메뉴 건너뛰기




Volumn 12, Issue 5, 2016, Pages

Reactome from a WikiPathways Perspective

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION; SEMANTICS; VISUALIZATION;

EID: 84975879813     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004941     Document Type: Article
Times cited : (36)

References (62)
  • 2
    • 84975867994 scopus 로고    scopus 로고
    • PathGuide the pathway resource list [18-07-2015]. Available from:
    • PathGuide the pathway resource list [18-07-2015]. Available from: http://pathguide.org/.
  • 3
    • 68749099453 scopus 로고    scopus 로고
    • Pathway databases and tools for their exploitation: benefits, current limitations and challenges
    • .;():
    • Bauer‐Mehren A, Furlong LI, Sanz F, Pathway databases and tools for their exploitation: benefits, current limitations and challenges. Molecular systems biology. 2009;5(1):290.
    • (2009) Molecular systems biology , vol.5 , Issue.1 , pp. 290
    • Bauer‐Mehren, A.1    Furlong, L.I.2    Sanz, F.3
  • 4
    • 77349123063 scopus 로고    scopus 로고
    • The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services
    • ..;():
    • van Iersel MP, Pico AR, Kelder T, Gao J, Ho I, Hanspers K, et al. The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC bioinformatics. 2010;11(1):5.
    • (2010) BMC bioinformatics , vol.11 , Issue.1 , pp. 5
    • van Iersel, M.P.1    Pico, A.R.2    Kelder, T.3    Gao, J.4    Ho, I.5    Hanspers, K.6
  • 5
    • 84975875778 scopus 로고    scopus 로고
    • WikiPathways Curation Protocol. Available from:
    • WikiPathways Curation Protocol. Available from: http://wikipathways.org/index.php/Help:Curation_Protocol.
  • 9
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • 14597658, ..;():–
    • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research. 2003;13(11):2498–504. 14597658
    • (2003) Genome research , vol.13 , Issue.11 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4    Wang, J.T.5    Ramage, D.6
  • 10
    • 84915746374 scopus 로고    scopus 로고
    • WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization
    • .;
    • Kutmon M, Lotia S, Evelo CT, Pico AR, WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization. F1000Research. 2014;3.
    • (2014) F1000Research , vol.3
    • Kutmon, M.1    Lotia, S.2    Evelo, C.T.3    Pico, A.R.4
  • 11
    • 84865098402 scopus 로고    scopus 로고
    • GO-Elite: a flexible solution for pathway and ontology over-representation
    • 22743224, ..;():–
    • Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, et al. GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinformatics. 2012;28(16):2209–10. doi: 10.1093/bioinformatics/bts36622743224
    • (2012) Bioinformatics , vol.28 , Issue.16 , pp. 2209-2210
    • Zambon, A.C.1    Gaj, S.2    Ho, I.3    Hanspers, K.4    Vranizan, K.5    Evelo, C.T.6
  • 12
    • 58149194608 scopus 로고    scopus 로고
    • SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system
    • ..;():–
    • Pico AR, Smirnov IV, Chang JS, Yeh R- F, Wiemels JL, Wiencke JK, et al. SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system. Nucleic acids research. 2009;37(suppl 1):D803–D9.
    • (2009) Nucleic acids research , vol.37 , pp. 803-809
    • Pico, A.R.1    Smirnov, I.V.2    Chang, J.S.3    Yeh R-, F.4    Wiemels, J.L.5    Wiencke, J.K.6
  • 13
    • 84885958793 scopus 로고    scopus 로고
    • WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks
    • ..;:
    • Hanumappa M, Preece J, Elser J, Nemeth D, Bono G, Wu K, et al. WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. Rice (N Y). 2013;6:14.
    • (2013) Rice (N Y) , vol.6 , pp. 14
    • Hanumappa, M.1    Preece, J.2    Elser, J.3    Nemeth, D.4    Bono, G.5    Wu, K.6
  • 14
    • 84975886840 scopus 로고    scopus 로고
    • WikiPathways plant portal. Available from:
    • WikiPathways plant portal. Available from: http://wikipathways.org/index.php/Portal:Plants.
