메뉴 건너뛰기




Volumn 8, Issue 11, 2013, Pages

DCGL v2.0: An R package for unveiling differential regulation from differential co-expression

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; GENE REGULATORY NETWORKS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE;

EID: 84894232727     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0079729     Document Type: Article
Times cited : (89)

References (37)
  • 1
    • 33749988857 scopus 로고    scopus 로고
    • Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer
    • DOI 10.1093/bioinformatics/btl392
    • Reverter A, Ingham A, Lehnert SA, Tan SH, Wang Y, et al. (2006) Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer. Bioinformatics 22: 2396-2404. (Pubitemid 44566969)
    • (2006) Bioinformatics , vol.22 , Issue.19 , pp. 2396-2404
    • Reverter, A.1    Ingham, A.2    Lehnert, S.A.3    Tan, S.-H.4    Wang, Y.5    Ratnakumar, A.6    Dalrymple, B.P.7
  • 2
    • 28944444652 scopus 로고    scopus 로고
    • Differential coexpression analysis using microarray data and its application to human cancer
    • DOI 10.1093/bioinformatics/bti722
    • Choi JK, Yu U, Yoo OJ, Kim S (2005) Differential coexpression analysis using microarray data and its application to human cancer. Bioinformatics 21: 4348-4355. (Pubitemid 41782924)
    • (2005) Bioinformatics , vol.21 , Issue.24 , pp. 4348-4355
    • Choi, J.K.1    Yu, U.2    Yoo, O.J.3    Kim, S.4
  • 3
    • 67649644714 scopus 로고    scopus 로고
    • Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks
    • van Nas A, Guhathakurta D, Wang SS, Yehya N, Horvath S, et al. (2009) Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks. Endocrinology 150: 1235-1249.
    • (2009) Endocrinology , vol.150 , pp. 1235-1249
    • Van Nas, A.1    Guhathakurta, D.2    Wang, S.S.3    Yehya, N.4    Horvath, S.5
  • 4
    • 68949098307 scopus 로고    scopus 로고
    • Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells
    • Mason MJ, Fan G, Plath K, Zhou Q, Horvath S (2009) Signed weighted gene co-expression network analysis of transcriptional regulation in murine embryonic stem cells. BMC Genomics 10: 327.
    • (2009) BMC Genomics , vol.10 , pp. 327
    • Mason, M.J.1    Fan, G.2    Plath, K.3    Zhou, Q.4    Horvath, S.5
  • 5
    • 79960892858 scopus 로고    scopus 로고
    • Link-based quantitative methods to identify differentially coexpressed genes and gene pairs
    • Yu H, Liu BH, Ye ZQ, Li C, Li YX, et al. (2011) Link-based quantitative methods to identify differentially coexpressed genes and gene pairs. BMC Bioinformatics 12: 315.
    • (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
  • 6
    • 77957813589 scopus 로고    scopus 로고
    • DCGL: An R package for identifying differentially coexpressed genes and links from gene expression microarray data
    • Liu BH, Yu H, Tu K, Li C, Li YX, et al. (2010) DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data. Bioinformatics 26: 2637-2638.
    • (2010) Bioinformatics , vol.26 , pp. 2637-2638
    • Liu, B.H.1    Yu, H.2    Tu, K.3    Li, C.4    Li, Y.X.5
  • 8
    • 70350682038 scopus 로고    scopus 로고
    • Statistical methods for gene set co-expression analysis
    • Choi Y, Kendziorski C (2009) Statistical methods for gene set co-expression analysis. Bioinformatics 25: 2780-2786.
    • (2009) Bioinformatics , vol.25 , pp. 2780-2786
    • Choi, Y.1    Kendziorski, C.2
  • 9
    • 67049159812 scopus 로고    scopus 로고
    • A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation
    • Hudson NJ, Reverter A, Dalrymple BP (2009) A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation. PLoS Comput Biol 5: e1000382.
    • (2009) PLoS Comput Biol , vol.5
    • Hudson, N.J.1    Reverter, A.2    Dalrymple, B.P.3
  • 10
    • 77951944593 scopus 로고    scopus 로고
    • Regulatory impact factors: Unraveling the transcriptional regulation of complex traits from expression data
    • Reverter A, Hudson NJ, Nagaraj SH, Perez-Enciso M, Dalrymple BP (2010) Regulatory impact factors: unraveling the transcriptional regulation of complex traits from expression data. Bioinformatics 26: 896-904.
