메뉴 건너뛰기




Volumn 22, Issue 5, 2015, Pages 278-284

Identification of commonly dysregulated genes in colorectal cancer by integrating analysis of RNA-Seq data and qRT-PCR validation

Author keywords

[No Author keywords available]

Indexed keywords

ADAMTS6 GENE; ADULT; AGED; ARTICLE; CARCINOGENESIS; CLINICAL ARTICLE; COLON ADENOCARCINOMA; COLON CANCER; CONTROLLED STUDY; DNAH5 GENE; FOXD4L4 GENE; GENE; GENE CONTROL; GENE FUNCTION; GENE IDENTIFICATION; HUMAN; MALE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RECTUM CANCER; RECTUM CARCINOMA; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; SIM2 GENE; COLORECTAL TUMOR; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; PROCEDURES; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY; STANDARDS;

EID: 84929288750     PISSN: 09291903     EISSN: 14765500     Source Type: Journal    
DOI: 10.1038/cgt.2015.20     Document Type: Article
Times cited : (31)

References (41)
  • 2
  • 3
    • 80053385552 scopus 로고    scopus 로고
    • Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion
    • Bass AJ, Lawrence MS, Brace LE, Ramos AH, Drier Y, Cibulskis K et al. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat Genet 2011;43:964-968.
    • (2011) Nat Genet , vol.43 , pp. 964-968
    • Bass, A.J.1    Lawrence, M.S.2    Brace, L.E.3    Ramos, A.H.4    Drier, Y.5    Cibulskis, K.6
  • 4
    • 10344260184 scopus 로고    scopus 로고
    • CpG island methylator phenotype in cancer
    • Issa JP. CpG island methylator phenotype in cancer. Nat Rev Cancer 2004;4:988-993.
    • (2004) Nat Rev Cancer , vol.4 , pp. 988-993
    • Issa, J.P.1
  • 5
    • 72449176846 scopus 로고    scopus 로고
    • Molecular origins of cancer: Molecular basis of colorectal cancer
    • Markowitz SD, Bertagnolli MM. Molecular origins of cancer: Molecular basis of colorectal cancer. N Engl J Med 2009;361:2449-2460.
    • (2009) N Engl J Med , vol.361 , pp. 2449-2460
    • Markowitz, S.D.1    Bertagnolli, M.M.2
  • 6
    • 84905005712 scopus 로고    scopus 로고
    • Focus on genetic and epigenetic events of colorectal cancer pathogenesis: Implications for molecular diagnosis
    • Zoratto F, Rossi L, Verrico M, Papa A, Basso E, Zullo A et al. Focus on genetic and epigenetic events of colorectal cancer pathogenesis: implications for molecular diagnosis. Tumour Biol 2014;35:6195-6206.
    • (2014) Tumour Biol , vol.35 , pp. 6195-6206
    • Zoratto, F.1    Rossi, L.2    Verrico, M.3    Papa, A.4    Basso, E.5    Zullo, A.6
  • 8
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008;18:1509-1517.
    • (2008) Genome Res , vol.18 , pp. 1509-1517
    • Marioni, J.C.1    Mason, C.E.2    Mane, S.M.3    Stephens, M.4    Gilad, Y.5
  • 9
    • 78650539308 scopus 로고    scopus 로고
    • From RNA-seq reads to differential expression results
    • Oshlack A, Robinson MD, Young MD. From RNA-seq reads to differential expression results. Genome Biol 2010;11:220.
    • (2010) Genome Biol , vol.11 , pp. 220
    • Oshlack, A.1    Robinson, M.D.2    Young, M.D.3
  • 10
    • 84889671824 scopus 로고    scopus 로고
    • Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5 -Aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets
    • Xu X, Zhang Y, Williams J, Antoniou E, McCombie WR, Wu S et al. Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5 -Aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets. BMC Bioinformatics 2013;14(Suppl 9):S1.
    • (2013) BMC Bioinformatics , vol.14 , pp. S1
    • Xu, X.1    Zhang, Y.2    Williams, J.3    Antoniou, E.4    McCombie, W.R.5    Wu, S.6
  • 12
    • 84930705383 scopus 로고    scopus 로고
    • Microarray meta -Analysis: From data to expression to biological relationships
    • Springer, Vienna, Austria
    • Feichtinger J, Thallinger GG, McFarlane RJ, Larcombe LD. Microarray meta -Analysis: From data to expression to biological relationships. In: Computational Medicine. Springer, Vienna, Austria 2012, pp 59-77.
    • (2012) Computational Medicine , pp. 59-77
    • Feichtinger, J.1    Thallinger, G.G.2    McFarlane, R.J.3    Larcombe, L.D.4
  • 13
    • 53149135477 scopus 로고    scopus 로고
    • Key issues in conducting a metaanalysis of gene expression microarray datasets
