메뉴 건너뛰기




Volumn 7, Issue SUPPL 5, 2013, Pages

Dynamic protein interaction modules in human hepatocellular carcinoma progression

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER STAGING; DISEASE COURSE; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENETICS; HUMAN; LIVER CELL CARCINOMA; LIVER TUMOR; METABOLISM; PATHOLOGY; PROTEIN ANALYSIS;

EID: 84889641190     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-7-S5-S2     Document Type: Article
Times cited : (24)

References (51)
  • 1
    • 84870330057 scopus 로고    scopus 로고
    • Protein-protein interaction networks: unraveling the wiring of molecular machines within the cell
    • 10.1093/bfgp/els036, 22908212
    • De Las Rivas J, Fontanillo C. Protein-protein interaction networks: unraveling the wiring of molecular machines within the cell. Brief Funct Genomics 2012, 11:489-496. 10.1093/bfgp/els036, 22908212.
    • (2012) Brief Funct Genomics , vol.11 , pp. 489-496
    • De Las Rivas, J.1    Fontanillo, C.2
  • 2
    • 58149271021 scopus 로고    scopus 로고
    • Integrated network analysis platform for protein-protein interactions
    • 10.1038/nmeth.1282, 19079255
    • Wu J, Vallenius T, Ovaska K, Westermarck J, Makela TP, Hautaniemi S. Integrated network analysis platform for protein-protein interactions. Nat Methods 2009, 6:75-77. 10.1038/nmeth.1282, 19079255.
    • (2009) Nat Methods , vol.6 , pp. 75-77
    • Wu, J.1    Vallenius, T.2    Ovaska, K.3    Westermarck, J.4    Makela, T.P.5    Hautaniemi, S.6
  • 3
    • 77952769823 scopus 로고    scopus 로고
    • Functional features, biological pathways, and protein interaction networks of addiction-related genes
    • 10.1002/cbdv.200900319, 2939034, 20491072
    • Sun J, Zhao Z. Functional features, biological pathways, and protein interaction networks of addiction-related genes. Chem Biodivers 2010, 7:1153-1162. 10.1002/cbdv.200900319, 2939034, 20491072.
    • (2010) Chem Biodivers , vol.7 , pp. 1153-1162
    • Sun, J.1    Zhao, Z.2
  • 4
    • 77952757170 scopus 로고    scopus 로고
    • Network analysis of ethanol-related candidate genes
    • 10.1002/cbdv.200900318, 2935470, 20491071
    • Guo AY, Sun J, Jia P, Zhao Z. Network analysis of ethanol-related candidate genes. Chem Biodivers 2010, 7:1142-1152. 10.1002/cbdv.200900318, 2935470, 20491071.
    • (2010) Chem Biodivers , vol.7 , pp. 1142-1152
    • Guo, A.Y.1    Sun, J.2    Jia, P.3    Zhao, Z.4
  • 5
    • 77950353931 scopus 로고    scopus 로고
    • Toward the dynamic interactome: it's about time
    • 10.1093/bib/bbp057, 2810115, 20061351
    • Przytycka TM, Singh M, Slonim DK. Toward the dynamic interactome: it's about time. Brief Bioinform 2010, 11:15-29. 10.1093/bib/bbp057, 2810115, 20061351.
    • (2010) Brief Bioinform , vol.11 , pp. 15-29
    • Przytycka, T.M.1    Singh, M.2    Slonim, D.K.3
  • 6
    • 84889660810 scopus 로고    scopus 로고
    • Identifying protein complexes and functional modules--from static PPI networks to dynamic PPI networks
    • Chen B, Fan W, Liu J, Wu FX. Identifying protein complexes and functional modules--from static PPI networks to dynamic PPI networks. Brief Bioinform 2013,
    • (2013) Brief Bioinform
    • Chen, B.1    Fan, W.2    Liu, J.3    Wu, F.X.4
  • 7
    • 0000801240 scopus 로고    scopus 로고
    • Discovering regulatory and signalling circuits in molecular interaction networks
    • 10.1093/bioinformatics/18.suppl_1.S233, 12169552
    • Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 2002, 18(Suppl 1):S233-240. 10.1093/bioinformatics/18.suppl_1.S233, 12169552.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Ideker, T.1    Ozier, O.2    Schwikowski, B.3    Siegel, A.F.4
  • 8
    • 35348891430 scopus 로고    scopus 로고
    • Network-based classification of breast cancer metastasis
    • 2063581, 17940530
    • Chuang HY, Lee E, Liu YT, Lee D, Ideker T. Network-based classification of breast cancer metastasis. Mol Syst Biol 2007, 3:140. 2063581, 17940530.
