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Volumn , Issue , 2012, Pages 49-55

Identifying novel glioma associated pathways based on integrated 'omics' data

Author keywords

glioma; meta analysis; omics data; pathway enrichment analysis

Indexed keywords

DATA SETS; DIFFERENTIALLY EXPRESSED GENE; EXPERIMENTAL VERIFICATION; EXPRESSION PROFILE; GENE LEVELS; GLIOMA; HIGH THROUGHPUT TECHNOLOGY; META-ANALYSIS; MICROARRAY DATA SETS; MICRORNA EXPRESSION; OMICS DATA; PATHWAY ENRICHMENT ANALYSIS; SYSTEM LEVELS;

EID: 84868670234     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ISB.2012.6314112     Document Type: Conference Paper
Times cited : (1)

References (41)
  • 1
    • 13444282534 scopus 로고    scopus 로고
    • Outcome signature genes in breast cancer: Is there a unique set?
    • Jan
    • L. Ein-Dor, I. Kela, G. Getz, D. Givol, and E. Domany, "Outcome signature genes in breast cancer: is there a unique set?" Bioinformatics, vol. 21, (no. 2), pp. 171-8, Jan 2005.
    • (2005) Bioinformatics , vol.21 , Issue.2 , pp. 171-178
    • Ein-Dor, L.1    Kela, I.2    Getz, G.3    Givol, D.4    Domany, E.5
  • 2
    • 26444608611 scopus 로고    scopus 로고
    • Discovering statistically significant pathways in expression profiling studies
    • Sep
    • L. Tian, S. A. Greenberg, S. W. Kong, J. Altschuler, I. S. Kohane, and P. J. Park, "Discovering statistically significant pathways in expression profiling studies," Proc Natl Acad Sci U S A, vol. 102, (no.38), pp. 13544-9, Sep 2005.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , Issue.38 , pp. 13544-13549
    • Tian, L.1    Greenberg, S.A.2    Kong, S.W.3    Altschuler, J.4    Kohane, I.S.5    Park, P.J.6
  • 3
    • 77952844021 scopus 로고    scopus 로고
    • Meta-analysis for pathway enrichment analysis when combining multiple genomic studies
    • Apr
    • K. Shen, and G.C. Tseng, "Meta-analysis for pathway enrichment analysis when combining multiple genomic studies," Bioinformatics, vol. 26, (no.10), pp. 1316-23, Apr 2010.
    • (2010) Bioinformatics , vol.26 , Issue.10 , pp. 1316-1323
    • Shen, K.1    Tseng, G.C.2
  • 4
    • 84856088642 scopus 로고    scopus 로고
    • Downregulation of RKIP is associated with poor outcome and malignant progression in gliomas
    • Jan
    • O. Martinho, S. Granja, T. Jaraquemada, C. Caeiro, V. Miranda-Goncalves, M. Honavar, et al., "Downregulation of RKIP is associated with poor outcome and malignant progression in gliomas," PLoS One, vol. 7, (no. 1), e30769, Jan 2012
    • (2012) PLoS One , vol.7 , Issue.1
    • Martinho, O.1    Granja, S.2    Jaraquemada, T.3    Caeiro, C.4    Miranda-Goncalves, V.5    Honavar, M.6
  • 5
    • 4944255253 scopus 로고    scopus 로고
    • Genetic pathways to glioblastoma: A population-based study
    • Oct
    • H. Ohgaki, P. Dessen, B. Jourde, S. Horstmann, T. Nishikawa, P. L. Di Patre, et al., "Genetic pathways to glioblastoma: a population-based study," Cancer Res, vol. 64. (no. 19), pp. 6892-9, Oct 2004.
    • (2004) Cancer Res , vol.64 , Issue.19 , pp. 6892-6899
    • Ohgaki, H.1    Dessen, P.2    Jourde, B.3    Horstmann, S.4    Nishikawa, T.5    Di Patre, P.L.6
  • 6
    • 69249160573 scopus 로고    scopus 로고
    • Systems biology reveals new strategies for personalizing cancer medicine and confirms the role of PTEN in resistance to trastuzumab
    • Aug
