메뉴 건너뛰기




Volumn 7, Issue , 2013, Pages

3Omics: A web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data

Author keywords

Analysis; Metabolomics; Omics integration; Proteomics; Systems biology; Transcriptomics; Visualization

Indexed keywords

ARSENIC TRIOXIDE; ORGANOARSENIC DERIVATIVE; OXIDE; RETINOIC ACID;

EID: 84880335552     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-7-64     Document Type: Article
Times cited : (149)

References (45)
  • 1
    • 33745659674 scopus 로고    scopus 로고
    • Combined transcript and metabolite profiling of Arabidopsis leaves reveals fundamental effects of the thiol-disulfide status on plant metabolism
    • 10.1104/pp.106.081208, 1475465, 16648214
    • Kolbe A, Oliver SN, Fernie AR, Stitt M, van Dongen JT, Geigenberger P. Combined transcript and metabolite profiling of Arabidopsis leaves reveals fundamental effects of the thiol-disulfide status on plant metabolism. Plant Physiol 2006, 141:412-422. 10.1104/pp.106.081208, 1475465, 16648214.
    • (2006) Plant Physiol , vol.141 , pp. 412-422
    • Kolbe, A.1    Oliver, S.N.2    Fernie, A.R.3    Stitt, M.4    van Dongen, J.T.5    Geigenberger, P.6
  • 2
    • 51649117334 scopus 로고    scopus 로고
    • Integrated transcriptomics, proteomics, and metabolomics analyses to survey ozone responses in the leaves of rice seedling
    • 10.1021/pr800128q, 18517257
    • Cho K, Shibato J, Agrawal GK, Jung YH, Kubo A, Jwa NS, Tamogami S, Satoh K, Kikuchi S, Higashi T, et al. Integrated transcriptomics, proteomics, and metabolomics analyses to survey ozone responses in the leaves of rice seedling. J Proteome Res 2008, 7:2980-2998. 10.1021/pr800128q, 18517257.
    • (2008) J Proteome Res , vol.7 , pp. 2980-2998
    • Cho, K.1    Shibato, J.2    Agrawal, G.K.3    Jung, Y.H.4    Kubo, A.5    Jwa, N.S.6    Tamogami, S.7    Satoh, K.8    Kikuchi, S.9    Higashi, T.10
  • 3
    • 27144452891 scopus 로고    scopus 로고
    • Systems toxicology: applications of toxicogenomics, transcriptomics, proteomics and metabolomics in toxicology
    • 10.1586/14789450.2.5.767, 16209655
    • Heijne WH, Kienhuis AS, van Ommen B, Stierum RH, Groten JP. Systems toxicology: applications of toxicogenomics, transcriptomics, proteomics and metabolomics in toxicology. Expert Rev Proteomics 2005, 2:767-780. 10.1586/14789450.2.5.767, 16209655.
    • (2005) Expert Rev Proteomics , vol.2 , pp. 767-780
    • Heijne, W.H.1    Kienhuis, A.S.2    van Ommen, B.3    Stierum, R.H.4    Groten, J.P.5
  • 5
    • 33845665396 scopus 로고    scopus 로고
    • Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior
    • 10.1104/pp.106.088534, 1676044, 17071647
    • Carrari F, Baxter C, Usadel B, Urbanczyk-Wochniak E, Zanor MI, Nunes-Nesi A, Nikiforova V, Centero D, Ratzka A, Pauly M, et al. Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior. Plant Physiol 2006, 142:1380-1396. 10.1104/pp.106.088534, 1676044, 17071647.
    • (2006) Plant Physiol , vol.142 , pp. 1380-1396
    • Carrari, F.1    Baxter, C.2    Usadel, B.3    Urbanczyk-Wochniak, E.4    Zanor, M.I.5    Nunes-Nesi, A.6    Nikiforova, V.7    Centero, D.8    Ratzka, A.9    Pauly, M.10
  • 6
    • 51449105863 scopus 로고    scopus 로고
    • Integrated pathway analysis of rat urine metabolic profiles and kidney transcriptomic profiles to elucidate the systems toxicology of model nephrotoxicants