    • (2007) Mol Syst Biol , vol.3 , pp. 140
    • Chuang, H.Y.1    Lee, E.2    Liu, Y.T.3    Lee, D.4    Ideker, T.5
  • 9
    • 46249128543 scopus 로고    scopus 로고
    • Identifying functional modules in protein-protein interaction networks: an integrated exact approach
    • 10.1093/bioinformatics/btn161, 2718639, 18586718
    • Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Muller T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 2008, 24:i223-231. 10.1093/bioinformatics/btn161, 2718639, 18586718.
    • (2008) Bioinformatics , vol.24
    • Dittrich, M.T.1    Klau, G.W.2    Rosenwald, A.3    Dandekar, T.4    Muller, T.5
  • 10
    • 3142706495 scopus 로고    scopus 로고
    • New methods for joint analysis of biological networks and expression data
    • 10.1093/bioinformatics/bth112, 15231545
    • Sohler F, Hanisch D, Zimmer R. New methods for joint analysis of biological networks and expression data. Bioinformatics 2004, 20:1517-1521. 10.1093/bioinformatics/bth112, 15231545.
    • (2004) Bioinformatics , vol.20 , pp. 1517-1521
    • Sohler, F.1    Hanisch, D.2    Zimmer, R.3
  • 11
    • 34248593385 scopus 로고    scopus 로고
    • Gene expression network analysis and applications to immunology
    • 10.1093/bioinformatics/btm019, 17267429
    • Nacu S, Critchley-Thorne R, Lee P, Holmes S. Gene expression network analysis and applications to immunology. Bioinformatics 2007, 23:850-858. 10.1093/bioinformatics/btm019, 17267429.
    • (2007) Bioinformatics , vol.23 , pp. 850-858
    • Nacu, S.1    Critchley-Thorne, R.2    Lee, P.3    Holmes, S.4
  • 12
    • 44449144053 scopus 로고    scopus 로고
    • Linking gene expression and functional network data in human heart failure
    • 10.1371/journal.pone.0001347, 2147076, 18094754
    • Camargo A, Azuaje F. Linking gene expression and functional network data in human heart failure. PLoS One 2007, 2:e1347. 10.1371/journal.pone.0001347, 2147076, 18094754.
    • (2007) PLoS One , vol.2
    • Camargo, A.1    Azuaje, F.2
  • 14
    • 34548583420 scopus 로고    scopus 로고
    • Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network
    • 10.1093/bioinformatics/btm294, 17545181
    • Guo Z, Wang L, Li Y, Gong X, Yao C, Ma W, Wang D, Zhu J, Zhang M, Yang D, et al. Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network. Bioinformatics 2007, 23:2121-2128. 10.1093/bioinformatics/btm294, 17545181.
    • (2007) Bioinformatics , vol.23 , pp. 2121-2128
    • Guo, Z.1    Wang, L.2    Li, Y.3    Gong, X.4    Yao, C.5    Ma, W.6    Wang, D.7    Zhu, J.8    Zhang, M.9    Yang, D.10
  • 16
    • 84860258459 scopus 로고    scopus 로고
    • Systematic identification of common functional modules related to heart failure with different etiologies
    • 10.1016/j.gene.2012.03.039, 22446039
    • Xiao Y, Xu C, Xu L, Guan J, Ping Y, Fan H, Li Y, Zhao H, Li X. Systematic identification of common functional modules related to heart failure with different etiologies. Gene 2012, 499:332-338. 10.1016/j.gene.2012.03.039, 22446039.
    • (2012) Gene , vol.499 , pp. 332-338
    • Xiao, Y.1    Xu, C.2    Xu, L.3    Guan, J.4    Ping, Y.5    Fan, H.6    Li, Y.7    Zhao, H.8    Li, X.9
  • 17
    • 84863596942 scopus 로고    scopus 로고
    • Combined gene expression and protein interaction analysis of dynamic modularity in glioma prognosis
    • 10.1007/s11060-011-0757-4, 22071792
    • Zhang X, Yang H, Gong B, Jiang C, Yang L. Combined gene expression and protein interaction analysis of dynamic modularity in glioma prognosis. J Neurooncol 2012, 107:281-288. 10.1007/s11060-011-0757-4, 22071792.