    • D. Faratian, A. Goltsov, G. Lebedeva, A. Sorokin, S. Moodie, P. Mullen, et al., "Systems biology reveals new strategies for personalizing cancer medicine and confirms the role of PTEN in resistance to trastuzumab," Cancer Res, vol. 69, (no. 16), pp. 6713-20, Aug 2009.
    • (2009) Cancer Res , vol.69 , Issue.16 , pp. 6713-6720
    • Faratian, D.1    Goltsov, A.2    Lebedeva, G.3    Sorokin, A.4    Moodie, S.5    Mullen, P.6
  • 7
    • 13144305047 scopus 로고    scopus 로고
    • Systems biology for cancer
    • Jan
    • I.G. Khalil, and C. Hill, "Systems biology for cancer," Curr Opin Oncol, vol. 17, (no. 1), pp. 44-8, Jan 2005.
    • (2005) Curr Opin Oncol , vol.17 , Issue.1 , pp. 44-48
    • Khalil, I.G.1    Hill, C.2
  • 8
    • 33749999763 scopus 로고    scopus 로고
    • Group testing for pathway analysis improves comparability of different microarray datasets
    • Oct
    • T. Manoli, N. Gretz, H. J. Grone, M. Kenzelmann, R. Eils, and B. Brors, "Group testing for pathway analysis improves comparability of different microarray datasets," Bioinformatics, vol. 22, (no. 20), pp. 2500-6, Oct 2006.
    • (2006) Bioinformatics , vol.22 , Issue.20 , pp. 2500-2506
    • Manoli, T.1    Gretz, N.2    Grone, H.J.3    Kenzelmann, M.4    Eils, R.5    Brors, B.6
  • 9
    • 79959713125 scopus 로고    scopus 로고
    • Identifying novel prostate cancer associated pathways based on integrative microarray data analysis
    • Jun
    • Y. Wang, J. J. Chen, Q. H. Li, H. Y. Wang, G. Q. Liu, Q. Jing, et al., "Identifying novel prostate cancer associated pathways based on integrative microarray data analysis," Comput Biol Chem, vol. 35, (no. 3), pp. 151-8, Jun 2011.
    • (2011) Comput Biol Chem , vol.35 , Issue.3 , pp. 151-158
    • Wang, Y.1    Chen, J.J.2    Li, Q.H.3    Wang, H.Y.4    Liu, G.Q.5    Jing, Q.6
  • 10
    • 33751377929 scopus 로고    scopus 로고
    • COPA - Cancer outlier profile analysis
    • Dec
    • J.W. MacDonald, and D. Ghosh, "COPA - cancer outlier profile analysis," Bioinformatics, vol. 22, (no. 23), pp. 2950-1, Dec 2006.
    • (2006) Bioinformatics , vol.22 , Issue.23 , pp. 2950-2951
    • MacDonald, J.W.1    Ghosh, D.2
  • 11
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Oct
    • A. Subramanian, P. Tamayo, V. K. Mootha, S. Mukherjee, B. L. Ebert, M. A. Gillette, et al., "Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles," Proc Natl Acad Sci U S A, vol. 102, (no.43), pp.15545-50, Oct 2005.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , Issue.43 , pp. 15545-15550
    • Subramanian, A.1    Tamayo, P.2    Mootha, V.K.3    Mukherjee, S.4    Ebert, B.L.5    Gillette, M.A.6
  • 12
    • 66049085403 scopus 로고    scopus 로고
    • Glioma stem cell lines expanded in adherent culture have tumor-specific phenotypes and are suitable for chemical and genetic screens
    • Jun
    • S. M. Pollard, K. Yoshikawa, I. D. Clarke, D. Danovi, S. Stricker, R. Russell, et al., "Glioma stem cell lines expanded in adherent culture have tumor-specific phenotypes and are suitable for chemical and genetic screens," Cell Stem Cell, vol. 4, (no. 6), pp. 568-80, Jun 2009.
    • (2009) Cell Stem Cell , vol.4 , Issue.6 , pp. 568-580
    • Pollard, S.M.1    Yoshikawa, K.2    Clarke, I.D.3    Danovi, D.4    Stricker, S.5    Russell, R.6
  • 13
    • 71549126830 scopus 로고    scopus 로고
    • Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology
    • Dec