  • 15
    • 84975857383 scopus 로고    scopus 로고
    • CIRM Stem Cell Pathways. Available from:
    • CIRM Stem Cell Pathways. Available from: http://www.wikipathways.org/index.php/Portal:CIRM.
  • 16
    • 84975868015 scopus 로고    scopus 로고
    • extracellular RNA research community. Available from:
    • extracellular RNA research community. Available from: http://www.wikipathways.org/index.php/Portal:ExRNA.
  • 17
    • 84975846883 scopus 로고    scopus 로고
    • Evelo CT
    • Waagmeester A, Deus H, Evelo CT. Exposing WikiPathways as Linked Open Data. 2011.
    • (2011)
    • Waagmeester, A.1    Deus, H.2
  • 18
    • 84975886794 scopus 로고    scopus 로고
    • WikiPathways Sparql queries. Available from:
    • WikiPathways Sparql queries. Available from: http://www.wikipathways.org/index.php/Help:WikiPathways_Sparql_queries.
  • 19
    • 84883258242 scopus 로고    scopus 로고
    • . In:;. p.–
    • Croft D, Building models using Reactome pathways as templates. In Silico Systems Biology: Springer; 2013. p. 273–83.
    • (2013) Silico Systems Biology , pp. 273-283
    • Croft, D.1
  • 20
    • 84871602426 scopus 로고    scopus 로고
    • Annotating cancer variants and anti-cancer therapeutics in reactome
    • 24213504, ..;():–
    • Milacic M, Haw R, Rothfels K, Wu G, Croft D, Hermjakob H, et al. Annotating cancer variants and anti-cancer therapeutics in reactome. Cancers. 2012;4(4):1180–211. doi: 10.3390/cancers404118024213504
    • (2012) Cancers , vol.4 , Issue.4 , pp. 1180-1211
    • Milacic, M.1    Haw, R.2    Rothfels, K.3    Wu, G.4    Croft, D.5    Hermjakob, H.6
  • 21
    • 79959846617 scopus 로고    scopus 로고
    • PSICQUIC and PSISCORE: accessing and scoring molecular interactions
    • 21716279, ..;():–
    • Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, et al. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nature methods. 2011;8(7):528–9. doi: 10.1038/nmeth.163721716279
    • (2011) Nature methods , vol.8 , Issue.7 , pp. 528-529
    • Aranda, B.1    Blankenburg, H.2    Kerrien, S.3    Brinkman, F.S.4    Ceol, A.5    Chautard, E.6
  • 22
    • 77952310528 scopus 로고    scopus 로고
    • Research a human functional protein interaction network and its application to cancer data analysis
    • 20482850, .;:
    • Wu G, Feng X, Stein L, Research a human functional protein interaction network and its application to cancer data analysis. Genome Biol. 2010;11:R53. doi: 10.1186/gb-2010-11-5-r5320482850
    • (2010) Genome Biol , vol.11 , pp. R53
    • Wu, G.1    Feng, X.2    Stein, L.3
  • 24
    • 84876560358 scopus 로고    scopus 로고
    • The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013
    • ..;():–
    • Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, et al. The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic acids research. 2013;41(D1):D456–D63.
    • (2013) Nucleic acids research , vol.41 , Issue.D1 , pp. 456-463
    • Hastings, J.1    de Matos, P.2    Dekker, A.3    Ennis, M.4    Harsha, B.5    Kale, N.6
  • 26
    • 84975809268 scopus 로고    scopus 로고
    • WikiPathways RDF. Available from:
    • WikiPathways RDF. Available from: http://wikipathways.org/index.php/Help:WikiPathways_RDF.
  • 28
    • 84975846907 scopus 로고    scopus 로고
    • GPML Description. Available from:
    • GPML Description. Available from: http://www.pathvisio.org/gpml/.
  • 29
    • 84975822885 scopus 로고    scopus 로고
    • Reactome Data Model. Available from:
    • Reactome Data Model. Available from: http://www.reactome.org/pages/documentation/data-model/.
  • 30
    • 84975822852 scopus 로고    scopus 로고
    • Portal:Reactome—WikiPathways 2015 [cited 2015 02-09-2015]. Available from:
    • Portal:Reactome—WikiPathways 2015 [cited 2015 02-09-2015]. Available from: http://wikipathways.org/index.php/Portal:Reactome.
