메뉴 건너뛰기




Volumn 15, Issue 5-6, 2015, Pages 981-996

Bioinformatics approaches for the functional interpretation of protein lists: From ontology term enrichment to network analysis

Author keywords

Bioinformatics; Data interpretation; Functional bioinformatics; Overrepresentation analysis; Pathways; Protein networks

Indexed keywords

PROTEIN; PROTEOME; TRANSCRIPTOME;

EID: 84924746762     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201400296     Document Type: Review
Times cited : (29)

References (181)
  • 2
    • 39149115688 scopus 로고    scopus 로고
    • Bioinformatics applications for pathway analysis of microarray data
    • Werner, T., Bioinformatics applications for pathway analysis of microarray data. Curr. Opin. Biotechnol. 2008, 19, 50-54.
    • (2008) Curr. Opin. Biotechnol. , vol.19 , pp. 50-54
    • Werner, T.1
  • 3
    • 84855710474 scopus 로고    scopus 로고
    • Combining literature text mining with microarray data: advances for system biology modeling
    • bbr018
    • Faro, A., Giordano, D., Spampinato, C., Combining literature text mining with microarray data: advances for system biology modeling. Brief. Bioinform. 2011, bbr018.
    • (2011) Brief. Bioinform.
    • Faro, A.1    Giordano, D.2    Spampinato, C.3
  • 4
    • 0037434977 scopus 로고    scopus 로고
    • Biomedical informatics for proteomics
    • Boguski, M. S., McIntosh, M. W., Biomedical informatics for proteomics. Nature 2003, 422, 233-237.
    • (2003) Nature , vol.422 , pp. 233-237
    • Boguski, M.S.1    McIntosh, M.W.2
  • 5
    • 33750600611 scopus 로고    scopus 로고
    • Proteome informatics I: bioinformatics tools for processing experimental data
    • Palagi, P. M., Hernandez, P., Walther, D., Appel, R. D., Proteome informatics I: bioinformatics tools for processing experimental data. Proteomics 2006, 6, 5435-44.
    • (2006) Proteomics , vol.6 , pp. 5435-5444
    • Palagi, P.M.1    Hernandez, P.2    Walther, D.3    Appel, R.D.4
  • 6
    • 67349208911 scopus 로고    scopus 로고
    • Bioinformatics analysis of mass spectrometry-based proteomics data sets
    • Kumar, C., Mann, M., Bioinformatics analysis of mass spectrometry-based proteomics data sets. Febs Lett. 2009, 583, 1703-1712.
    • (2009) Febs Lett. , vol.583 , pp. 1703-1712
    • Kumar, C.1    Mann, M.2
  • 7
    • 77949732319 scopus 로고    scopus 로고
    • From proteome lists to biological impact- tools and strategies for the analysis of large MS data sets
    • Malik, R., Dulla, K., Nigg, E. A., Körner, R., From proteome lists to biological impact- tools and strategies for the analysis of large MS data sets. Proteomics 2010, 10, 1270-1283.
    • (2010) Proteomics , vol.10 , pp. 1270-1283
    • Malik, R.1    Dulla, K.2    Nigg, E.A.3    Körner, R.4
  • 8
    • 79551483264 scopus 로고    scopus 로고
    • Discussion on common data analysis strategies used in MS-based proteomics
    • Matthiesen, R., Azevedo, L., Amorim, A., Carvalho, A.S., Discussion on common data analysis strategies used in MS-based proteomics. Proteomics 2011, 11, 604-619.
    • (2011) Proteomics , vol.11 , pp. 604-619
    • Matthiesen, R.1    Azevedo, L.2    Amorim, A.3    Carvalho, A.S.4
  • 9
    • 84896400808 scopus 로고    scopus 로고
    • Computational proteomics: designing a comprehensive analytical strategy
    • Goh, W. W. B., Wong, L., Computational proteomics: designing a comprehensive analytical strategy. Drug Discov. Today 2014, 19, 266-274.
    • (2014) Drug Discov. Today , vol.19 , pp. 266-274
    • Goh, W.W.B.1    Wong, L.2
  • 10
    • 33750601225 scopus 로고    scopus 로고
    • Proteome informatics II: Bioinformatics for comparative proteomics
    • Lisacek, F., Cohen-Boulakia, S., Appel, R. D., Proteome informatics II: Bioinformatics for comparative proteomics. Proteomics 2006, 6, 5445-5466.
    • (2006) Proteomics , vol.6 , pp. 5445-5466
    • Lisacek, F.1    Cohen-Boulakia, S.2    Appel, R.D.3
  • 12
    • 24644470505 scopus 로고    scopus 로고
    • Ontological analysis of gene expression data: current tools, limitations, and open problems
    • Khatri, P., Drăghici, S., Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 2005, 21, 3587-3595.
    • (2005) Bioinformatics , vol.21 , pp. 3587-3595
    • Khatri, P.1    Drăghici, S.2
  • 13
    • 35748978819 scopus 로고    scopus 로고
    • Fun&Co: identification of key functional differences in transcriptomes
    • Gamberoni, G., Lamma, E., Lodo, G., Marchesini, J. et al., Fun&Co: identification of key functional differences in transcriptomes. Bioinformatics 2007, 23, 2725-2732.
    • (2007) Bioinformatics , vol.23 , pp. 2725-2732
    • Gamberoni, G.1    Lamma, E.2    Lodo, G.3    Marchesini, J.4
  • 14
    • 34249663294 scopus 로고    scopus 로고
    • Analyzing gene expression data in terms of gene sets: methodological issues
    • Goeman, J. J., Bühlmann, P., Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 2007, 23, 980-987.
    • (2007) Bioinformatics , vol.23 , pp. 980-987
    • Goeman, J.J.1    Bühlmann, P.2
  • 15
    • 48449105128 scopus 로고    scopus 로고
    • CoPub: a literature-based keyword enrichment tool for microarray data analysis
    • Frijters, R., Heupers, B., Beek, P. van, Bouwhuis, M. et al., CoPub: a literature-based keyword enrichment tool for microarray data analysis. Nucleic Acids Res. 2008, 36, W406-W410.
    • (2008) Nucleic Acids Res. , vol.36 , pp. W406-W410
    • Frijters, R.1    Heupers, B.2    Beek, P.v.3    Bouwhuis, M.4
  • 16
    • 58549112996 scopus 로고    scopus 로고
    • Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
    • Huang, D. W., Sherman, B. T., Lempicki, R. A., Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009, 37, 1-13.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 1-13
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 17
    • 79959410946 scopus 로고    scopus 로고
    • From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems
    • Geistlinger, L., Csaba, G., Küffner, R., Mulder, N., Zimmer, R., From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. Bioinformatics 2011, 27, i366-i373.
    • (2011) Bioinformatics , vol.27 , pp. i366-i373
    • Geistlinger, L.1    Csaba, G.2    Küffner, R.3    Mulder, N.4    Zimmer, R.5
  • 18
    • 79956322553 scopus 로고    scopus 로고
    • Global quantification of mammalian gene expression control
    • Schwanhäusser, B., Busse, D., Li, N., Dittmar, G. et al., Global quantification of mammalian gene expression control. Nature 2011, 473, 337-342.
    • (2011) Nature , vol.473 , pp. 337-342
    • Schwanhäusser, B.1    Busse, D.2    Li, N.3    Dittmar, G.4
  • 19
    • 84874805815 scopus 로고    scopus 로고
    • The challenge of the proteome dynamic range and its implications for in-depth proteomics
    • Zubarev, R. A., The challenge of the proteome dynamic range and its implications for in-depth proteomics. Proteomics 2013, 13, 723-726.
    • (2013) Proteomics , vol.13 , pp. 723-726
    • Zubarev, R.A.1
  • 20
    • 79951747696 scopus 로고    scopus 로고
    • The necessity of adjusting tests of protein category enrichment in discovery proteomics
    • Louie, B., Higdon, R., Kolker, E., The necessity of adjusting tests of protein category enrichment in discovery proteomics. Bioinformatics 2010, 26, 3007-3011.
    • (2010) Bioinformatics , vol.26 , pp. 3007-3011
    • Louie, B.1    Higdon, R.2    Kolker, E.3
  • 21
    • 84901599553 scopus 로고    scopus 로고
    • A draft map of the human proteome
    • Kim, M. S., Pinto, S. M., Getnet, D., Nirujogi, R. S. et al., A draft map of the human proteome. Nature 2014, 509, 575-581.