    • (2012) J Neurooncol , vol.107 , pp. 281-288
    • Zhang, X.1    Yang, H.2    Gong, B.3    Jiang, C.4    Yang, L.5
  • 18
    • 77957892202 scopus 로고    scopus 로고
    • Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy
    • 10.1186/1752-0509-4-138, 2978157, 20950417
    • Lin CC, Hsiang JT, Wu CY, Oyang YJ, Juan HF, Huang HC. Dynamic functional modules in co-expressed protein interaction networks of dilated cardiomyopathy. BMC Syst Biol 2010, 4:138. 10.1186/1752-0509-4-138, 2978157, 20950417.
    • (2010) BMC Syst Biol , vol.4 , pp. 138
    • Lin, C.C.1    Hsiang, J.T.2    Wu, C.Y.3    Oyang, Y.J.4    Juan, H.F.5    Huang, H.C.6
  • 19
    • 84870321974 scopus 로고    scopus 로고
    • Differentially co-expressed interacting protein pairs discriminate samples under distinct stages of HIV type 1 infection
    • Yoon D, Kim H, Suh-Kim H, Park RW, Lee K. Differentially co-expressed interacting protein pairs discriminate samples under distinct stages of HIV type 1 infection. BMC Syst Biol 2011, 5(Suppl 2):S1.
    • (2011) BMC Syst Biol , vol.5 , Issue.SUPPL. 2
    • Yoon, D.1    Kim, H.2    Suh-Kim, H.3    Park, R.W.4    Lee, K.5
  • 20
    • 84879066322 scopus 로고    scopus 로고
    • ToP: A Trend-of-Disease-Progression Procedure Works Well for Identifying Cancer Genes from Multi-State Cohort Gene Expression Data for Human Colorectal Cancer
    • 10.1371/journal.pone.0065683, 3683052, 23799036
    • Chung FH, Lee HH, Lee HC. ToP: A Trend-of-Disease-Progression Procedure Works Well for Identifying Cancer Genes from Multi-State Cohort Gene Expression Data for Human Colorectal Cancer. PLoS One 2013, 8:e65683. 10.1371/journal.pone.0065683, 3683052, 23799036.
    • (2013) PLoS One , vol.8
    • Chung, F.H.1    Lee, H.H.2    Lee, H.C.3
  • 21
    • 77953913791 scopus 로고    scopus 로고
    • From 'differential expression' to 'differential networking' - identification of dysfunctional regulatory networks in diseases
    • 10.1016/j.tig.2010.05.001, 20570387
    • de la Fuente A. From 'differential expression' to 'differential networking' - identification of dysfunctional regulatory networks in diseases. Trends Genet 2010, 26:326-333. 10.1016/j.tig.2010.05.001, 20570387.
    • (2010) Trends Genet , vol.26 , pp. 326-333
    • de la Fuente, A.1
  • 22
    • 70350682038 scopus 로고    scopus 로고
    • Statistical methods for gene set co-expression analysis
    • 10.1093/bioinformatics/btp502, 2781749, 19689953
    • Choi Y, Kendziorski C. Statistical methods for gene set co-expression analysis. Bioinformatics 2009, 25:2780-2786. 10.1093/bioinformatics/btp502, 2781749, 19689953.
    • (2009) Bioinformatics , vol.25 , pp. 2780-2786
    • Choi, Y.1    Kendziorski, C.2
  • 23
    • 79960892858 scopus 로고    scopus 로고
    • Link-based quantitative methods to identify differentially coexpressed genes and gene pairs
    • 10.1186/1471-2105-12-315, 3199761, 21806838
    • Yu H, Liu BH, Ye ZQ, Li C, Li YX, Li YY. Link-based quantitative methods to identify differentially coexpressed genes and gene pairs. BMC Bioinformatics 2011, 12:315. 10.1186/1471-2105-12-315, 3199761, 21806838.
    • (2011) BMC Bioinformatics , vol.12 , pp. 315
    • Yu, H.1    Liu, B.H.2    Ye, Z.Q.3    Li, C.4    Li, Y.X.5    Li, Y.Y.6
  • 24
    • 79961125191 scopus 로고    scopus 로고
    • Integrative network analysis identifies key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma
    • 10.1186/1755-8794-4-62, 3212927, 21824427
    • Zheng S, Tansey WP, Hiebert SW, Zhao Z. Integrative network analysis identifies key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma. BMC Med Genomics 2011, 4:62. 10.1186/1755-8794-4-62, 3212927, 21824427.