  • 31
    • 30044440098 scopus 로고    scopus 로고
    • Molecular interaction maps of bioregulatory networks: a general rubric for systems biology
    • 16267266, .;():–
    • Kohn KW, Aladjem MI, Weinstein JN, Pommier Y, Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Molecular biology of the cell. 2006;17(1):1–13. 16267266
    • (2006) Molecular biology of the cell , vol.17 , Issue.1 , pp. 1-13
    • Kohn, K.W.1    Aladjem, M.I.2    Weinstein, J.N.3    Pommier, Y.4
  • 32
    • 84975799971 scopus 로고    scopus 로고
    • D'Eustachio P. Abacavir transport and metabolism [Homo sapiens]
    • D'Eustachio P. Abacavir transport and metabolism [Homo sapiens].
  • 33
    • 84975799979 scopus 로고    scopus 로고
    • Reactome Team, Bohler A,. Abacavir transport and metabolism (Homo sapiens). Available from:
    • Reactome Team, Bohler A,. Abacavir transport and metabolism (Homo sapiens). Available from: http://wikipathways.org/index.php/Pathway:WP2712.
  • 36
    • 84890871773 scopus 로고    scopus 로고
    • Epidemiology, diagnosis, and management of polycystic ovary syndrome
    • .;:
    • Sirmans SM, Pate KA, Epidemiology, diagnosis, and management of polycystic ovary syndrome. Clinical epidemiology. 2014;6:1.
    • (2014) Clinical epidemiology , vol.6 , pp. 1
    • Sirmans, S.M.1    Pate, K.A.2
  • 37
    • 0346186090 scopus 로고    scopus 로고
    • Revised 2003 consensus on diagnostic criteria and long-term health risks related to polycystic ovary syndrome (PCOS)
    • .;():
    • Rotterdam E, ASRM-Sponsored PRevised 2003 consensus on diagnostic criteria and long-term health risks related to polycystic ovary syndrome (PCOS). Human Reproduction (Oxford, England). 2004;19(1):41.
    • (2004) Human Reproduction (Oxford, England) , vol.19 , Issue.1 , pp. 41
    • Rotterdam, E.1
  • 38
    • 84867251597 scopus 로고    scopus 로고
    • Differential gene expression in granulosa cells from polycystic ovary syndrome patients with and without insulin resistance: identification of susceptibility gene sets through network analysis
    • Kaur S, Archer KJ, Devi MG, Kriplani A, Strauss JF, IIISingh R, Differential gene expression in granulosa cells from polycystic ovary syndrome patients with and without insulin resistance: identification of susceptibility gene sets through network analysis. The Journal of Clinical Endocrinology & Metabolism. 2012.
    • (2012) The Journal of Clinical Endocrinology & Metabolism
    • Kaur, S.1    Archer, K.J.2    Devi, M.G.3    Kriplani, A.4    Strauss, J.F.5    Singh, R.6
  • 39
    • 84882239458 scopus 로고    scopus 로고
    • User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis. org
    • ..;():–
    • Eijssen LM, Jaillard M, Adriaens ME, Gaj S, de Groot PJ, Müller M, et al. User-friendly solutions for microarray quality control and pre-processing on ArrayAnalysis. org. Nucleic acids research. 2013;41(W1):W71–W6.
    • (2013) Nucleic acids research , vol.41 , Issue.1 , pp. 71-76
    • Eijssen, L.M.1    Jaillard, M.2    Adriaens, M.E.3    Gaj, S.4    de Groot, P.J.5    Müller, M.6
  • 40
    • 84975849394 scopus 로고    scopus 로고
    • :;
    • Dutta A, Adding automated Statistical Analysis and Biological Evaluation modules to www.arrayanalysis.org: Maastricht University; 2011.
    • (2011)
    • Dutta, A.1
  • 41
    • 84951167236 scopus 로고    scopus 로고
    • Microarray analysis of Long non-coding RNA expression profiles in human gastric cells and tissues with Helicobacter pylori Infection
    • ..;():
    • Zhu H, Wang Q, Yao Y, Fang J, Sun F, Ni Y, et al. Microarray analysis of Long non-coding RNA expression profiles in human gastric cells and tissues with Helicobacter pylori Infection. BMC medical genomics. 2015;8(1):1.