    • (2014) Nature , vol.509 , pp. 575-581
    • Kim, M.S.1    Pinto, S.M.2    Getnet, D.3    Nirujogi, R.S.4
  • 22
    • 84901611036 scopus 로고    scopus 로고
    • Mass-spectrometry-based draft of the human proteome
    • Wilhelm, M., Schlegl, J., Hahne, H., Gholami, A. M. et al., Mass-spectrometry-based draft of the human proteome. Nature 2014, 509, 582-587.
    • (2014) Nature , vol.509 , pp. 582-587
    • Wilhelm, M.1    Schlegl, J.2    Hahne, H.3    Gholami, A.M.4
  • 23
    • 84896693880 scopus 로고    scopus 로고
    • Machine learning applications in proteomics research: How the past can boost the future
    • Kelchtermans, P., Bittremieux, W., De Grave, K., Degroeve, S. et al., Machine learning applications in proteomics research: How the past can boost the future. Proteomics 2014, 14, 353-366.
    • (2014) Proteomics , vol.14 , pp. 353-366
    • Kelchtermans, P.1    Bittremieux, W.2    De Grave, K.3    Degroeve, S.4
  • 24
    • 0036746362 scopus 로고    scopus 로고
    • Evaluation of proteome reference maps for cross-species identification of proteins by peptide mass fingerprinting
    • Mathesius, U., Imin, N., Chen, H., Djordjevic, M. A. et al., Evaluation of proteome reference maps for cross-species identification of proteins by peptide mass fingerprinting. Proteomics 2002, 2, 1288-1303.
    • (2002) Proteomics , vol.2 , pp. 1288-1303
    • Mathesius, U.1    Imin, N.2    Chen, H.3    Djordjevic, M.A.4
  • 25
    • 1542720728 scopus 로고    scopus 로고
    • Construction of a two-dimensional gel electrophoresis protein database for the Nicotiana tabacum cv. Bright Yellow-2 cell suspension culture
    • Laukens, K., Deckers, P., Esmans, E., Van Onckelen, H., Witters, E., Construction of a two-dimensional gel electrophoresis protein database for the Nicotiana tabacum cv. Bright Yellow-2 cell suspension culture. Proteomics 2004, 4, 720-727.
    • (2004) Proteomics , vol.4 , pp. 720-727
    • Laukens, K.1    Deckers, P.2    Esmans, E.3    Van Onckelen, H.4    Witters, E.5
  • 26
    • 80052033624 scopus 로고    scopus 로고
    • Protein identification using MS/MS data
    • Cottrell, J. S., Protein identification using MS/MS data. J. Proteomics 2011, 74, 1842-1851.
    • (2011) J. Proteomics , vol.74 , pp. 1842-1851
    • Cottrell, J.S.1
  • 27
    • 77958549006 scopus 로고    scopus 로고
    • Large-scale protein interactome mapping: strategies and opportunities
    • Lievens, S., Eyckerman, S., Lemmens, I., Tavernier, J., Large-scale protein interactome mapping: strategies and opportunities. Expert Rev. Proteomics 2010, 7, 679-690.
    • (2010) Expert Rev. Proteomics , vol.7 , pp. 679-690
    • Lievens, S.1    Eyckerman, S.2    Lemmens, I.3    Tavernier, J.4
  • 28
    • 77955608634 scopus 로고    scopus 로고
    • Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana
    • Van Leene, J., Hollunder, J., Eeckhout, D., Persiau, G. et al., Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol. Syst. Biol. 2010, 6, 397.
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 397
    • Van Leene, J.1    Hollunder, J.2    Eeckhout, D.3    Persiau, G.4
  • 29
    • 84898612068 scopus 로고    scopus 로고
    • Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism
    • Corominas, R., Yang, X., Lin, G. N., Kang, S. et al., Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. Nat. Commun. 2014, 5, 3650.
    • (2014) Nat. Commun. , vol.5 , pp. 3650
    • Corominas, R.1    Yang, X.2    Lin, G.N.3    Kang, S.4
  • 30
    • 77955444211 scopus 로고    scopus 로고
    • Application of chemoproteomics to drug discovery: identification of a clinical candidate targeting Hsp90
    • Fadden, P., Huang, K. H., Veal, J. M., Steed, P. M. et al., Application of chemoproteomics to drug discovery: identification of a clinical candidate targeting Hsp90. Chem. Biol. 2010, 17, 686-694.
    • (2010) Chem. Biol. , vol.17 , pp. 686-694
    • Fadden, P.1    Huang, K.H.2    Veal, J.M.3    Steed, P.M.4
  • 31
    • 84890641204 scopus 로고    scopus 로고
    • The coming of age of phosphoproteomics-from large data sets to inference of protein functions
    • Roux, P. P., Thibault, P., The coming of age of phosphoproteomics-from large data sets to inference of protein functions. Mol. Cell. Proteomics 2013, 12, 3453-3464.
    • (2013) Mol. Cell. Proteomics , vol.12 , pp. 3453-3464
    • Roux, P.P.1    Thibault, P.2
  • 32
    • 84857817395 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics strategies for protease cleavage site identification
    • Van den Berg, B. H. J., Tholey, A., Mass spectrometry-based proteomics strategies for protease cleavage site identification. Proteomics 2012, 12, 516-529.
    • (2012) Proteomics , vol.12 , pp. 516-529
    • Van den Berg, B.H.J.1    Tholey, A.2
  • 33
    • 84865576726 scopus 로고    scopus 로고
    • Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present
    • Bantscheff, M., Lemeer, S., Savitski, M. M., Kuster, B., Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal. Bioanal. Chem. 2012, 404, 939-965.
    • (2012) Anal. Bioanal. Chem. , vol.404 , pp. 939-965
    • Bantscheff, M.1    Lemeer, S.2    Savitski, M.M.3    Kuster, B.4
  • 34
    • 79551500036 scopus 로고    scopus 로고
    • Less label, more free: approaches in label-free quantitative mass spectrometry
    • Neilson, K. A., Ali, N. A., Muralidharan, S., Mirzaei, M. et al., Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics 2011, 11, 535-553.
    • (2011) Proteomics , vol.11 , pp. 535-553
    • Neilson, K.A.1    Ali, N.A.2    Muralidharan, S.3    Mirzaei, M.4
  • 35
    • 84878075017 scopus 로고    scopus 로고
    • Statistical methods for quantitative mass spectrometry proteomic experiments with labeling
    • Oberg, A. L., Mahoney, D. W., Statistical methods for quantitative mass spectrometry proteomic experiments with labeling. BMC Bioinformatics 2012, 13, S7.
    • (2012) BMC Bioinformatics , vol.13 , pp. S7
    • Oberg, A.L.1    Mahoney, D.W.2
  • 36
    • 84882589554 scopus 로고    scopus 로고
    • Topologically inferring risk-active pathways toward precise cancer classification by directed random walk
    • Liu, W., Li, C., Xu, Y., Yang, H. et al., Topologically inferring risk-active pathways toward precise cancer classification by directed random walk. Bioinformatics 2013, 29, 2169-2177.
    • (2013) Bioinformatics , vol.29 , pp. 2169-2177
    • Liu, W.1    Li, C.2    Xu, Y.3    Yang, H.4
  • 37
    • 84873987395 scopus 로고    scopus 로고
    • A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments
    • Matzke, M. M., Brown, J. N., Gritsenko, M. A., Metz, T. O. et al., A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments. Proteomics 2013, 13, 493-503.
    • (2013) Proteomics , vol.13 , pp. 493-503
    • Matzke, M.M.1    Brown, J.N.2    Gritsenko, M.A.3    Metz, T.O.4
  • 39
    • 79952197936 scopus 로고    scopus 로고
    • Statistics in experimental design, preprocessing, and analysis of proteomics data
    • Jung, K., Statistics in experimental design, preprocessing, and analysis of proteomics data. Methods Mol. Biol. 2011, 696, 259-272.