    • (2010) Bioinformatics , vol.26 , pp. 896-904
    • Reverter, A.1    Hudson, N.J.2    Nagaraj, S.H.3    Perez-Enciso, M.4    Dalrymple, B.P.5
  • 12
    • 84875834246 scopus 로고    scopus 로고
    • Studying the Differential Co-expression of MicroRNAs Reveals Significant Role of White Matter in Early Alzheimer's Progression
    • Accepted
    • Bhattacharyya M, Bandyopadhyay S (2013) Studying the Differential Co-expression of MicroRNAs Reveals Significant Role of White Matter in Early Alzheimer's Progression. Molecular BioSystems: Accepted.
    • (2013) Molecular BioSystems
    • Bhattacharyya, M.1    Bandyopadhyay, S.2
  • 13
    • 34547649056 scopus 로고    scopus 로고
    • CoXpress: Differential co-expression in gene expression data
    • Watson M (2006) CoXpress: differential co-expression in gene expression data. BMC Bioinformatics 7: 509.
    • (2006) BMC Bioinformatics , vol.7 , pp. 509
    • Watson, M.1
  • 14
    • 84875380606 scopus 로고    scopus 로고
    • DiffCorr: An R package to analyze and visualize differential correlations in biological networks
    • Fukushima A (2013) DiffCorr: an R package to analyze and visualize differential correlations in biological networks. Gene 518: 209-214.
    • (2013) Gene , vol.518 , pp. 209-214
    • Fukushima, A.1
  • 15
    • 84875654974 scopus 로고    scopus 로고
    • Analysis of crucial molecules involved in herniated discs and degenerative disc disease
    • Sao Paulo
    • Qu Z, Miao W, Zhang Q, Wang Z, Fu C, et al. (2013) Analysis of crucial molecules involved in herniated discs and degenerative disc disease. Clinics (Sao Paulo) 68: 225-230.
    • (2013) Clinics , vol.68 , pp. 225-230
    • Qu, Z.1    Miao, W.2    Zhang, Q.3    Wang, Z.4    Fu, C.5
  • 16
    • 84871675217 scopus 로고    scopus 로고
    • Gene expression profiling combined with bioinformatics analysis identify biomarkers for Parkinson disease
    • Diao H, Li X, Hu S, Liu Y (2012) Gene expression profiling combined with bioinformatics analysis identify biomarkers for Parkinson disease. PLoS One 7: e52319.
    • (2012) PLoS One , vol.7
    • Diao, H.1    Li, X.2    Hu, S.3    Liu, Y.4
  • 17
    • 84878403356 scopus 로고    scopus 로고
    • Microarray gene expression profiling analysis combined with bioinformatics in multiple sclerosis
    • Liu M, Hou X, Zhang P, Hao Y, Yang Y, et al. (2013) Microarray gene expression profiling analysis combined with bioinformatics in multiple sclerosis. Mol Biol Rep 40: 3731-3737.
    • (2013) Mol Biol Rep , vol.40 , pp. 3731-3737
    • Liu, M.1    Hou, X.2    Zhang, P.3    Hao, Y.4    Yang, Y.5
  • 18
    • 84878720357 scopus 로고    scopus 로고
    • Identification of transcription regulatory relationships in rheumatoid arthritis and osteoarthritis
    • Li G, Han N, Li Z, Lu Q (2013) Identification of transcription regulatory relationships in rheumatoid arthritis and osteoarthritis. Clin Rheumatol.
    • (2013) Clin Rheumatol
    • Li, G.1    Han, N.2    Li, Z.3    Lu, Q.4
  • 19
    • 58049198442 scopus 로고    scopus 로고
    • Human gene coexpression landscape: Confident network derived from tissue transcriptomic profiles
    • Prieto C, Risueno A, Fontanillo C, De las Rivas J (2008) Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles. PLoS One 3: e3911.