    • Ramasamy A, Mondry A, Holmes CC, Altman DG. Key issues in conducting a metaanalysis of gene expression microarray datasets. PLoS Med 2008;5:e184.
    • (2008) PLoS Med , vol.5 , pp. e184
    • Ramasamy, A.1    Mondry, A.2    Holmes, C.C.3    Altman, D.G.4
  • 14
    • 84899073808 scopus 로고    scopus 로고
    • Differential meta -Analysis of RNA-seq data from multiple studies
    • Rau A, Marot G, Jaffrezic F. Differential meta -Analysis of RNA-seq data from multiple studies. BMC Bioinformatics 2014;15:91.
    • (2014) BMC Bioinformatics , vol.15 , pp. 91
    • Rau, A.1    Marot, G.2    Jaffrezic, F.3
  • 15
    • 84876100832 scopus 로고    scopus 로고
    • Systems biology approach to identify gene network signatures for colorectal cancer
    • Sonachalam M, Shen J, Huang H, Wu X. Systems biology approach to identify gene network signatures for colorectal cancer. Front Genet 2012;3:80.
    • (2012) Front Genet , vol.3 , pp. 80
    • Sonachalam, M.1    Shen, J.2    Huang, H.3    Wu, X.4
  • 16
    • 84864190709 scopus 로고    scopus 로고
    • A network-based gene expression signature informs prognosis and treatment for colorectal cancer patients
    • Shi M, Beauchamp RD, Zhang B. A network-based gene expression signature informs prognosis and treatment for colorectal cancer patients. PloS One 2012;7:e41292.
    • (2012) PloS One , vol.7 , pp. e41292
    • Shi, M.1    Beauchamp, R.D.2    Zhang, B.3
  • 18
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
    • Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010;28:511-515.
    • (2010) Nat Biotechnol , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.A.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    Van Baren, M.J.6
  • 19
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009;25:1105-1111.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 20
    • 33747885673 scopus 로고    scopus 로고
    • Bioconductor: An open source framework for bioinformatics and computational biology
    • Reimers M, Carey VJ. Bioconductor: an open source framework for bioinformatics and computational biology. Method Enzymol 2006;411:119-134.
    • (2006) Method Enzymol , vol.411 , pp. 119-134
    • Reimers, M.1    Carey, V.J.2
  • 21
    • 84864494098 scopus 로고    scopus 로고
    • GeneCodis3: A nonredundant and modular enrichment analysis tool for functional genomics
    • Tabas-Madrid D, Nogales-Cadenas R, Pascual-Montano A. GeneCodis3: a nonredundant and modular enrichment analysis tool for functional genomics. Nucleic Acid Res 2012;40:W478-W483.
    • (2012) Nucleic Acid Res , vol.40 , pp. W478-W483
    • Tabas-Madrid, D.1    Nogales-Cadenas, R.2    Pascual-Montano, A.3
  • 24
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software environment for integrated models of biomolecular interaction networks
    • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome 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    Wang, J.T.5    Ramage, D.6
  • 26
    • 84874840067 scopus 로고    scopus 로고
    • High-mobility group box 2 (HMGB2) modulates radioresponse and is downregulated by p53 in colorectal cancer cell
    • Shin YJ, Kim MS, Kim MS, Lee J, Kang M, Jeong JH. High-mobility group box 2 (HMGB2) modulates radioresponse and is downregulated by p53 in colorectal cancer cell. Cancer Biol Ther 2013;14:213-221.
    • (2013) Cancer Biol Ther , vol.14 , pp. 213-221
    • Shin, Y.J.1    Kim, M.S.2    Kim, M.S.3    Lee, J.4    Kang, M.5    Jeong, J.H.6
  • 27
    • 84864436663 scopus 로고    scopus 로고
    • A comprehensive characterization of genome-wide copy number aberrations in colorectal cancer reveals novel oncogenes and patterns of alterations
    • Xie T, D'Ario G, Lamb JR, Martin E, Wang K, Tejpar S et al. A comprehensive characterization of genome-wide copy number aberrations in colorectal cancer reveals novel oncogenes and patterns of alterations. PloS One 2012;7:e42001.
    • (2012) PloS One , vol.7 , pp. e42001
    • Xie, T.1    D'Ario, G.2    Lamb, J.R.3    Martin, E.4    Wang, K.5    Tejpar, S.6
  • 29
    • 34447574683 scopus 로고    scopus 로고
    • Differential expression in normal -Adenoma-carcinoma sequence suggests complex molecular carcinogenesis in colon
    • Lee S, Bang S, Song K, Lee I. Differential expression in normal -Adenoma-carcinoma sequence suggests complex molecular carcinogenesis in colon. Oncol Rep 2006;16:747-754.