    • (2011) Methods Mol. Biol. , vol.696 , pp. 259-272
    • Jung, K.1
  • 41
    • 84860833500 scopus 로고    scopus 로고
    • The UniProt consortium, reorganizing the protein space at the universal protein resource (UniProt)
    • The UniProt consortium, reorganizing the protein space at the universal protein resource (UniProt). Nucleic Acids Res. 2011, 40, D71-D75.
    • (2011) Nucleic Acids Res. , vol.40 , pp. D71-D75
  • 42
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D. et al., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25, 25-29.
    • (2000) Nat. Genet. , vol.25 , pp. 25-29
    • Ashburner, M.1    Ball, C.A.2    Blake, J.A.3    Botstein, D.4
  • 43
    • 80053188682 scopus 로고    scopus 로고
    • Literature-aided interpretation of gene expression data with the weighted global test
    • Jelier, R., Goeman, J. J., Hettne, K. M., Schuemie, M. J. et al., Literature-aided interpretation of gene expression data with the weighted global test. Brief. Bioinform. 2011, 12, 518-529.
    • (2011) Brief. Bioinform. , vol.12 , pp. 518-529
    • Jelier, R.1    Goeman, J.J.2    Hettne, K.M.3    Schuemie, M.J.4
  • 44
    • 84878483493 scopus 로고    scopus 로고
    • Biases in the experimental annotations of protein function and their effect on our understanding of protein function space
    • Schnoes, A. M., Ream, D. C., Thorman, A. W., Babbitt, P. C., Friedberg, I., Biases in the experimental annotations of protein function and their effect on our understanding of protein function space. Plos Comput. Biol. 2013, 9, e1003063.
    • (2013) Plos Comput. Biol. , vol.9 , pp. e1003063
    • Schnoes, A.M.1    Ream, D.C.2    Thorman, A.W.3    Babbitt, P.C.4    Friedberg, I.5
  • 45
    • 84904723024 scopus 로고    scopus 로고
    • Gene set analysis methods: statistical models and methodological differences
    • Maciejewski, H., Gene set analysis methods: statistical models and methodological differences. Brief. Bioinform. 2014, 15, 504-518.
    • (2014) Brief. Bioinform. , vol.15 , pp. 504-518
    • Maciejewski, H.1
  • 48
    • 0038175144 scopus 로고    scopus 로고
    • GoMiner: a resource for biological interpretation of genomic and proteomic data
    • R28
    • Zeeberg, B. R., Feng, W., Wang, G., Wang, M. D. et al., GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol. 2003, 4, R28.
    • (2003) Genome Biol. , vol.4
    • Zeeberg, B.R.1    Feng, W.2    Wang, G.3    Wang, M.D.4
  • 49
    • 24044440971 scopus 로고    scopus 로고
    • BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks
    • Maere, S., Heymans, K., Kuiper, M., BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinformatics 2005, 21, 3448-3449.
    • (2005) Bioinformatics , vol.21 , pp. 3448-3449
    • Maere, S.1    Heymans, K.2    Kuiper, M.3
  • 50
    • 33747846582 scopus 로고    scopus 로고
    • WEGO: a web tool for plotting GO annotations
    • Ye, J., Fang, L., Zheng, H., Zhang, Y. et al., WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 2006, 34, W293-297.
    • (2006) Nucleic Acids Res. , vol.34 , pp. W293-W297
    • Ye, J.1    Fang, L.2    Zheng, H.3    Zhang, Y.4
  • 52
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang, D. W., Sherman, B. T., Lempicki, R. A., Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2008, 4, 44-57.
    • (2008) Nat. Protoc. , vol.4 , pp. 44-57
    • Huang, D.W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 53
    • 48449104617 scopus 로고    scopus 로고
    • GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis
    • Zheng, Q., Wang, X. J., GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res. 2008, 36, W358-W363.
    • (2008) Nucleic Acids Res. , vol.36 , pp. W358-W363
    • Zheng, Q.1    Wang, X.J.2
  • 54
    • 64549104807 scopus 로고    scopus 로고
    • ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
    • Bindea, G., Mlecnik, B., Hackl, H., Charoentong, P. et al., ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 2009, 25, 1091-1093.
    • (2009) Bioinformatics , vol.25 , pp. 1091-1093
    • Bindea, G.1    Mlecnik, B.2    Hackl, H.3    Charoentong, P.4
  • 55
    • 77954299992 scopus 로고    scopus 로고
    • agriGO: a GO analysis toolkit for the agricultural community
    • Du, Z., Zhou, X., Ling, Y., Zhang, Z., Su, Z., agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res. 2010, 38, W64-W70.
    • (2010) Nucleic Acids Res. , vol.38 , pp. W64-W70
    • Du, Z.1    Zhou, X.2    Ling, Y.3    Zhang, Z.4    Su, Z.5
  • 56
    • 77951968341 scopus 로고    scopus 로고
    • GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach
    • Zhang, S., Cao, J., Kong, Y. M., Scheuermann, R. H., GO-Bayes: Gene Ontology-based overrepresentation analysis using a Bayesian approach. Bioinformatics 2010, 26, 905-911.
    • (2010) Bioinformatics , vol.26 , pp. 905-911
    • Zhang, S.1    Cao, J.2    Kong, Y.M.3    Scheuermann, R.H.4
  • 57
    • 84880617636 scopus 로고    scopus 로고
    • WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013
    • Wang, J., Duncan, D., Shi, Z., Zhang, B., WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Nucleic Acids Res. 2013, 41, W77-W83.
    • (2013) Nucleic Acids Res. , vol.41 , pp. W77-W83
    • Wang, J.1    Duncan, D.2    Shi, Z.3    Zhang, B.4
  • 59
    • 0035999977 scopus 로고    scopus 로고
    • A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments
    • Pan, W., A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 2002, 18, 546-554.
    • (2002) Bioinformatics , vol.18 , pp. 546-554
    • Pan, W.1
  • 60
    • 84871206169 scopus 로고    scopus 로고
    • Fold change and p-value cutoffs significantly alter microarray interpretations
    • Dalman, M. R., Deeter, A., Nimishakavi, G., Duan, Z. H., Fold change and p-value cutoffs significantly alter microarray interpretations. BMC Bioinformatics 2012, 13, S11.
    • (2012) BMC Bioinformatics , vol.13 , pp. S11
    • Dalman, M.R.1    Deeter, A.2    Nimishakavi, G.3    Duan, Z.H.4
  • 61
    • 43149116763 scopus 로고    scopus 로고
    • Gene-set approach for expression pattern analysis
    • Nam, D., Kim, S. Y., Gene-set approach for expression pattern analysis. Brief. Bioinform. 2008, 9, 189-197.
    • (2008) Brief. Bioinform. , vol.9 , pp. 189-197
    • Nam, D.1    Kim, S.Y.2
  • 62
    • 36448946146 scopus 로고    scopus 로고
    • Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis
    • Grossmann, S., Bauer, S., Robinson, P. N., Vingron, M., Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis. Bioinformatics 2007, 23, 3024-3031.
    • (2007) Bioinformatics , vol.23 , pp. 3024-3031
    • Grossmann, S.1    Bauer, S.2    Robinson, P.N.3    Vingron, M.4
  • 63
    • 40249110012 scopus 로고    scopus 로고
    • ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization
    • Huang, W. L., Tung, C. W., Ho, S. W., Hwang, S. F., Ho, S. Y., ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization. BMC Bioinformatics 2008, 9, 80.
    • (2008) BMC Bioinformatics , vol.9 , pp. 80
    • Huang, W.L.1    Tung, C.W.2    Ho, S.W.3    Hwang, S.F.4    Ho, S.Y.5
  • 64
    • 77953212372 scopus 로고    scopus 로고
    • Gene ontology analysis for RNA-seq: accounting for selection bias
    • R14
    • Young, M. D., Wakefield, M. J., Smyth, G. K., Oshlack, A., Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010, 11, R14.
    • (2010) Genome Biol. , vol.11
    • Young, M.D.1    Wakefield, M.J.2    Smyth, G.K.3    Oshlack, A.4
  • 65
    • 26844457138 scopus 로고    scopus 로고
    • Pancreatic cancer proteome: the proteins that underlie invasion, metastasis, and immunologic escape
    • Chen, R., Yi, E. C., Donohoe, S., Pan, S. et al., Pancreatic cancer proteome: the proteins that underlie invasion, metastasis, and immunologic escape. Gastroenterology 2005, 129, 1187-1197.