    • (2008) PLoS One , vol.3
    • Prieto, C.1    Risueno, A.2    Fontanillo, C.3    De Las Rivas, J.4
  • 20
    • 14944378943 scopus 로고    scopus 로고
    • Technical Reports. Biometric Research Branch, Available
    • Simon RaL A (2006) BRB Array Tools Users Guide. Technical Reports. Biometric Research Branch, National Cancer Institute. Available: http://linus.nci.nih.gov/,brb/download-full-new.html.
    • (2006) BRB Array Tools Users Guide
    • Simon RaL, A.1
  • 21
    • 34548550573 scopus 로고    scopus 로고
    • Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process
    • DOI 10.1093/bioinformatics/btm309
    • Elo LL, Jarvenpaa H, Oresic M, Lahesmaa R, Aittokallio T (2007) Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinformatics 23: 2096-2103. (Pubitemid 47394109)
    • (2007) Bioinformatics , vol.23 , Issue.16 , pp. 2096-2103
    • Elo, L.L.1    Jarvenpaa, H.2    Oresic, M.3    Lahesmaa, R.4    Aittokallio, T.5
  • 22
    • 72749114315 scopus 로고    scopus 로고
    • Identifying genes for establishing a multigenic test for hepatocellular carcinoma surveillance in hepatitis C virus-positive cirrhotic patients
    • Archer KJ, Mas VR, David K, Maluf DG, Bornstein K, et al. (2009) Identifying genes for establishing a multigenic test for hepatocellular carcinoma surveillance in hepatitis C virus-positive cirrhotic patients. Cancer Epidemiol Biomarkers Prev 18: 2929-2932.
    • (2009) Cancer Epidemiol Biomarkers Prev , vol.18 , pp. 2929-2932
    • Archer, K.J.1    Mas, V.R.2    David, K.3    Maluf, D.G.4    Bornstein, K.5
  • 23
    • 77954364953 scopus 로고    scopus 로고
    • Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data
    • Essaghir A, Toffalini F, Knoops L, Kallin A, van Helden J, et al. (2010) Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data. Nucleic Acids Res 38: e120.
    • (2010) Nucleic Acids Res , vol.38
    • Essaghir, A.1    Toffalini, F.2    Knoops, L.3    Kallin, A.4    Van Helden, J.5
  • 24
    • 78650839537 scopus 로고    scopus 로고
    • TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information
    • Liu Q, Tan Y, Huang T, Ding G, Tu Z, et al. (2010) TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information. BMC Bioinformatics 11 Suppl 11: S5.
    • (2010) BMC Bioinformatics , vol.11 , Issue.SUPPL. 11
    • Liu, Q.1    Tan, Y.2    Huang, T.3    Ding, G.4    Tu, Z.5
  • 25
    • 27544454913 scopus 로고    scopus 로고
    • Identifying active transcription factors and kinases from expression data using pathway queries
    • DOI 10.1093/bioinformatics/bti1120
    • Sohler F, Zimmer R (2005) Identifying active transcription factors and kinases from expression data using pathway queries. Bioinformatics 21 Suppl 2: ii115-122. (Pubitemid 41535438)
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Sohler, F.1    Zimmer, R.2
  • 26
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • DOI 10.1038/30918
    • Watts DJ, Strogatz SH (1998) Collective dynamics of 'small-world' networks. Nature 393: 440-442. (Pubitemid 28292183)
    • (1998) Nature , vol.393 , Issue.6684 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 27
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Smyth GK (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3.