    • (2015) BMC medical genomics , vol.8 , Issue.1 , pp. 1
    • Zhu, H.1    Wang, Q.2    Yao, Y.3    Fang, J.4    Sun, F.5    Ni, Y.6
  • 42
    • 84943254286 scopus 로고    scopus 로고
    • Pathway Analysis Based on a Genome-Wide Association Study of Polycystic Ovary Syndrome
    • 26308735, .;():
    • Shim U, Kim H-N, Lee H, Oh J-Y, Sung Y-A, Kim H-L, Pathway Analysis Based on a Genome-Wide Association Study of Polycystic Ovary Syndrome. PloS one. 2015;10(8):e0136609. doi: 10.1371/journal.pone.013660926308735
    • (2015) PloS one , vol.10 , Issue.8 , pp. e0136609
    • Shim, U.1    Kim, H.-N.2    Lee, H.3    Oh, J.-Y.4    Sung, Y.-A.5    Kim, H.-L.6
  • 43
    • 84930676348 scopus 로고    scopus 로고
    • Pathway-based gene signatures predicting clinical outcome of lung adenocarcinoma
    • .;
    • Chang Y-H, Chen C-M, Chen H-Y, Yang P-C, Pathway-based gene signatures predicting clinical outcome of lung adenocarcinoma. Scientific reports. 2015;5.
    • (2015) Scientific reports , pp. 5
    • Chang, Y.-H.1    Chen, C.-M.2    Chen, H.-Y.3    Yang, P.-C.4
  • 44
    • 84975849397 scopus 로고    scopus 로고
    • Reactome Team, Bohler A, Willighagen E. Toll-Like Receptors Cascades (Homo sapiens). Available from:
    • Reactome Team, Bohler A, Willighagen E. Toll-Like Receptors Cascades (Homo sapiens). Available from: http://wikipathways.org/index.php/Pathway:WP2775.
  • 46
    • 77956383646 scopus 로고    scopus 로고
    • Cellularity and adipogenic profile of the abdominal subcutaneous adipose tissue from obese adolescents: association with insulin resistance and hepatic steatosis
    • 20805387, ..;():–
    • Kursawe R, Eszlinger M, Narayan D, Liu T, Bazuine M, Cali AM, et al. Cellularity and adipogenic profile of the abdominal subcutaneous adipose tissue from obese adolescents: association with insulin resistance and hepatic steatosis. Diabetes. 2010;59(9):2288–96. doi: 10.2337/db10-011320805387
    • (2010) Diabetes , vol.59 , Issue.9 , pp. 2288-2296
    • Kursawe, R.1    Eszlinger, M.2    Narayan, D.3    Liu, T.4    Bazuine, M.5    Cali, A.M.6
  • 47
    • 84887317809 scopus 로고    scopus 로고
    • A comprehensive molecular interaction map for Hepatitis B virus and drug designing of a novel inhibitor for Hepatitis BX protein
    • 21904432, .;():
    • Jitendra S, Nanda A, Kaur S, Singh M, A comprehensive molecular interaction map for Hepatitis B virus and drug designing of a novel inhibitor for Hepatitis BX protein. Bioinformation. 2011;7(1):9. 21904432
    • (2011) Bioinformation , vol.7 , Issue.1 , pp. 9
    • Jitendra, S.1    Nanda, A.2    Kaur, S.3    Singh, M.4
  • 48
    • 84862810266 scopus 로고    scopus 로고
    • Proteomic analysis of acquired tamoxifen resistance in MCF-7 cells reveals expression signatures associated with enhanced migration
    • 22417809, ..;():
    • Zhou C, Zhong Q, Rhodes LV, Townley I, Bratton MR, Zhang Q, et al. Proteomic analysis of acquired tamoxifen resistance in MCF-7 cells reveals expression signatures associated with enhanced migration. Breast Cancer Res. 2012;14(2):R45. 22417809
    • (2012) Breast Cancer Res , vol.14 , Issue.2 , pp. R45
    • Zhou, C.1    Zhong, Q.2    Rhodes, L.V.3    Townley, I.4    Bratton, M.R.5    Zhang, Q.6
  • 49
    • 79955776933 scopus 로고    scopus 로고
    • Alterations in hepatic one-carbon metabolism and related pathways following a high-fat dietary intervention
    • 21303933, ..;():–
    • Rubio-Aliaga I, de Roos B, Sailer M, McLoughlin GA, Boekschoten MV, van Erk M, et al. Alterations in hepatic one-carbon metabolism and related pathways following a high-fat dietary intervention. Physiological genomics. 2011;43(8):408–16. doi: 10.1152/physiolgenomics.00179.201021303933
    • (2011) Physiological genomics , vol.43 , Issue.8 , pp. 408-416
    • Rubio-Aliaga, I.1    de Roos, B.2    Sailer, M.3    McLoughlin, G.A.4    Boekschoten, M.V.5    van Erk, M.6
  • 50
    • 77952470286 scopus 로고    scopus 로고
    • Pattern recognition via the toll-like receptor system in the human female genital tract
    • .;
    • Nasu K, Narahara H, Pattern recognition via the toll-like receptor system in the human female genital tract. Mediators of inflammation. 2010;2010.