    • (2005) Gastroenterology , vol.129 , pp. 1187-1197
    • Chen, R.1    Yi, E.C.2    Donohoe, S.3    Pan, S.4
  • 66
    • 84901599553 scopus 로고    scopus 로고
    • A draft map of the human proteome
    • Kim, M. S., Pinto, S. M., Getnet, D., Nirujogi, R. S. et al., A draft map of the human proteome. Nature 2014, 509, 575-581.
    • (2014) Nature , vol.509 , pp. 575-581
    • Kim, M.S.1    Pinto, S.M.2    Getnet, D.3    Nirujogi, R.S.4
  • 67
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S. et al., Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 15545-15550.
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 15545-15550
    • Subramanian, A.1    Tamayo, P.2    Mootha, V.K.3    Mukherjee, S.4
  • 68
    • 35548988505 scopus 로고    scopus 로고
    • Computation of significance scores of unweighted Gene Set Enrichment Analyses
    • Keller, A., Backes, C., Lenhof, H. P., Computation of significance scores of unweighted Gene Set Enrichment Analyses. BMC Bioinformatics 2007, 8, 290.
    • (2007) BMC Bioinformatics , vol.8 , pp. 290
    • Keller, A.1    Backes, C.2    Lenhof, H.P.3
  • 69
    • 84893380809 scopus 로고    scopus 로고
    • Human cognitive ability is influenced by genetic variation in components of postsynaptic signalling complexes assembled by NMDA receptors and MAGUK proteins
    • Hill, W. D., Davies, G., van de Lagemaat, L. N., Christoforou, A. et al., Human cognitive ability is influenced by genetic variation in components of postsynaptic signalling complexes assembled by NMDA receptors and MAGUK proteins. Transl. Psychiatry 2014, 4, e341.
    • (2014) Transl. Psychiatry , vol.4 , pp. e341
    • Hill, W.D.1    Davies, G.2    van de Lagemaat, L.N.3    Christoforou, A.4
  • 70
    • 78149289532 scopus 로고    scopus 로고
    • In Situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection (LCM)-LC/MS: Annotation by protein set enrichment analysis (PSEA) and gene ontology (GO)
    • mcp.M110.000398.
    • Cha, S., Imielinski, M. B., Rejtar, T., Richardson, E. A. et al., In Situ proteomic analysis of human breast cancer epithelial cells using laser capture microdissection (LCM)-LC/MS: Annotation by protein set enrichment analysis (PSEA) and gene ontology (GO). Mol. Cell. Proteomics 2010, mcp.M110.000398.
    • (2010) Mol. Cell. Proteomics
    • Cha, S.1    Imielinski, M.B.2    Rejtar, T.3    Richardson, E.A.4
  • 71
  • 72
    • 84891760956 scopus 로고    scopus 로고
    • Data, information, knowledge and principle: back to metabolism in KEGG
    • Kanehisa, M., Goto, S., Sato, Y., Kawashima, M. et al., Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 2014, 42, D199-D205.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D199-D205
    • Kanehisa, M.1    Goto, S.2    Sato, Y.3    Kawashima, M.4
  • 73
    • 25444472585 scopus 로고    scopus 로고
    • Pathway level analysis of gene expression using singular value decomposition
    • Tomfohr, J., Lu, J., Kepler, T. B., Pathway level analysis of gene expression using singular value decomposition. BMC Bioinformatics 2005, 6, 225.
    • (2005) BMC Bioinformatics , vol.6 , pp. 225
    • Tomfohr, J.1    Lu, J.2    Kepler, T.B.3
  • 74
    • 33748198771 scopus 로고    scopus 로고
    • Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles
    • Edelman, E., Porrello, A., Guinney, J., Balakumaran, B. et al., Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles. Bioinformatics 2006, 22, e108-e116.
    • (2006) Bioinformatics , vol.22 , pp. e108-e116
    • Edelman, E.1    Porrello, A.2    Guinney, J.3    Balakumaran, B.4
  • 76
    • 26444608611 scopus 로고    scopus 로고
    • Discovering statistically significant pathways in expression profiling studies
    • Tian, L., Greenberg, S. A., Kong, S. W., Altschuler, J. et al., Discovering statistically significant pathways in expression profiling studies. Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 13544-13549.
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 13544-13549
    • Tian, L.1    Greenberg, S.A.2    Kong, S.W.3    Altschuler, J.4
  • 77
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini, Y., Hochberg, Y., Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol. 1995, 57, 289-300.
    • (1995) J. R. Stat. Soc. Ser. B Methodol. , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 78
    • 84896716464 scopus 로고    scopus 로고
    • A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity
    • Tarca, A. L., Bhatti, G., Romero, R., A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity. Plos One 2013, 8, e79217.
    • (2013) Plos One , vol.8 , pp. e79217
    • Tarca, A.L.1    Bhatti, G.2    Romero, R.3
  • 79
    • 13444274300 scopus 로고    scopus 로고
    • MEGO: gene functional module expression based on gene ontology
    • Tu, K., Yu, H., Zhu, M., MEGO: gene functional module expression based on gene ontology. Biotechniques 2005, 38, 277-283.
    • (2005) Biotechniques , vol.38 , pp. 277-283
    • Tu, K.1    Yu, H.2    Zhu, M.3
  • 80
    • 25444502609 scopus 로고    scopus 로고
    • PAGE: parametric analysis of gene set enrichment
    • Kim, S. Y., Volsky, D. J., PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics 2005, 6, 144.
    • (2005) BMC Bioinformatics , vol.6 , pp. 144
    • Kim, S.Y.1    Volsky, D.J.2
  • 81
  • 83
    • 0038054341 scopus 로고    scopus 로고
    • PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
    • Mootha, V. K., Lindgren, C. M., Eriksson, K. F., Subramanian, A. et al., PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet. 2003, 34, 267-273.
    • (2003) Nat. Genet. , vol.34 , pp. 267-273
    • Mootha, V.K.1    Lindgren, C.M.2    Eriksson, K.F.3    Subramanian, A.4
  • 84
    • 84861793773 scopus 로고    scopus 로고
    • Gene set enrichment analysis: performance evaluation and usage guidelines
    • Hung, J. H., Yang, T. H., Hu, Z., Weng, Z., DeLisi, C., Gene set enrichment analysis: performance evaluation and usage guidelines. Brief. Bioinform. 2012, 13, 281-291.
    • (2012) Brief. Bioinform. , vol.13 , pp. 281-291
    • Hung, J.H.1    Yang, T.H.2    Hu, Z.3    Weng, Z.4    DeLisi, C.5
  • 86
    • 77956524952 scopus 로고    scopus 로고
    • De-correlating expression in gene-set analysis
    • Nam, D., De-correlating expression in gene-set analysis. Bioinformatics 2010, 26, i511-i516.
    • (2010) Bioinformatics , vol.26 , pp. i511-i516
    • Nam, D.1
  • 87
    • 84861123691 scopus 로고    scopus 로고
    • Ten years of pathway analysis: current approaches and outstanding challenges
    • Khatri, P., Sirota, M., Butte, A. J., Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput. Biol. 2012, 8, e1002375.
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002375
    • Khatri, P.1    Sirota, M.2    Butte, A.J.3
  • 88
    • 84880544162 scopus 로고    scopus 로고
    • Gene-set analysis is severely biased when applied to genome-wide methylation data
    • Geeleher, P., Hartnett, L., Egan, L. J., Golden, A. et al., Gene-set analysis is severely biased when applied to genome-wide methylation data. Bioinformatics 2013, 29, 1851-1857.
    • (2013) Bioinformatics , vol.29 , pp. 1851-1857
    • Geeleher, P.1    Hartnett, L.2    Egan, L.J.3    Golden, A.4
  • 89
    • 47349105353 scopus 로고    scopus 로고
    • Anni 2.0: a multipurpose text-mining tool for the life sciences
    • R96
    • Jelier, R., Schuemie, M. J., Veldhoven, A., Dorssers, L. C. et al., Anni 2.0: a multipurpose text-mining tool for the life sciences. Genome Biol. 2008, 9, R96.