    • 10.1021/tx800061w, 18656965
    • Xu EY, Perlina A, Vu H, Troth SP, Brennan RJ, Aslamkhan AG, Xu Q. Integrated pathway analysis of rat urine metabolic profiles and kidney transcriptomic profiles to elucidate the systems toxicology of model nephrotoxicants. Chem Res Toxicol 2008, 21:1548-1561. 10.1021/tx800061w, 18656965.
    • (2008) Chem Res Toxicol , vol.21 , pp. 1548-1561
    • Xu, E.Y.1    Perlina, A.2    Vu, H.3    Troth, S.P.4    Brennan, R.J.5    Aslamkhan, A.G.6    Xu, Q.7
  • 7
    • 75949130452 scopus 로고    scopus 로고
    • Combining tissue transcriptomics and urine metabolomics for breast cancer biomarker identification
    • 10.1093/bioinformatics/btp558, 19783829
    • Nam H, Chung BC, Kim Y, Lee K, Lee D. Combining tissue transcriptomics and urine metabolomics for breast cancer biomarker identification. Bioinformatics 2009, 25:3151-3157. 10.1093/bioinformatics/btp558, 19783829.
    • (2009) Bioinformatics , vol.25 , pp. 3151-3157
    • Nam, H.1    Chung, B.C.2    Kim, Y.3    Lee, K.4    Lee, D.5
  • 8
    • 79951529195 scopus 로고    scopus 로고
    • Integrated metabolome and transcriptome analysis of the NCI60 dataset
    • Su G, Burant CF, Beecher CW, Athey BD, Meng F. Integrated metabolome and transcriptome analysis of the NCI60 dataset. BMC Bioinforma 2011, 12(1):36.
    • (2011) BMC Bioinforma , vol.12 , Issue.1 , pp. 36
    • Su, G.1    Burant, C.F.2    Beecher, C.W.3    Athey, B.D.4    Meng, F.5
  • 10
    • 33645241830 scopus 로고    scopus 로고
    • VANTED: a system for advanced data analysis and visualization in the context of biological networks
    • Junker BH, Klukas C, Schreiber F. VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinforma 2006, 7:109.
    • (2006) BMC Bioinforma , vol.7 , pp. 109
    • Junker, B.H.1    Klukas, C.2    Schreiber, F.3
  • 11
    • 67849122322 scopus 로고    scopus 로고
    • VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
    • 10.1093/nar/gkp406, 2703932, 19465394
    • Hu Z, Hung JH, Wang Y, Chang YC, Huang CL, Huyck M, DeLisi C. VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res 2009, 37:W115-121. 10.1093/nar/gkp406, 2703932, 19465394.
    • (2009) Nucleic Acids Res , vol.37
    • Hu, Z.1    Hung, J.H.2    Wang, Y.3    Chang, Y.C.4    Huang, C.L.5    Huyck, M.6    DeLisi, C.7
  • 14
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • 10.1101/gr.1239303, 403769, 14597658
    • 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, 13:2498-2504. 10.1101/gr.1239303, 403769, 14597658.
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5    Ramage, D.6    Amin, N.7    Schwikowski, B.8    Ideker, T.9
  • 15
    • 70350638951 scopus 로고    scopus 로고
    • Interaction techniques for selecting and manipulating subgraphs in network visualizations
    • McGuffin MJ, Jurisica I. Interaction techniques for selecting and manipulating subgraphs in network visualizations. IEEE Trans Vis Comput Graph 2009, 15:937-944.
    • (2009) IEEE Trans Vis Comput Graph , vol.15 , pp. 937-944
    • McGuffin, M.J.1    Jurisica, I.2
  • 16
    • 54949110152 scopus 로고    scopus 로고
    • Cerebral: visualizing multiple experimental conditions on a graph with biological context
    • Barsky A, Munzner T, Gardy J, Kincaid R. Cerebral: visualizing multiple experimental conditions on a graph with biological context. IEEE Trans Vis Comput Graph 2008, 14:1253-1260.