    • (2011) BMC Med Genomics , vol.4 , pp. 62
    • Zheng, S.1    Tansey, W.P.2    Hiebert, S.W.3    Zhao, Z.4
  • 28
    • 14944375587 scopus 로고    scopus 로고
    • Immunology of hepatitis B virus and hepatitis C virus infection
    • 10.1038/nri1573, 15738952
    • Rehermann B, Nascimbeni M. Immunology of hepatitis B virus and hepatitis C virus infection. Nat Rev Immunol 2005, 5:215-229. 10.1038/nri1573, 15738952.
    • (2005) Nat Rev Immunol , vol.5 , pp. 215-229
    • Rehermann, B.1    Nascimbeni, M.2
  • 30
    • 84861625981 scopus 로고    scopus 로고
    • Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma
    • 10.1038/ng.2256, 3819251, 22561517
    • Guichard C, Amaddeo G, Imbeaud S, Ladeiro Y, Pelletier L, Maad IB, Calderaro J, Bioulac-Sage P, Letexier M, Degos F, et al. Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma. Nat Genet 2012, 44:694-698. 10.1038/ng.2256, 3819251, 22561517.
    • (2012) Nat Genet , vol.44 , pp. 694-698
    • Guichard, C.1    Amaddeo, G.2    Imbeaud, S.3    Ladeiro, Y.4    Pelletier, L.5    Maad, I.B.6    Calderaro, J.7    Bioulac-Sage, P.8    Letexier, M.9    Degos, F.10
  • 31
    • 84874019016 scopus 로고    scopus 로고
    • Pathway Interaction Database
    • Pathway Interaction Database. , http://pid.nci.nih.gov/
  • 32
    • 84880534247 scopus 로고    scopus 로고
    • Genetic Variations of the CTNNA1 And The CTNNB1 Genes in Sporadic Colorectal Cancer in Polish Population
    • Sygut A, Przybylowska K, Ferenc T, Dziki L, Spychalski M, Mik M, Dziki A. Genetic Variations of the CTNNA1 And The CTNNB1 Genes in Sporadic Colorectal Cancer in Polish Population. Pol Przegl Chir 2012, 84:560-564.
    • (2012) Pol Przegl Chir , vol.84 , pp. 560-564
    • Sygut, A.1    Przybylowska, K.2    Ferenc, T.3    Dziki, L.4    Spychalski, M.5    Mik, M.6    Dziki, A.7
  • 33
    • 84866462100 scopus 로고    scopus 로고
    • Role of cellular senescence in hepatic wound healing and carcinogenesis
    • 10.1016/j.ejcb.2012.08.002, 22980320
    • Ramakrishna G, Anwar T, Angara RK, Chatterjee N, Kiran S, Singh S. Role of cellular senescence in hepatic wound healing and carcinogenesis. Eur J Cell Biol 2012, 91:739-747. 10.1016/j.ejcb.2012.08.002, 22980320.
    • (2012) Eur J Cell Biol , vol.91 , pp. 739-747
    • Ramakrishna, G.1    Anwar, T.2    Angara, R.K.3    Chatterjee, N.4    Kiran, S.5    Singh, S.6
  • 35
    • 80053300659 scopus 로고    scopus 로고
    • Genome-wide copy number analyses identified novel cancer genes in hepatocellular carcinoma
    • 10.1002/hep.24495, 21688285
    • Jia D, Wei L, Guo W, Zha R, Bao M, Chen Z, Zhao Y, Ge C, Zhao F, Chen T, et al. Genome-wide copy number analyses identified novel cancer genes in hepatocellular carcinoma. Hepatology 2011, 54:1227-1236. 10.1002/hep.24495, 21688285.
    • (2011) Hepatology , vol.54 , pp. 1227-1236
    • Jia, D.1    Wei, L.2    Guo, W.3    Zha, R.4    Bao, M.5    Chen, Z.6    Zhao, Y.7    Ge, C.8    Zhao, F.9    Chen, T.10
  • 36
    • 70449702094 scopus 로고    scopus 로고
    • Transcriptional analysis of doxorubicin-induced cytotoxicity and resistance in human hepatocellular carcinoma cell lines
    • 10.1111/j.1478-3231.2009.02081.x, 19627484
    • Wang J, Chan JY, Fong CC, Tzang CH, Fung KP, Yang M. Transcriptional analysis of doxorubicin-induced cytotoxicity and resistance in human hepatocellular carcinoma cell lines. Liver Int 2009, 29:1338-1347. 10.1111/j.1478-3231.2009.02081.x, 19627484.