    • (2004) Stat Appl Genet Mol Biol , vol.3 , pp. 3
    • Smyth, G.K.1
  • 28
    • 34848897208 scopus 로고    scopus 로고
    • Novel serum biomarker candidates for liver fibrosis in hepatitis C patients
    • DOI 10.1373/clinchem.2007.089144
    • Gangadharan B, Antrobus R, Dwek RA, Zitzmann N (2007) Novel serum biomarker candidates for liver fibrosis in hepatitis C patients. Clin Chem 53: 1792-1799. (Pubitemid 47509672)
    • (2007) Clinical Chemistry , vol.53 , Issue.10 , pp. 1792-1799
    • Gangadharan, B.1    Antrobus, R.2    Dwek, R.A.3    Zitzmann, N.4
  • 29
    • 70350104779 scopus 로고    scopus 로고
    • SKP2 and CKS1 promote degradation of cell cycle regulators and are associated with hepatocellular carcinoma prognosis
    • Calvisi DF, Ladu S, Pinna F, Frau M, Tomasi ML, et al. (2009) SKP2 and CKS1 promote degradation of cell cycle regulators and are associated with hepatocellular carcinoma prognosis. Gastroenterology 137: 1816-1826 e1811-1810
    • (2009) Gastroenterology , vol.137
    • Calvisi, D.F.1    Ladu, S.2    Pinna, F.3    Frau, M.4    Tomasi, M.L.5
  • 30
    • 0036232664 scopus 로고    scopus 로고
    • Transcription factor EGR-1 inhibits growth of hepatocellular carcinoma and esophageal carcinoma cell lines
    • Hao MW, Liang YR, Liu YF, Liu L, Wu MY, et al. (2002) Transcription factor EGR-1 inhibits growth of hepatocellular carcinoma and esophageal carcinoma cell lines. World J Gastroenterol 8: 203-207. (Pubitemid 34414865)
    • (2002) World Journal of Gastroenterology , vol.8 , Issue.2 , pp. 203-207
    • Hao, M.-W.1    Liang, Y.-R.2    Liu, Y.-F.3    Liu, L.4    Wu, M.-Y.5    Yang, H.-X.6
  • 31
    • 58949102772 scopus 로고    scopus 로고
    • ZIC1 is downregulated through promoter hypermethylation in gastric cancer
    • Wang LJ, Jin HC, Wang X, Lam EK, Zhang JB, et al. (2009) ZIC1 is downregulated through promoter hypermethylation in gastric cancer. Biochem Biophys Res Commun 379: 959-963.
    • (2009) Biochem Biophys Res Commun , vol.379 , pp. 959-963
    • Wang, L.J.1    Jin, H.C.2    Wang, X.3    Lam, E.K.4    Zhang, J.B.5
  • 32
    • 79951922993 scopus 로고    scopus 로고
    • ZIC1 is downregulated through promoter hypermethylation, and functions as a tumor suppressor gene in colorectal cancer
    • Gan L, Chen S, Zhong J, Wang X, Lam EK, et al. (2011) ZIC1 is downregulated through promoter hypermethylation, and functions as a tumor suppressor gene in colorectal cancer. PLoS One 6: e16916.
    • (2011) PLoS One , vol.6
    • Gan, L.1    Chen, S.2    Zhong, J.3    Wang, X.4    Lam, E.K.5
  • 33
    • 80053334666 scopus 로고    scopus 로고
    • DNA methylation of ZIC1 and KLOTHO gene promoters in colorectal carcinomas and its clinicopathological significance
    • Gan LH, Pan J, Chen SJ, Zhong J, Wang LJ (2011) DNA methylation of ZIC1 and KLOTHO gene promoters in colorectal carcinomas and its clinicopathological significance. Zhejiang Da Xue Xue Bao Yi Xue Ban 40: 309-314.
    • (2011) Zhejiang Da Xue Xue Bao Yi Xue Ban , vol.40 , pp. 309-314
    • Gan, L.H.1    Pan, J.2    Chen, S.J.3    Zhong, J.4    Wang, L.J.5
  • 35
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang da W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
    • (2009) Nat Protoc , vol.4 , pp. 44-57
    • Huang Da, W.1    Sherman, B.T.2    Lempicki, R.A.3
  • 36
    • 33646141149 scopus 로고    scopus 로고
    • Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies
    • Hu Z, Willsky GR (2006) Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies. BMC Bioinformatics 7: 12.
    • (2006) BMC Bioinformatics , vol.7 , pp. 12
    • Hu, Z.1    Willsky, G.R.2
  • 37
    • 77953913791 scopus 로고    scopus 로고
    • From 'differential expression' to 'differential networking' - identification of dysfunctional regulatory networks in diseases
    • de la Fuente A (2010) From 'differential expression' to 'differential networking' - identification of dysfunctional regulatory networks in diseases. Trends Genet 26: 326-333.
    • (2010) Trends Genet , vol.26 , pp. 326-333
    • De La Fuente, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.