    • (2008) IEEE Trans Vis Comput Graph , vol.14 , pp. 1253-1260
    • Barsky, A.1    Munzner, T.2    Gardy, J.3    Kincaid, R.4
  • 17
    • 33644873677 scopus 로고    scopus 로고
    • Pathguide: a pathway resource list
    • 10.1093/nar/gkj126, 1347488, 16381921
    • Bader GD, Cary MP, Sander C. Pathguide: a pathway resource list. Nucleic Acids Res 2006, 34:D504-506. 10.1093/nar/gkj126, 1347488, 16381921.
    • (2006) Nucleic Acids Res , vol.34
    • Bader, G.D.1    Cary, M.P.2    Sander, C.3
  • 18
    • 27744493624 scopus 로고    scopus 로고
    • KEGG-based pathway visualization tool for complex omics data
    • Arakawa K, Kono N, Yamada Y, Mori H, Tomita M. KEGG-based pathway visualization tool for complex omics data. In Silico Biol 2005, 5:419-423.
    • (2005) In Silico Biol , vol.5 , pp. 419-423
    • Arakawa, K.1    Kono, N.2    Yamada, Y.3    Mori, H.4    Tomita, M.5
  • 19
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • 10.1093/nar/28.1.27, 102409, 10592173
    • Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 20
    • 78650572031 scopus 로고    scopus 로고
    • Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data
    • 10.1093/bioinformatics/btq594, 3008637, 21098431
    • Garcia-Alcalde F, Garcia-Lopez F, Dopazo J, Conesa A. Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data. Bioinformatics 2011, 27:137-139. 10.1093/bioinformatics/btq594, 3008637, 21098431.
    • (2011) Bioinformatics , vol.27 , pp. 137-139
    • Garcia-Alcalde, F.1    Garcia-Lopez, F.2    Dopazo, J.3    Conesa, A.4
  • 21
    • 71049126880 scopus 로고    scopus 로고
    • Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example
    • 10.1186/1752-0509-3-82, 2744654, 19698148
    • Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, Huser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A. Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. BMC Syst Biol 2009, 3:82. 10.1186/1752-0509-3-82, 2744654, 19698148.
    • (2009) BMC Syst Biol , vol.3 , pp. 82
    • Neuweger, H.1    Persicke, M.2    Albaum, S.P.3    Bekel, T.4    Dondrup, M.5    Huser, A.T.6    Winnebald, J.7    Schneider, J.8    Kalinowski, J.9    Goesmann, A.10
  • 22
    • 27244440204 scopus 로고    scopus 로고
    • KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps
    • 10.1104/pp.105.060525, 1176402, 16010003
    • Tokimatsu T, Sakurai N, Suzuki H, Ohta H, Nishitani K, Koyama T, Umezawa T, Misawa N, Saito K, Shibata D. KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps. Plant Physiol 2005, 138:1289-1300. 10.1104/pp.105.060525, 1176402, 16010003.
    • (2005) Plant Physiol , vol.138 , pp. 1289-1300
    • Tokimatsu, T.1    Sakurai, N.2    Suzuki, H.3    Ohta, H.4    Nishitani, K.5    Koyama, T.6    Umezawa, T.7    Misawa, N.8    Saito, K.9    Shibata, D.10
  • 23
    • 12144291195 scopus 로고    scopus 로고
    • MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes
    • 10.1111/j.1365-313X.2004.02016.x, 14996223
    • Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 2004, 37:914-939. 10.1111/j.1365-313X.2004.02016.x, 14996223.
    • (2004) Plant J , vol.37 , pp. 914-939
    • Thimm, O.1    Blasing, O.2    Gibon, Y.3    Nagel, A.4    Meyer, S.5    Kruger, P.6    Selbig, J.7    Muller, L.A.8    Rhee, S.Y.9    Stitt, M.10
  • 25
    • 8844222709 scopus 로고    scopus 로고
    • PaVESy: Pathway Visualization and Editing System
