mus musculus. Genome Biology 2008, 9:S8. 10.1186/gb-2008-9-s1-s8, 2447542, 18613952.
    • (2008) Genome Biology , vol.9
    • Tasan, M.1    Tian, W.2    Hill, D.3    Gibbons, F.4    Blake, J.5    Roth, F.6
  • 20
    • 47549104748 scopus 로고    scopus 로고
    • Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function
    • 10.1186/gb-2008-9-s1-s7, 2447541, 18613951
    • Tian W, Zhang L, Tasan M, Gibbons F, King O, Park J, Wunderlich Z, Cherry JM, Roth F. Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome Biology 2008, 9:S7. 10.1186/gb-2008-9-s1-s7, 2447541, 18613951.
    • (2008) Genome Biology , vol.9
    • Tian, W.1    Zhang, L.2    Tasan, M.3    Gibbons, F.4    King, O.5    Park, J.6    Wunderlich, Z.7    Cherry, J.M.8    Roth, F.9
  • 23
    • 38049054726 scopus 로고    scopus 로고
    • Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs
    • 10.1101/gr.6654808, 2134779, 18042645
    • Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, Zhang MQ, Green RD, Ren B. Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res 2008, 18:46-59. 10.1101/gr.6654808, 2134779, 18042645.
    • (2008) Genome Res , vol.18 , pp. 46-59
    • Barrera, L.O.1    Li, Z.2    Smith, A.D.3    Arden, K.C.4    Cavenee, W.K.5    Zhang, M.Q.6    Green, R.D.7    Ren, B.8
  • 26
    • 58149197592 scopus 로고    scopus 로고
    • The Mouse Genome Database genotypes::phenotypes
    • 10.1093/nar/gkn886, 2686566, 18981050, the Mouse Genome Database Group
    • Blake JA, Bult CJ, Eppig JT, Kadin JA, Richardson JE, . the Mouse Genome Database Group The Mouse Genome Database genotypes::phenotypes. Nucl Acids Res 2009, 37:D712-D719. 10.1093/nar/gkn886, 2686566, 18981050, the Mouse Genome Database Group.
    • (2009) Nucl Acids Res , vol.37
    • Blake, J.A.1    Bult, C.J.2    Eppig, J.T.3    Kadin, J.A.4    Richardson, J.E.5
  • 27
    • 33744975264 scopus 로고    scopus 로고
    • L2L: a simple tool for discovering the hidden significance in microarray expression data
    • 10.1186/gb-2005-6-9-r81, 1242216, 16168088
    • Newman JC, Weiner AM. L2L: a simple tool for discovering the hidden significance in microarray expression data. Genome Biol 2005, 6:R81. 10.1186/gb-2005-6-9-r81, 1242216, 16168088.
    • (2005) Genome Biol , vol.6
    • Newman, J.C.1    Weiner, A.M.2
  • 29
    • 33747875436 scopus 로고    scopus 로고
    • Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset
    • 10.1093/bioinformatics/btl184, 1617036, 16709591
    • Liu X, Sivaganesan S, Yeung KY, Guo J, Bumgarner RE, Medvedovic M. Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset. Bioinformatics 2006, 22:1737-1744. 10.1093/bioinformatics/btl184, 1617036, 16709591.
    • (2006) Bioinformatics , vol.22 , pp. 1737-1744
    • Liu, X.1    Sivaganesan, S.2    Yeung, K.Y.3    Guo, J.4    Bumgarner, R.E.5    Medvedovic, M.6
  • 30
    • 0036739286 scopus 로고    scopus 로고
    • Bayesian infinite mixture model based clustering of gene expression profiles
    • 10.1093/bioinformatics/18.9.1194, 12217911
    • Medvedovic M, Sivaganesan S. Bayesian infinite mixture model based clustering of gene expression profiles. Bioinformatics 2002, 18:1194-1206. 10.1093/bioinformatics/18.9.1194, 12217911.
    • (2002) Bioinformatics , vol.18 , pp. 1194-1206
    • Medvedovic, M.1    Sivaganesan, S.2
  • 31
    • 69549095896 scopus 로고    scopus 로고
    • CLEAN: CLustering Enrichment ANalysis
    • 10.1186/1471-2105-10-234, 2734555, 19640299
    • Freudenberg JM, Joshi VK, Hu Z, Medvedovic M. CLEAN: CLustering Enrichment ANalysis. BMC Bioinformatics 2009, 10:234. 10.1186/1471-2105-10-234, 2734555, 19640299.
    • (2009) BMC Bioinformatics , vol.10 , pp. 234
    • Freudenberg, J.M.1    Joshi, V.K.2    Hu, Z.3    Medvedovic, M.4
  • 32
    • 9444225935 scopus 로고    scopus 로고
    • Java Treeview--extensible visualization of microarray data
    • 10.1093/bioinformatics/bth349, 15180930
    • Saldanha AJ. Java Treeview--extensible visualization of microarray data. Bioinformatics 2004, 20:3246-3248. 10.1093/bioinformatics/bth349, 15180930.
    • (2004) Bioinformatics , vol.20 , pp. 3246-3248
    • Saldanha, A.J.1
  • 33
    • 0029960055 scopus 로고    scopus 로고
    • TRANSFAC: a database on transcription factors and their DNA binding sites
    • 10.1093/nar/24.1.238, 145586, 8594589
    • Wingender E, Dietze P, Karas H, Knuppel R. TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res 1996, 24:238-241. 10.1093/nar/24.1.238, 145586, 8594589.