    • (2009) Liver Int , vol.29 , pp. 1338-1347
    • Wang, J.1    Chan, J.Y.2    Fong, C.C.3    Tzang, C.H.4    Fung, K.P.5    Yang, M.6
  • 37
    • 70449671065 scopus 로고    scopus 로고
    • The effect of Scutellaria baicalensis on the signaling network in hepatocellular carcinoma cells
    • 10.1080/01635580902803719, 19838925
    • Ye F, Che Y, McMillen E, Gorski J, Brodman D, Saw D, Jiang B, Zhang DY. The effect of Scutellaria baicalensis on the signaling network in hepatocellular carcinoma cells. Nutr Cancer 2009, 61:530-537. 10.1080/01635580902803719, 19838925.
    • (2009) Nutr Cancer , vol.61 , pp. 530-537
    • Ye, F.1    Che, Y.2    McMillen, E.3    Gorski, J.4    Brodman, D.5    Saw, D.6    Jiang, B.7    Zhang, D.Y.8
  • 40
    • 70350672533 scopus 로고    scopus 로고
    • Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms
    • 10.1093/nar/gkp638, 2764428, 19671526
    • Tu K, Yu H, Hua YJ, Li YY, Liu L, Xie L, Li YX. Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms. Nucleic Acids Res 2009, 37:5969-5980. 10.1093/nar/gkp638, 2764428, 19671526.
    • (2009) Nucleic Acids Res , vol.37 , pp. 5969-5980
    • Tu, K.1    Yu, H.2    Hua, Y.J.3    Li, Y.Y.4    Liu, L.5    Xie, L.6    Li, Y.X.7
  • 41
    • 77951076168 scopus 로고    scopus 로고
    • Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis
    • 10.1186/1752-0509-4-47, 2873318, 20406493
    • Gu J, Chen Y, Li S, Li Y. Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis. BMC Syst Biol 2010, 4:47. 10.1186/1752-0509-4-47, 2873318, 20406493.
    • (2010) BMC Syst Biol , vol.4 , pp. 47
    • Gu, J.1    Chen, Y.2    Li, S.3    Li, Y.4
  • 42
    • 84875834246 scopus 로고    scopus 로고
    • Studying the differential co-expression of microRNAs reveals significant role of white matter in early Alzheimer's progression
    • 10.1039/c2mb25434d, 23344858
    • Bhattacharyya M, Bandyopadhyay S. Studying the differential co-expression of microRNAs reveals significant role of white matter in early Alzheimer's progression. Mol Biosyst 2013, 9:457-466. 10.1039/c2mb25434d, 23344858.
    • (2013) Mol Biosyst , vol.9 , pp. 457-466
    • Bhattacharyya, M.1    Bandyopadhyay, S.2
  • 43
    • 84870532154 scopus 로고    scopus 로고
    • Gene Expression Omnibus
    • Gene Expression Omnibus. , http://www.ncbi.nlm.nih.gov/geo/
  • 46
    • 80052259779 scopus 로고    scopus 로고
    • Hepatitis C Virus Protein Interaction Database
    • Hepatitis C Virus Protein Interaction Database. , http://cbrc.kaust.edu.sa/hcvpro/
  • 47
    • 84889663785 scopus 로고    scopus 로고
    • Cancer Gene Consensus
    • Cancer Gene Consensus. , http://www.sanger.ac.uk/genetics/CGP/Census/symbol.shtml
  • 48
    • 84889679384 scopus 로고    scopus 로고
    • MSigDB
    • MSigDB. , http://www.broadinstitute.org/gsea/msigdb/search.jsp
  • 49
    • 0001165055 scopus 로고
    • Frequency Distribution of the Values of the Correlation Coefficient in Samples from an Indefinitely Large Population
    • Fisher RA. Frequency Distribution of the Values of the Correlation Coefficient in Samples from an Indefinitely Large Population. Biometrika 1915, 10:507-521.
    • (1915) Biometrika , vol.10 , pp. 507-521
    • Fisher, R.A.1
  • 50
    • 33846689706 scopus 로고    scopus 로고
    • Using GOstats to test gene lists for GO term association
    • 10.1093/bioinformatics/btl567, 17098774
    • Falcon S, Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics 2007, 23:257-258. 10.1093/bioinformatics/btl567, 17098774.
    • (2007) Bioinformatics , vol.23 , pp. 257-258
    • Falcon, S.1    Gentleman, R.2
  • 51
    • 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 Statist Soc B 1995, 57:289-300.
    • (1995) J R Statist Soc B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.