    • (2008) Genome Biol. , vol.9
    • Jelier, R.1    Schuemie, M.J.2    Veldhoven, A.3    Dorssers, L.C.4
  • 91
    • 0038017587 scopus 로고    scopus 로고
    • Mining microarray expression data by literature profiling
    • research0055.1-research0055.16.
    • Chaussabel, D., Sher, A., Mining microarray expression data by literature profiling. Genome Biol. 2002, 3, research0055.1-research0055.16.
    • (2002) Genome Biol. , vol.3
    • Chaussabel, D.1    Sher, A.2
  • 92
    • 25444530343 scopus 로고    scopus 로고
    • CoPub Mapper: mining MEDLINE based on search term co-publication
    • Alako, B. T., Veldhoven, A., Baal, S. van, Jelier, R. et al., CoPub Mapper: mining MEDLINE based on search term co-publication. BMC Bioinformatics 2005, 6, 51.
    • (2005) BMC Bioinformatics , vol.6 , pp. 51
    • Alako, B.T.1    Veldhoven, A.2    Baal, S.v.3    Jelier, R.4
  • 94
    • 84907030251 scopus 로고    scopus 로고
    • GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms
    • Wang, J. H., Zhao, L. F., Lin, P., Su, X. R. et al., GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms. Bioinformatics 2014, 30, 2534-2536.
    • (2014) Bioinformatics , vol.30 , pp. 2534-2536
    • Wang, J.H.1    Zhao, L.F.2    Lin, P.3    Su, X.R.4
  • 95
    • 0035042776 scopus 로고    scopus 로고
    • A literature network of human genes for high-throughput analysis of gene expression
    • Jenssen, T. K., Laegreid, A., Komorowski, J., Hovig, E., A literature network of human genes for high-throughput analysis of gene expression. Nat. Genet. 2001, 28, 21-28.
    • (2001) Nat. Genet. , vol.28 , pp. 21-28
    • Jenssen, T.K.1    Laegreid, A.2    Komorowski, J.3    Hovig, E.4
  • 96
    • 4844222294 scopus 로고    scopus 로고
    • TXTGate: profiling gene groups with text-based information
    • R43
    • Glenisson, P., Coessens, B., Vooren, S. V., Mathys, J. et al., TXTGate: profiling gene groups with text-based information. Genome Biol. 2004, 5, R43.
    • (2004) Genome Biol. , vol.5
    • Glenisson, P.1    Coessens, B.2    Vooren, S.V.3    Mathys, J.4
  • 97
    • 77957703420 scopus 로고    scopus 로고
    • Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization)
    • Tjioe, E., Berry, M. W., Homayouni, R., Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization). BMC Bioinformatics 2010, 11, S14.
    • (2010) BMC Bioinformatics , vol.11 , pp. S14
    • Tjioe, E.1    Berry, M.W.2    Homayouni, R.3
  • 98
    • 77949510039 scopus 로고    scopus 로고
    • LAITOR-literature assistant for identification of terms co-occurrences and relationships
    • Barbosa-Silva, A., Soldatos, T. G., Magalhães, I. L., Pavlopoulos, G. A. et al., LAITOR-literature assistant for identification of terms co-occurrences and relationships. BMC Bioinformatics 2010, 11, 70.
    • (2010) BMC Bioinformatics , vol.11 , pp. 70
    • Barbosa-Silva, A.1    Soldatos, T.G.2    Magalhães, I.L.3    Pavlopoulos, G.A.4
  • 99
    • 82455162310 scopus 로고    scopus 로고
    • PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries
    • Barbosa-Silva, A., Fontaine, J. F., Donnard, E. R., Stussi, F. et al., PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics 2011, 12, 435.
    • (2011) BMC Bioinformatics , vol.12 , pp. 435
    • Barbosa-Silva, A.1    Fontaine, J.F.2    Donnard, E.R.3    Stussi, F.4
  • 100
    • 84884507478 scopus 로고    scopus 로고
    • CoCiter: An efficient tool to infer gene function by assessing the significance of literature co-citation
    • Qiao, N., Huang, Y., Naveed, H., Green, C. D., Han, J. D. J., CoCiter: An efficient tool to infer gene function by assessing the significance of literature co-citation. PLoS One 2013, 8, e74074.
    • (2013) PLoS One , vol.8 , pp. e74074
    • Qiao, N.1    Huang, Y.2    Naveed, H.3    Green, C.D.4    Han, J.D.J.5
  • 101
    • 79955797347 scopus 로고    scopus 로고
    • Network-based pipeline for analyzing ms data: an application toward liver cancer
    • Goh, W. W. B., Lee, Y. H., Zubaidah, R. M., Jin, J. et al., Network-based pipeline for analyzing ms data: an application toward liver cancer. J. Proteome Res. 2011, 10, 2261-2272.
    • (2011) J. Proteome Res. , vol.10 , pp. 2261-2272
    • Goh, W.W.B.1    Lee, Y.H.2    Zubaidah, R.M.3    Jin, J.4
  • 102
    • 84859242507 scopus 로고    scopus 로고
    • How advancement in biological network analysis methods empowers proteomics
    • Goh, W. W. B., Lee, Y. H., Chung, M., Wong, L., How advancement in biological network analysis methods empowers proteomics. Proteomics 2012, 12, 550-563.
    • (2012) Proteomics , vol.12 , pp. 550-563
    • Goh, W.W.B.1    Lee, Y.H.2    Chung, M.3    Wong, L.4
  • 103
    • 84872184001 scopus 로고    scopus 로고
    • Enhancing the utility of proteomics signature profiling (PSP) with pathway derived Subnets (PDSs), performance analysis and specialised ontologies
    • Goh, W. W. B., Fan, M., Low, H. S., Sergot, M., Wong, L., Enhancing the utility of proteomics signature profiling (PSP) with pathway derived Subnets (PDSs), performance analysis and specialised ontologies. BMC Genomics 2013, 14, 35.
    • (2013) BMC Genomics , vol.14 , pp. 35
    • Goh, W.W.B.1    Fan, M.2    Low, H.S.3    Sergot, M.4    Wong, L.5
  • 104
    • 84887625418 scopus 로고    scopus 로고
    • Networks in proteomics analysis of cancer
    • Goh, W. W. B., Wong, L., Networks in proteomics analysis of cancer. Curr. Opin. Biotechnol. 2013, 24, 1122-1128.
    • (2013) Curr. Opin. Biotechnol. , vol.24 , pp. 1122-1128
    • Goh, W.W.B.1    Wong, L.2
  • 105
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: a software environment for integrated models of biomolecular interaction networks
    • Shannon, P., Markiel, A., Ozier, O., Baliga, N. S. et al., Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13, 2498-2504.
    • (2003) Genome Res. , vol.13 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.S.4
  • 106
    • 65449162644 scopus 로고    scopus 로고
    • A survey of visualization tools for biological network analysis
    • Pavlopoulos, G. A., Wegener, A. L., Schneider, R., A survey of visualization tools for biological network analysis. Biodata Min. 2008, 1, 12.
    • (2008) Biodata Min. , vol.1 , pp. 12
    • Pavlopoulos, G.A.1    Wegener, A.L.2    Schneider, R.3
  • 108
    • 69249122100 scopus 로고    scopus 로고
    • Network-assisted protein identification and data interpretation in shotgun proteomics
    • Li, J., Zimmerman, L. J., Park, B. H., Tabb, D. L. et al., Network-assisted protein identification and data interpretation in shotgun proteomics. Mol. Syst. Biol. 2009, 5.
    • (2009) Mol. Syst. Biol. , vol.5
    • Li, J.1    Zimmerman, L.J.2    Park, B.H.3    Tabb, D.L.4
  • 109
    • 77952909304 scopus 로고    scopus 로고
    • Candidate Serological biomarkers for cancer identified from the secretomes of 23 cancer cell lines and the human protein atlas
    • Wu, C. C., Hsu, C. W., Chen, C. D., Yu, C. J. et al., Candidate Serological biomarkers for cancer identified from the secretomes of 23 cancer cell lines and the human protein atlas. Mol. Cell. Proteomics 2010, 9, 1100-1117.
    • (2010) Mol. Cell. Proteomics , vol.9 , pp. 1100-1117
    • Wu, C.C.1    Hsu, C.W.2    Chen, C.D.3    Yu, C.J.4
  • 110
    • 84862333922 scopus 로고    scopus 로고
    • Integrated proteomic, transcriptomic, and biological network analysis of breast carcinoma reveals molecular features of tumorigenesis and clinical relapse
    • M111.014910.