    • 10.1093/bioinformatics/bth278, 15105280
    • Lüdemann A, Weicht D, Selbig J, Kopka J. PaVESy: Pathway Visualization and Editing System. Bioinformatics 2004, 20:2841-2844. 10.1093/bioinformatics/bth278, 15105280.
    • (2004) Bioinformatics , vol.20 , pp. 2841-2844
    • Lüdemann, A.1    Weicht, D.2    Selbig, J.3    Kopka, J.4
  • 26
    • 80052000539 scopus 로고    scopus 로고
    • Ingenuity Pathway Analysis
    • Ingenuity Pathway Analysis. http://www.ingenuity.com/.
  • 27
    • 3042786293 scopus 로고    scopus 로고
    • A gene network for navigating the literature
    • 10.1038/ng0704-664, 15226743
    • Hoffmann R, Valencia A. A gene network for navigating the literature. Nat Genet 2004, 36:664-664. 10.1038/ng0704-664, 15226743.
    • (2004) Nat Genet , vol.36 , pp. 664-664
    • Hoffmann, R.1    Valencia, A.2
  • 28
    • 84888044295 scopus 로고    scopus 로고
    • IHOP
    • iHOP. http://www.ihop-net.org.
  • 29
    • 14844326483 scopus 로고    scopus 로고
    • Computational prediction of human metabolic pathways from the complete human genome
    • 10.1186/gb-2004-6-1-r2, 549063, 15642094
    • Romero P, Wagg J, Green M, Kaiser D, Krummenacker M, Karp P. Computational prediction of human metabolic pathways from the complete human genome. Genome Biology 2004, 6:R2. 10.1186/gb-2004-6-1-r2, 549063, 15642094.
    • (2004) Genome Biology , vol.6
    • Romero, P.1    Wagg, J.2    Green, M.3    Kaiser, D.4    Krummenacker, M.5    Karp, P.6
  • 30
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • da Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.
    • (2009) Nat Protoc , vol.4 , pp. 44-57
    • da Huang, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 31
    • 78651317908 scopus 로고    scopus 로고
    • Entrez Gene: gene-centered information at NCBI
    • 10.1093/nar/gkq1237, 3013746, 21115458
    • Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2011, 39:D52-57. 10.1093/nar/gkq1237, 3013746, 21115458.
    • (2011) Nucleic Acids Res , vol.39
    • Maglott, D.1    Ostell, J.2    Pruitt, K.D.3    Tatusova, T.4
  • 33
    • 67849104638 scopus 로고    scopus 로고
    • PubChem: a public information system for analyzing bioactivities of small molecules
    • 10.1093/nar/gkp456, 2703903, 19498078
    • Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Bryant SH. PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Research 2009, 37:W623-W633. 10.1093/nar/gkp456, 2703903, 19498078.
    • (2009) Nucleic Acids Research , vol.37
    • Wang, Y.1    Xiao, J.2    Suzek, T.O.3    Zhang, J.4    Wang, J.5    Bryant, S.H.6
  • 35
    • 78650575601 scopus 로고    scopus 로고
    • Includes R soruce code and/or documentation contributed by (in alphabetical order): Bolker B, Bonebakker L, Gentleman R, Liaw WHA, Lumley T, Maechler M, Magnusson A, Moeller S, Schwartz M, Venables B
    • Warnes GR, Includes R soruce code and/or documentation contributed by (in alphabetical order): Bolker B, Bonebakker L, Gentleman R, Liaw WHA, Lumley T, Maechler M, Magnusson A, Moeller S, Schwartz M, Venables B gplots: Various R programming tools for plotting data 2010, Includes R soruce code and/or documentation contributed by (in alphabetical order): Bolker B, Bonebakker L, Gentleman R, Liaw WHA, Lumley T, Maechler M, Magnusson A, Moeller S, Schwartz M, Venables B.
    • (2010) gplots: Various R programming tools for plotting data