    • (2010) Mediators of inflammation , pp. 2010
    • Nasu, K.1    Narahara, H.2
  • 52
    • 84055172781 scopus 로고    scopus 로고
    • Is PCOS an inflammatory process?
    • 22192135, .;():–
    • Duleba AJ, Dokras A, Is PCOS an inflammatory process?Fertility and sterility. 2012;97(1):7–12. doi: 10.1016/j.fertnstert.2011.11.02322192135
    • (2012) Fertility and sterility , vol.97 , Issue.1 , pp. 7-12
    • Duleba, A.J.1    Dokras, A.2
  • 53
    • 38349016581 scopus 로고    scopus 로고
    • Toll-like receptors in female reproductive tract and their menstrual cycle dependent expression
    • 17493683, .;():–
    • Aflatoonian R, Fazeli A, Toll-like receptors in female reproductive tract and their menstrual cycle dependent expression. Journal of reproductive immunology. 2008;77(1):7–13. 17493683
    • (2008) Journal of reproductive immunology , vol.77 , Issue.1 , pp. 7-13
    • Aflatoonian, R.1    Fazeli, A.2
  • 54
    • 84934327756 scopus 로고    scopus 로고
    • Higher circulating leukocytes in women with PCOS is reversed by aerobic exercise
    • Covington JD, Tam CS, Pasarica M, Redman LM, Higher circulating leukocytes in women with PCOS is reversed by aerobic exercise. Biochimie. 2014.
    • (2014) Biochimie
    • Covington, J.D.1    Tam, C.S.2    Pasarica, M.3    Redman, L.M.4
  • 55
    • 84975892705 scopus 로고    scopus 로고
    • Bohler A, Wu G, Pradhana LA. Reactome converter source code. Available from:
    • Bohler A, Wu G, Pradhana LA. Reactome converter source code. Available from: https://github.com/wikipathways/reactome2gpml-converter.
  • 56
    • 84975892713 scopus 로고    scopus 로고
    • The Developement team of Reactome. Reactome Curator Tool 2015. Available from:
    • The Developement team of Reactome. Reactome Curator Tool 2015. Available from: https://github.com/reactome/CuratorTool.
  • 58
    • 84975867962 scopus 로고    scopus 로고
    • Java Scripts Available from:
    • Java Scripts Available from: https://github.com/pennatula/Utilities.
  • 61
    • 84975877447 scopus 로고    scopus 로고
    • Bohler A. ComplexViz Plugin source code 2015. Available from:,
    • Bohler A. ComplexViz Plugin source code 2015. Available from:, https://github.com/pennatula/ComplexViz.
  • 62
    • 84975794266 scopus 로고    scopus 로고
    • Bohler A. User Guide for the ComplexViz Plugin 2015. Available from:
    • Bohler A. User Guide for the ComplexViz Plugin 2015. Available from: https://github.com/pennatula/ComplexViz/wiki/User-Guide-for-the-ComplexViz-Plugin.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.