    • Imielinski, M., Cha, S., Rejtar, T., Richardson, E. A. et al., Integrated proteomic, transcriptomic, and biological network analysis of breast carcinoma reveals molecular features of tumorigenesis and clinical relapse. Mol. Cell. Proteomics 2012, 11, M111.014910.
    • (2012) Mol. Cell. Proteomics , vol.11
    • Imielinski, M.1    Cha, S.2    Rejtar, T.3    Richardson, E.A.4
  • 112
    • 77449089538 scopus 로고    scopus 로고
    • A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics
    • Van Damme, E., Laukens, K., Dang, T. H., Van Ostade, X., A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics. Int. J. Biol. Sci. 2010, 6, 51-67.
    • (2010) Int. J. Biol. Sci. , vol.6 , pp. 51-67
    • Van Damme, E.1    Laukens, K.2    Dang, T.H.3    Van Ostade, X.4
  • 113
    • 34548400259 scopus 로고    scopus 로고
    • A systems biology approach for pathway level analysis
    • Draghici, S., Khatri, P., Tarca, A. L., Amin, K. et al., A systems biology approach for pathway level analysis. Genome Res. 2007, 17, 1537-1545.
    • (2007) Genome Res. , vol.17 , pp. 1537-1545
    • Draghici, S.1    Khatri, P.2    Tarca, A.L.3    Amin, K.4
  • 114
    • 77956480115 scopus 로고    scopus 로고
    • Consistency, comprehensiveness, and compatibility of pathway databases
    • Soh, D., Dong, D., Guo, Y., Wong, L., Consistency, comprehensiveness, and compatibility of pathway databases. BMC Bioinformatics 2010, 11, 449.
    • (2010) BMC Bioinformatics , vol.11 , pp. 449
    • Soh, D.1    Dong, D.2    Guo, Y.3    Wong, L.4
  • 115
    • 35748935228 scopus 로고    scopus 로고
    • Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases
    • Cavalieri, D., Castagnini, C., Toti, S., Maciag, K. et al., Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases. Bioinforma. Oxf. Engl. 2007, 23, 2631-2632.
    • (2007) Bioinforma. Oxf. Engl. , vol.23 , pp. 2631-2632
    • Cavalieri, D.1    Castagnini, C.2    Toti, S.3    Maciag, K.4
  • 116
    • 84891540477 scopus 로고    scopus 로고
    • Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures
    • Foroushani, A. B. K., Brinkman, F. S. L., Lynn, D. J., Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures. PeerJ 2013, 1, e229.
    • (2013) PeerJ , vol.1 , pp. e229
    • Foroushani, A.B.K.1    Brinkman, F.S.L.2    Lynn, D.J.3
  • 117
    • 84876090381 scopus 로고    scopus 로고
    • Pathway Distiller-multisource biological pathway consolidation
    • Doderer, M. S., Anguiano, Z., Suresh, U., Dashnamoorthy, R. et al., Pathway Distiller-multisource biological pathway consolidation. BMC Genomics 2012, 13, 1-16.
    • (2012) BMC Genomics , vol.13 , pp. 1-16
    • Doderer, M.S.1    Anguiano, Z.2    Suresh, U.3    Dashnamoorthy, R.4
  • 118
    • 58149177166 scopus 로고    scopus 로고
    • Reactome knowledgebase of human biological pathways and processes
    • Matthews, L., Gopinath, G., Gillespie, M., Caudy, M. et al., Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 2009, 37, D619-622.
    • (2009) Nucleic Acids Res. , vol.37 , pp. D619-D622
    • Matthews, L.1    Gopinath, G.2    Gillespie, M.3    Caudy, M.4
  • 120
    • 27244436714 scopus 로고    scopus 로고
    • Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
    • Karp, P. D., Ouzounis, C. A., Moore-Kochlacs, C., Goldovsky, L. et al., Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 2005, 33, 6083-6089.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 6083-6089
    • Karp, P.D.1    Ouzounis, C.A.2    Moore-Kochlacs, C.3    Goldovsky, L.4
  • 121
    • 78651332286 scopus 로고    scopus 로고
    • Pathway Commons, a web resource for biological pathway data
    • Cerami, E. G., Gross, B. E., Demir, E., Rodchenkov, I. et al., Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011, 39, D685-D690.
    • (2011) Nucleic Acids Res. , vol.39 , pp. D685-D690
    • Cerami, E.G.1    Gross, B.E.2    Demir, E.3    Rodchenkov, I.4
  • 122
    • 84874969184 scopus 로고    scopus 로고
    • PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees
    • Mi, H., Muruganujan, A., Thomas, P. D., PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 2013, 41, D377-D386.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D377-D386
    • Mi, H.1    Muruganujan, A.2    Thomas, P.D.3
  • 123
    • 14644430468 scopus 로고    scopus 로고
    • Calculating the statistical significance of changes in pathway activity from gene expression data
    • Rahnenführer, J., Domingues, F. S., Maydt, J., Lengauer, T., Calculating the statistical significance of changes in pathway activity from gene expression data. Stat. Appl. Genet. Mol. Biol. 2004, 3, 1-29.
    • (2004) Stat. Appl. Genet. Mol. Biol. , vol.3 , pp. 1-29
    • Rahnenführer, J.1    Domingues, F.S.2    Maydt, J.3    Lengauer, T.4
  • 124
    • 84866495994 scopus 로고    scopus 로고
    • PathNet: a tool for pathway analysis using topological information
    • Dutta, B., Wallqvist, A., Reifman, J., PathNet: a tool for pathway analysis using topological information. Source Code Biol. Med. 2012, 7, 10.
    • (2012) Source Code Biol. Med. , vol.7 , pp. 10
    • Dutta, B.1    Wallqvist, A.2    Reifman, J.3
  • 126
    • 77949365759 scopus 로고    scopus 로고
    • Identification of functional modules that correlate with phenotypic difference: the influence of network topology
    • R23
    • Hung, J. H., Whitfield, T. W., Yang, T. H., Hu, Z. et al., Identification of functional modules that correlate with phenotypic difference: the influence of network topology. Genome Biol. 2010, 11, R23.
    • (2010) Genome Biol. , vol.11
    • Hung, J.H.1    Whitfield, T.W.2    Yang, T.H.3    Hu, Z.4
  • 127
    • 61749083981 scopus 로고    scopus 로고
    • Analysis of Gene Sets Based on the Underlying Regulatory Network
    • Shojaie, A., Michailidis, G., Analysis of Gene Sets Based on the Underlying Regulatory Network. J. Comput. Biol. 2009, 16, 407-426.
    • (2009) J. Comput. Biol. , vol.16 , pp. 407-426
    • Shojaie, A.1    Michailidis, G.2
  • 128
    • 84866238676 scopus 로고    scopus 로고
    • Gains in Power from Structured Two-Sample Tests of Means on Graphs
    • Jacob, L., Neuvial, P., Dudoit, S., Gains in Power from Structured Two-Sample Tests of Means on Graphs. Ann. Appl. Stat. 2012, 6, 561-600.
    • (2012) Ann. Appl. Stat. , vol.6 , pp. 561-600
    • Jacob, L.1    Neuvial, P.2    Dudoit, S.3
  • 129
    • 84893009656 scopus 로고    scopus 로고
    • Methods and approaches in the topology-based analysis of biological pathways
    • Mitrea, C., Taghavi, Z., Bokanizad, B., Hanoudi, S. et al., Methods and approaches in the topology-based analysis of biological pathways. Front. Physiol. 2013, 4, 278.
    • (2013) Front. Physiol. , vol.4 , pp. 278
    • Mitrea, C.1    Taghavi, Z.2    Bokanizad, B.3    Hanoudi, S.4
  • 130
    • 77955505357 scopus 로고    scopus 로고
    • Protein-Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks
    • De Las Rivas, J., Fontanillo, C., Protein-Protein Interactions Essentials: Key Concepts to Building and Analyzing Interactome Networks. Plos Comput Biol 2010, 6, e1000807.