    • (1996) Nucleic Acids Res , vol.24 , pp. 238-241
    • Wingender, E.1    Dietze, P.2    Karas, H.3    Knuppel, R.4
  • 35
    • 26444546442 scopus 로고    scopus 로고
    • From The Cover: An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival
    • 10.1073/pnas.0506230102, 1197273,1197273, 16141321
    • Miller LD, Smeds J, George J, Vega VB, Vergara L, Ploner A, Pawitan Y, Hall P, Klaar S, Liu ET, et al. From The Cover: An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. PNAS 2005, 102:13550-13555. 10.1073/pnas.0506230102, 1197273,1197273, 16141321.
    • (2005) PNAS , vol.102 , pp. 13550-13555
    • Miller, L.D.1    Smeds, J.2    George, J.3    Vega, V.B.4    Vergara, L.5    Ploner, A.6    Pawitan, Y.7    Hall, P.8    Klaar, S.9    Liu, E.T.10
  • 36
    • 33746894693 scopus 로고    scopus 로고
    • Gene Expression Signature in Organized and Growth-Arrested Mammary Acini Predicts Good Outcome in Breast Cancer
    • 10.1158/0008-5472.CAN-06-0515, 16849555
    • Fournier MV, Martin KJ, Kenny PA, Xhaja K, Bosch I, Yaswen P, Bissell MJ. Gene Expression Signature in Organized and Growth-Arrested Mammary Acini Predicts Good Outcome in Breast Cancer. Cancer Res 2006, 66:7095-7102. 10.1158/0008-5472.CAN-06-0515, 16849555.
    • (2006) Cancer Res , vol.66 , pp. 7095-7102
    • Fournier, M.V.1    Martin, K.J.2    Kenny, P.A.3    Xhaja, K.4    Bosch, I.5    Yaswen, P.6    Bissell, M.J.7
  • 38
    • 17844386351 scopus 로고    scopus 로고
    • Anti-proliferative effect of estrogen in breast cancer cells that re-express ER{alpha} is mediated by aberrant regulation of cell cycle genes
    • 10.1677/jme.1.01677, 15821115
    • Moggs JG, Murphy TC, Lim FL, Moore DJ, Stuckey R, Antrobus K, Kimber I, Orphanides G. Anti-proliferative effect of estrogen in breast cancer cells that re-express ER{alpha} is mediated by aberrant regulation of cell cycle genes. J Mol Endocrinol 2005, 34:535-551. 10.1677/jme.1.01677, 15821115.
    • (2005) J Mol Endocrinol , vol.34 , pp. 535-551
    • Moggs, J.G.1    Murphy, T.C.2    Lim, F.L.3    Moore, D.J.4    Stuckey, R.5    Antrobus, K.6    Kimber, I.7    Orphanides, G.8
  • 39
    • 33644872577 scopus 로고    scopus 로고
    • Limma: linear models for microarray data
    • New York: Springer, Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W
    • Smyth GK. Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions using R and Bioconductor 2005, 397-420. New York: Springer, Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W.
    • (2005) Bioinformatics and Computational Biology Solutions using R and Bioconductor , pp. 397-420
    • Smyth, G.K.1
  • 40
    • 58349105009 scopus 로고    scopus 로고
    • LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data
    • 10.1093/bioinformatics/btn592, 2639007, 19038984
    • Sartor MA, Leikauf GD, Medvedovic M. LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data. Bioinformatics 2009, 25:211-217. 10.1093/bioinformatics/btn592, 2639007, 19038984.
    • (2009) Bioinformatics , vol.25 , pp. 211-217
    • Sartor, M.A.1    Leikauf, G.D.2    Medvedovic, M.3
  • 41
    • 44649117905 scopus 로고    scopus 로고
    • Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
    • 10.1016/j.cell.2008.04.043, 18555785
    • Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, et al. Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells. Cell 2008, 133:1106-1117. 10.1016/j.cell.2008.04.043, 18555785.
    • (2008) Cell , vol.133 , pp. 1106-1117
    • Chen, X.1    Xu, H.2    Yuan, P.3    Fang, F.4    Huss, M.5    Vega, V.B.6    Wong, E.7    Orlov, Y.L.8    Zhang, W.9    Jiang, J.10
  • 43
    • 35949000033 scopus 로고    scopus 로고
    • A comprehensive ChIPGCochip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members
    • 10.1101/gr.6783507, 2045138, 17908821
    • Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, Farnham PJ. A comprehensive ChIPGCochip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res 2007, 17:1550-1561. 10.1101/gr.6783507, 2045138, 17908821.
    • (2007) Genome Res , vol.17 , pp. 1550-1561
    • Xu, X.1    Bieda, M.2    Jin, V.X.3    Rabinovich, A.4    Oberley, M.J.5    Green, R.6    Farnham, P.J.7
  • 44
    • 0035868379 scopus 로고    scopus 로고
    • Expression analysis using DNA microarrays demonstrates that E2F-1 up-regulates expression of DNA replication genes including replication protein A2 3
    • 10.1038/sj.onc.1204230, 11313881
    • Kalma Y, Marash L, Lamed Y, Ginsberg D. Expression analysis using DNA microarrays demonstrates that E2F-1 up-regulates expression of DNA replication genes including replication protein A2 3. Oncogene 2001, 20:1379-1387. 10.1038/sj.onc.1204230, 11313881.
    • (2001) Oncogene , vol.20 , pp. 1379-1387
    • Kalma, Y.1    Marash, L.2    Lamed, Y.3    Ginsberg, D.4


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