    • (2006) Oncol Rep , vol.16 , pp. 747-754
    • Lee, S.1    Bang, S.2    Song, K.3    Lee, I.4
  • 30
    • 84899486093 scopus 로고    scopus 로고
    • Insulinlike growth factor 2 mRNA-binding protein 1 (IGF2BP1) is an important protumorigenic factor in hepatocellular carcinoma
    • Gutschner T, Hammerle M, Pazaitis N, Bley N, Fiskin E, Uckelmann H et al. Insulinlike growth factor 2 mRNA-binding protein 1 (IGF2BP1) is an important protumorigenic factor in hepatocellular carcinoma. Hepatology 2014;59:1900-1911.
    • (2014) Hepatology , vol.59 , pp. 1900-1911
    • Gutschner, T.1    Hammerle, M.2    Pazaitis, N.3    Bley, N.4    Fiskin, E.5    Uckelmann, H.6
  • 31
    • 0037447077 scopus 로고    scopus 로고
    • Identification of Down's syndrome critical locus gene SIM2-s as a drug therapy target for solid tumors
    • DeYoung MP, Tress M, Narayanan R. Identification of Down's syndrome critical locus gene SIM2-s as a drug therapy target for solid tumors. Proc Natl Acad Sci USA 2003;100:4760-4765.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 4760-4765
    • DeYoung, M.P.1    Tress, M.2    Narayanan, R.3
  • 32
    • 49649113927 scopus 로고    scopus 로고
    • Characterization of an acrosome protein VAD1.2/AEP2 which is differentially expressed in spermatogenesis
    • Lee KF, Tam YT, Zuo Y, Cheong AW, Pang RT, Lee NP et al. Characterization of an acrosome protein VAD1.2/AEP2 which is differentially expressed in spermatogenesis. Mol Hum Reprod 2008;14:465-474.
    • (2008) Mol Hum Reprod , vol.14 , pp. 465-474
    • Lee, K.F.1    Tam, Y.T.2    Zuo, Y.3    Cheong, A.W.4    Pang, R.T.5    Lee, N.P.6
  • 33
    • 79955146210 scopus 로고    scopus 로고
    • Gene expression profile of ADAMs and ADAMTSs metalloproteinases in normal and malignant plasma cells and in the bone marrow environment
    • e8
    • Bret C, Hose D, Reme T, Kassambara A, Seckinger A, Meissner T et al. Gene expression profile of ADAMs and ADAMTSs metalloproteinases in normal and malignant plasma cells and in the bone marrow environment. Exp Hematol 2011;39:546-557 e8.
    • (2011) Exp Hematol , vol.39 , pp. 546-557
    • Bret, C.1    Hose, D.2    Reme, T.3    Kassambara, A.4    Seckinger, A.5    Meissner, T.6
  • 34
  • 35
    • 84155174835 scopus 로고    scopus 로고
    • Differences in gene expression profiles and carcinogenesis pathways between colon and rectal cancer
    • Li JN, Zhao L, Wu J, Wu B, Yang H, Zhang HH et al. Differences in gene expression profiles and carcinogenesis pathways between colon and rectal cancer. J Digestive Dis 2012;13:24-32.
    • (2012) J Digestive Dis , vol.13 , pp. 24-32
    • Li, J.N.1    Zhao, L.2    Wu, J.3    Wu, B.4    Yang, H.5    Zhang, H.H.6
  • 38
    • 84864544413 scopus 로고    scopus 로고
    • Intraclonal heterogeneity and distinct molecular mechanisms characterize the development of t (4;14) and t (11;14) myeloma
    • Walker BA, Wardell CP, Melchor L, Hulkki S, Potter NE, Johnson DC et al. Intraclonal heterogeneity and distinct molecular mechanisms characterize the development of t (4;14) and t (11;14) myeloma. Blood 2012;120:1077-1086.
    • (2012) Blood , vol.120 , pp. 1077-1086
    • Walker, B.A.1    Wardell, C.P.2    Melchor, L.3    Hulkki, S.4    Potter, N.E.5    Johnson, D.C.6
  • 39
    • 75949126139 scopus 로고    scopus 로고
    • AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia
    • Lin C, Smith ER, Takahashi H, Lai KC, Martin-Brown S, Florens L et al. AFF4, a component of the ELL/P-TEFb elongation complex and a shared subunit of MLL chimeras, can link transcription elongation to leukemia. Mol Cell 2010;37:429-437.
    • (2010) Mol Cell , vol.37 , pp. 429-437
    • Lin, C.1    Smith, E.R.2    Takahashi, H.3    Lai, K.C.4    Martin-Brown, S.5    Florens, L.6
  • 40
    • 79951762304 scopus 로고    scopus 로고
    • A mutation in the type II hair keratin KRT86 gene in a Han family with monilethrix
    • Wu J, Lin Y, Xu W, Li Z, Fan W. A mutation in the type II hair keratin KRT86 gene in a Han family with monilethrix. J Biomed Res 2011;25:49-55.
    • (2011) J Biomed Res , vol.25 , pp. 49-55
    • Wu, J.1    Lin, Y.2    Xu, W.3    Li, Z.4    Fan, W.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.