    • (2010) Plos Comput Biol , vol.6 , pp. e1000807
    • De Las Rivas, J.1    Fontanillo, C.2
  • 131
    • 84864092600 scopus 로고    scopus 로고
    • A quick guide to biomolecular network studies: Construction, analysis, applications, and resources
    • Tang, H., Zhong, F., Xie, H., A quick guide to biomolecular network studies: Construction, analysis, applications, and resources. Biochem. Biophys. Res. Commun. 2012, 424, 7-11.
    • (2012) Biochem. Biophys. Res. Commun. , vol.424 , pp. 7-11
    • Tang, H.1    Zhong, F.2    Xie, H.3
  • 132
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
    • Xenarios, I., Salwínski, L., Duan, X. J., Higney, P. et al., DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 2002, 30, 303-305.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 303-305
    • Xenarios, I.1    Salwínski, L.2    Duan, X.J.3    Higney, P.4
  • 135
    • 84859204939 scopus 로고    scopus 로고
    • The IntAct molecular interaction database in 2012
    • Kerrien, S., Aranda, B., Breuza, L., Bridge, A. et al., The IntAct molecular interaction database in 2012. Nucleic Acids Res. 2012, 40, D841-D846.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D841-D846
    • Kerrien, S.1    Aranda, B.2    Breuza, L.3    Bridge, A.4
  • 136
    • 84860918589 scopus 로고    scopus 로고
    • MINT, the molecular interaction database: 2012 update
    • Licata, L., Briganti, L., Peluso, D., Perfetto, L. et al., MINT, the molecular interaction database: 2012 update. Nucleic Acids Res. 2012, 40, D857-D861.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D857-D861
    • Licata, L.1    Briganti, L.2    Peluso, D.3    Perfetto, L.4
  • 137
    • 77949431355 scopus 로고    scopus 로고
    • Lists2Networks: Integrated analysis of gene/protein lists
    • Lachmann, A., Ma'ayan, A., Lists2Networks: Integrated analysis of gene/protein lists. BMC Bioinformatics 2010, 11, 87.
    • (2010) BMC Bioinformatics , vol.11 , pp. 87
    • Lachmann, A.1    Ma'ayan, A.2
  • 138
    • 84856918212 scopus 로고    scopus 로고
    • HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores
    • Schaefer, M. H., Fontaine, J. F., Vinayagam, A., Porras, P. et al., HIPPIE: Integrating Protein Interaction Networks with Experiment Based Quality Scores. PLoS One 2012, 7, e31826.
    • (2012) PLoS One , vol.7 , pp. e31826
    • Schaefer, M.H.1    Fontaine, J.F.2    Vinayagam, A.3    Porras, P.4
  • 139
    • 84876100615 scopus 로고    scopus 로고
    • Enrichr : interactive and collaborative HTML5 gene list enrichment analysis tool
    • Chen, E. Y., Tan, C. M., Kou, Y., Duan, Q. et al., Enrichr : interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 2013, 14, 128.
    • (2013) BMC Bioinformatics , vol.14 , pp. 128
    • Chen, E.Y.1    Tan, C.M.2    Kou, Y.3    Duan, Q.4
  • 140
    • 65549102777 scopus 로고    scopus 로고
    • Protein-protein interaction databases: keeping up with growing interactomes
    • Lehne, B., Schlitt, T., Protein-protein interaction databases: keeping up with growing interactomes. Hum. Genomics 2009, 3, 291-297.
    • (2009) Hum. Genomics , vol.3 , pp. 291-297
    • Lehne, B.1    Schlitt, T.2
  • 141
    • 84891799734 scopus 로고    scopus 로고
    • The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases
    • Orchard, S., Ammari, M., Aranda, B., Breuza, L. et al., The MIntAct project-IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. 2014, 42, D358-D363.
    • (2014) Nucleic Acids Res. , vol.42 , pp. D358-D363
    • Orchard, S.1    Ammari, M.2    Aranda, B.3    Breuza, L.4
  • 142
    • 84876515907 scopus 로고    scopus 로고
    • STRING v9.1: protein-protein interaction networks, with increased coverage and integration
    • Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M. et al., STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013, 41, D808-D815.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D808-D815
    • Franceschini, A.1    Szklarczyk, D.2    Frankild, S.3    Kuhn, M.4
  • 143
    • 80052844300 scopus 로고    scopus 로고
    • The representation of protein complexes in the Protein Ontology (PRO)
    • Bult, C. J., Drabkin, H. J., Evsikov, A., Natale, D. et al., The representation of protein complexes in the Protein Ontology (PRO). BMC Bioinformatics 2011, 12, 371.
    • (2011) BMC Bioinformatics , vol.12 , pp. 371
    • Bult, C.J.1    Drabkin, H.J.2    Evsikov, A.3    Natale, D.4
  • 144
    • 84910679144 scopus 로고    scopus 로고
    • Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database
    • Khoury, G. A., Baliban, R. C., Floudas, C. A., Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database. Sci. Reports 2011, 1.
    • (2011) Sci. Reports , vol.1
    • Khoury, G.A.1    Baliban, R.C.2    Floudas, C.A.3
  • 145
    • 84902031172 scopus 로고    scopus 로고
    • Evolution and functional cross-talk of protein post-translational modifications
    • Beltrao, P., Bork, P., Krogan, N. J., van Noort, V., Evolution and functional cross-talk of protein post-translational modifications. Mol. Syst. Biol. 2013, 9, 714.
    • (2013) Mol. Syst. Biol. , vol.9 , pp. 714
    • Beltrao, P.1    Bork, P.2    Krogan, N.J.3    van Noort, V.4
  • 146
    • 84864184970 scopus 로고    scopus 로고
    • Deciphering a global network of functionally associated post-translational modifications
    • Minguez, P., Parca, L., Diella, F., Mende, D. R. et al., Deciphering a global network of functionally associated post-translational modifications. Mol. Syst. Biol. 2012, 8, 599.
    • (2012) Mol. Syst. Biol. , vol.8 , pp. 599
    • Minguez, P.1    Parca, L.2    Diella, F.3    Mende, D.R.4
  • 147
    • 77953292595 scopus 로고    scopus 로고
    • Post-translational modifications in signal integration
    • Deribe, Y. L., Pawson, T., Dikic, I., Post-translational modifications in signal integration. Nat. Struct. Mol. Biol. 2010, 17, 666-672.
    • (2010) Nat. Struct. Mol. Biol. , vol.17 , pp. 666-672
    • Deribe, Y.L.1    Pawson, T.2    Dikic, I.3
  • 148
    • 77952956167 scopus 로고    scopus 로고
    • Decoding signalling networks by mass spectrometry-based proteomics
    • Choudhary, C., Mann, M., Decoding signalling networks by mass spectrometry-based proteomics. Nat. Rev. Mol. Cell Biol. 2010, 11, 427-439.
    • (2010) Nat. Rev. Mol. Cell Biol. , vol.11 , pp. 427-439
    • Choudhary, C.1    Mann, M.2
  • 149
    • 33644876212 scopus 로고    scopus 로고
    • dbPTM: an information repository of protein post-translational modification
    • Lee, T. Y., dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res. 2006, 34, D622-D627.
    • (2006) Nucleic Acids Res. , vol.34 , pp. D622-D627
    • Lee, T.Y.1
  • 150
    • 78651277460 scopus 로고    scopus 로고
    • PHOSIDA 2011: the posttranslational modification database
    • Gnad, F., Gunawardena, J., Mann, M., PHOSIDA 2011: the posttranslational modification database. Nucleic Acids Res. 2010, 39, D253-D260.
    • (2010) Nucleic Acids Res. , vol.39 , pp. D253-D260
    • Gnad, F.1    Gunawardena, J.2    Mann, M.3
  • 151
    • 78651320816 scopus 로고    scopus 로고
    • Phospho.ELM: a database of phosphorylation sites-update 2011
    • Dinkel, H., Chica, C., Via, A., Gould, C. M. et al., Phospho.ELM: a database of phosphorylation sites-update 2011. Nucleic Acids Res. 2010, 39, D261-D267.