    • Warnes, G.R.1
  • 36
    • 52649157604 scopus 로고    scopus 로고
    • An algorithm for thorough background subtraction from high-resolution LC/MS data: application for detection of glutathione-trapped reactive metabolites
    • 10.1002/jms.1390, 18300330
    • Zhang H, Yang Y. An algorithm for thorough background subtraction from high-resolution LC/MS data: application for detection of glutathione-trapped reactive metabolites. J Mass Spectrom 2008, 43:1181-1190. 10.1002/jms.1390, 18300330.
    • (2008) J Mass Spectrom , vol.43 , pp. 1181-1190
    • Zhang, H.1    Yang, Y.2
  • 37
    • 84874651821 scopus 로고    scopus 로고
    • Google Chart Tools
    • Google Chart Tools. https://developers.google.com/chart/.
  • 39
    • 77956550520 scopus 로고    scopus 로고
    • MetPA: a web-based metabolomics tool for pathway analysis and visualization
    • 10.1093/bioinformatics/btq418, 20628077
    • Xia J, Wishart DS. MetPA: a web-based metabolomics tool for pathway analysis and visualization. Bioinformatics 2010, 26:2342-2344. 10.1093/bioinformatics/btq418, 20628077.
    • (2010) Bioinformatics , vol.26 , pp. 2342-2344
    • Xia, J.1    Wishart, D.S.2
  • 40
    • 12244286062 scopus 로고    scopus 로고
    • Role of the Promyelocytic Leukemia Body in the Dynamic Interaction between the Androgen Receptor and Steroid Receptor Coactivator-1 in Living Cells
    • 10.1210/me.2002-0165, 12511612
    • Rivera OJ, Song CS, Centonze VE, Lechleiter JD, Chatterjee B, Roy AK. Role of the Promyelocytic Leukemia Body in the Dynamic Interaction between the Androgen Receptor and Steroid Receptor Coactivator-1 in Living Cells. Molecular Endocrinology 2003, 17:128-140. 10.1210/me.2002-0165, 12511612.
    • (2003) Molecular Endocrinology , vol.17 , pp. 128-140
    • Rivera, O.J.1    Song, C.S.2    Centonze, V.E.3    Lechleiter, J.D.4    Chatterjee, B.5    Roy, A.K.6
  • 41
    • 0037064106 scopus 로고    scopus 로고
    • Ligand-independent Activation of the Androgen Receptor by Interleukin-6 and the Role of Steroid Receptor Coactivator-1 in Prostate Cancer Cells
    • 10.1074/jbc.M203313200, 12163482
    • Ueda T, Mawji NR, Bruchovsky N, Sadar MD. Ligand-independent Activation of the Androgen Receptor by Interleukin-6 and the Role of Steroid Receptor Coactivator-1 in Prostate Cancer Cells. Journal of Biological Chemistry 2002, 277:38087-38094. 10.1074/jbc.M203313200, 12163482.
    • (2002) Journal of Biological Chemistry , vol.277 , pp. 38087-38094
    • Ueda, T.1    Mawji, N.R.2    Bruchovsky, N.3    Sadar, M.D.4
  • 43
    • 4444363680 scopus 로고    scopus 로고
    • Comparative proteomic analysis of all-trans-retinoic acid treatment reveals systematic posttranscriptional control mechanisms in acute promyelocytic leukemia
    • 10.1182/blood-2004-01-0046, 15142884
    • Harris MN, Ozpolat B, Abdi F, Gu S, Legler A, Mawuenyega KG, Tirado-Gomez M, Lopez-Berestein G, Chen X. Comparative proteomic analysis of all-trans-retinoic acid treatment reveals systematic posttranscriptional control mechanisms in acute promyelocytic leukemia. Blood 2004, 104:1314-1323. 10.1182/blood-2004-01-0046, 15142884.
    • (2004) Blood , vol.104 , pp. 1314-1323
    • Harris, M.N.1    Ozpolat, B.2    Abdi, F.3    Gu, S.4    Legler, A.5    Mawuenyega, K.G.6    Tirado-Gomez, M.7    Lopez-Berestein, G.8    Chen, X.9


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.