    • (2010) Nucleic Acids Res. , vol.39 , pp. D261-D267
    • Dinkel, H.1    Chica, C.2    Via, A.3    Gould, C.M.4
  • 152
    • 84857047339 scopus 로고    scopus 로고
    • PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
    • Hornbeck, P. V., Kornhauser, J. M., Tkachev, S., Zhang, B. et al., PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 2012, 40, D261-D270.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D261-D270
    • Hornbeck, P.V.1    Kornhauser, J.M.2    Tkachev, S.3    Zhang, B.4
  • 153
    • 84901788851 scopus 로고    scopus 로고
    • KinomeXplorer: an integrated platform for kinome biology studies
    • Horn, H., Schoof, E. M., Kim, J., Robin, X. et al., KinomeXplorer: an integrated platform for kinome biology studies. Nat. Methods 2014, 11, 603-604.
    • (2014) Nat. Methods , vol.11 , pp. 603-604
    • Horn, H.1    Schoof, E.M.2    Kim, J.3    Robin, X.4
  • 154
    • 65149105339 scopus 로고    scopus 로고
    • A post-translational modification code for transcription factors: sorting through a sea of signals
    • Benayoun, B. A., Veitia, R. A., A post-translational modification code for transcription factors: sorting through a sea of signals. Trends Cell Biol. 2009, 19, 189-197.
    • (2009) Trends Cell Biol. , vol.19 , pp. 189-197
    • Benayoun, B.A.1    Veitia, R.A.2
  • 155
    • 84874957680 scopus 로고    scopus 로고
    • PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins
    • Minguez, P., Letunic, I., Parca, L., Bork, P., PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins. Nucleic Acids Res. 2013, 41, D306-D311.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D306-D311
    • Minguez, P.1    Letunic, I.2    Parca, L.3    Bork, P.4
  • 156
    • 79953044960 scopus 로고    scopus 로고
    • Genome-wide transcription factor binding: beyond direct target regulation
    • MacQuarrie, K. L., Fong, A. P., Morse, R. H., Tapscott, S. J., Genome-wide transcription factor binding: beyond direct target regulation. Trends Genet. 2011, 27, 141-148.
    • (2011) Trends Genet. , vol.27 , pp. 141-148
    • MacQuarrie, K.L.1    Fong, A.P.2    Morse, R.H.3    Tapscott, S.J.4
  • 157
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-dna interactions
    • Johnson, D. S., Mortazavi, A., Myers, R. M., Wold, B., Genome-wide mapping of in vivo protein-dna interactions. Science 2007, 316, 1497-1502.
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 158
    • 46049087782 scopus 로고    scopus 로고
    • The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
    • Wingender, E., The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief. Bioinform. 2008, 9, 326-332.
    • (2008) Brief. Bioinform. , vol.9 , pp. 326-332
    • Wingender, E.1
  • 159
  • 160
    • 33845311536 scopus 로고    scopus 로고
    • Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping
    • Walhout, A. J. M., Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res. 2006, 16, 1445-1454.
    • (2006) Genome Res. , vol.16 , pp. 1445-1454
    • Walhout, A.J.M.1
  • 161
  • 162
    • 63849315606 scopus 로고    scopus 로고
    • High-resolution DNA-binding specificity analysis of yeast transcription factors
    • Zhu, C., Byers, K. J. R. P., McCord, R. P., Shi, Z. et al., High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res. 2009, 19, 556-566.
    • (2009) Genome Res. , vol.19 , pp. 556-566
    • Zhu, C.1    Byers, K.J.R.P.2    McCord, R.P.3    Shi, Z.4
  • 163
    • 77950920903 scopus 로고    scopus 로고
    • Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
    • Hafner, M., Landthaler, M., Burger, L., Khorshid, M. et al., Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010, 141, 129-141.
    • (2010) Cell , vol.141 , pp. 129-141
    • Hafner, M.1    Landthaler, M.2    Burger, L.3    Khorshid, M.4
  • 164
    • 77949426688 scopus 로고    scopus 로고
    • A Novel microRNA and transcription factor mediated regulatory network in schizophrenia
    • Guo, A. Y., Sun, J., Jia, P., Zhao, Z., A Novel microRNA and transcription factor mediated regulatory network in schizophrenia. BMC Syst. Biol. 2010, 4, 10.
    • (2010) BMC Syst. Biol. , vol.4 , pp. 10
    • Guo, A.Y.1    Sun, J.2    Jia, P.3    Zhao, Z.4
  • 167
    • 11844278458 scopus 로고    scopus 로고
    • Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets
    • Lewis, B. P., Burge, C. B., Bartel, D. P., Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets. Cell 2005, 120, 15-20.
    • (2005) Cell , vol.120 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 168
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U., Segal, E., The role of site accessibility in microRNA target recognition. Nat. Genet. 2007, 39, 1278-1284.
    • (2007) Nat. Genet. , vol.39 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 169
    • 33746061228 scopus 로고    scopus 로고
    • Function of the MAPK scaffold protein, Ste5, requires a cryptic PH domain
    • Garrenton, L. S., Young, S. L., Thorner, J., Function of the MAPK scaffold protein, Ste5, requires a cryptic PH domain. Genes Dev. 2006, 20, 1946-1958.
    • (2006) Genes Dev. , vol.20 , pp. 1946-1958
    • Garrenton, L.S.1    Young, S.L.2    Thorner, J.3
  • 170
    • 79955770162 scopus 로고    scopus 로고
    • Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information
    • Good, M. C., Zalatan, J. G., Lim, W. A., Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information. Science 2011, 332, 680-686.
    • (2011) Science , vol.332 , pp. 680-686
    • Good, M.C.1    Zalatan, J.G.2    Lim, W.A.3
  • 171
  • 172
    • 79958139420 scopus 로고    scopus 로고
    • Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications
    • Remmerie, N., De Vijlder, T., Laukens, K., Dang, T. H. et al., Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications. Phytochemistry 2011, 72, 1192-1218.
    • (2011) Phytochemistry , vol.72 , pp. 1192-1218
    • Remmerie, N.1    De Vijlder, T.2    Laukens, K.3    Dang, T.H.4
  • 173
    • 77952833904 scopus 로고    scopus 로고
    • BioCarta. Biotech Softw
    • Nishimura, D., BioCarta. Biotech Softw. Internet Rep. 2001, 2, 117-120.
    • (2001) Internet Rep. , vol.2 , pp. 117-120
    • Nishimura, D.1
  • 174
    • 0037245913 scopus 로고    scopus 로고
    • BIND: the Biomolecular Interaction Network Database
    • Bader, G. D., Betel, D., Hogue, C. W. V., BIND: the Biomolecular Interaction Network Database. Nucl. Acids Res. 2003, 31, 248-250.
    • (2003) Nucl. Acids Res. , vol.31 , pp. 248-250
    • Bader, G.D.1    Betel, D.2    Hogue, C.W.V.3
  • 175
    • 84864037265 scopus 로고    scopus 로고
    • INOH: ontology-based highly structured database of signal transduction pathways
    • bar052-bar052
    • Yamamoto, S., Sakai, N., Nakamura, H., Fukagawa, H. et al., INOH: ontology-based highly structured database of signal transduction pathways. Database 2011, 2011, bar052-bar052.
    • (2011) Database , vol.2011
    • Yamamoto, S.1    Sakai, N.2    Nakamura, H.3    Fukagawa, H.4
  • 177
    • 3142665525 scopus 로고    scopus 로고
    • GOstat: find statistically overrepresented Gene Ontologies within a group of genes
    • Beißbarth, T., Speed, T. P., GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 2004, 20, 1464-1465.
    • (2004) Bioinformatics , vol.20 , pp. 1464-1465
    • Beißbarth, T.1    Speed, T.P.2
  • 178
    • 0345832338 scopus 로고    scopus 로고
    • A global test for groups of genes: testing association with a clinical outcome
    • Goeman, J. J., Geer, S. A. van de, Kort, F. de, Houwelingen, H. C. van, A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 2004, 20, 93-99.
    • (2004) Bioinformatics , vol.20 , pp. 93-99
    • Goeman, J.J.1    Geer, S.A.v.d.2    Kort, F.d.3    Houwelingen, H.C.v.4
  • 179
    • 84872202078 scopus 로고    scopus 로고
    • GSVA: gene set variation analysis for microarray and RNA-seq data
    • Hänzelmann, S., Castelo, R., Guinney, J., GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics 2013, 14, 7.
    • (2013) BMC Bioinformatics , vol.14 , pp. 7
    • Hänzelmann, S.1    Castelo, R.2    Guinney, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.