    • L. A. M. Gravendeel, M. C. M. Kouwenhoven, O. Gevaert, J. J. de Rooi, A. P. Stubbs, J. E. Duijm, et al., "Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology," Cancer Res, vol. 69, (no. 23), pp. 9065-72, Dec 2009.
    • (2009) Cancer Res , vol.69 , Issue.23 , pp. 9065-9072
    • Gravendeel, L.A.M.1    Kouwenhoven, M.C.M.2    Gevaert, O.3    De Rooi, J.J.4    Stubbs, A.P.5    Duijm, J.E.6
  • 14
    • 60549087374 scopus 로고    scopus 로고
    • Correlation analysis between single-nucleotide polymorphism and expression arrays in gliomas identifies potentially relevant target genes
    • Feb
    • Y. Kotliarov, S. Kotliarova, N. Charong, A. G. Li, J. Walling, E. Aquilanti, et al., "Correlation analysis between single-nucleotide polymorphism and expression arrays in gliomas identifies potentially relevant target genes," Cancer Res, vol. 69, (no. 4), pp. 1596-603, Feb 2009.
    • (2009) Cancer Res , vol.69 , Issue.4 , pp. 1596-1603
    • Kotliarov, Y.1    Kotliarova, S.2    Charong, N.3    Li, A.G.4    Walling, J.5    Aquilanti, E.6
  • 15
    • 3042694117 scopus 로고    scopus 로고
    • Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression
    • Jun
    • D. R. Rhodes, J. J. Yu, K. Shanker, N. Deshpande, R. Varambally, D. Ghosh, et al., "Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression," Proc Natl Acad Sci U S A, vol. 101, (no. 25), pp. 9309-14, Jun 2004.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , Issue.25 , pp. 9309-9314
    • Rhodes, D.R.1    Yu, J.J.2    Shanker, K.3    Deshpande, N.4    Varambally, R.5    Ghosh, D.6
  • 16
    • 39049097168 scopus 로고    scopus 로고
    • Median absolute deviation to improve hit selection for genome-scale RNAi screens
    • Feb
    • N. J. Chung, X. D. Zhang, A. Kreamer, L. Locco, P. F. Kuan, S. Bartz, et al., "Median absolute deviation to improve hit selection for genome-scale RNAi screens," J Biomol Screen, vol. 13, (no. 2), pp. 149-58, Feb 2008.
    • (2008) J Biomol Screen , vol.13 , Issue.2 , pp. 149-158
    • Chung, N.J.1    Zhang, X.D.2    Kreamer, A.3    Locco, L.4    Kuan, P.F.5    Bartz, S.6
  • 17
    • 0035687492 scopus 로고    scopus 로고
    • Identifying differentially expressed genes in cDNA microarray experiments
    • K. A. Baggerly, K. R. Coombes, K. R. Hess, D. N. Stivers, L. V. Abruzzo, and W. Zhang, "Identifying differentially expressed genes in cDNA microarray experiments," J Comput Biol, vol. 8, (no. 6), pp. 639-59, 2001.
    • (2001) J Comput Biol , vol.8 , Issue.6 , pp. 639-659
    • Baggerly, K.A.1    Coombes, K.R.2    Hess, K.R.3    Stivers, D.N.4    Abruzzo, L.V.5    Zhang, W.6
  • 18
    • 34648817312 scopus 로고    scopus 로고
    • Cancer outlier differential gene expression detection
    • Jul
    • B. Wu, "Cancer outlier differential gene expression detection," Biostatistics, vol. 8, (no. 3), pp. 566-75, Jul 2007.
    • (2007) Biostatistics , vol.8 , Issue.3 , pp. 566-575
    • Wu, B.1
  • 19
    • 45849096393 scopus 로고    scopus 로고
    • MOST: Detecting cancer differential gene expression
    • Jul
    • H. Lian, "MOST: detecting cancer differential gene expression," Biostatistics, vol. 9, (no. 3), pp. 411-8, Jul 2008.
    • (2008) Biostatistics , vol.9 , Issue.3 , pp. 411-418
    • Lian, H.1
  • 20
    • 18144365478 scopus 로고    scopus 로고
    • MicroRNA biogenesis and cancer
    • May
    • R. I. Gregory, and R. Shiekhattar, "MicroRNA biogenesis and cancer," Cancer Res, vol. 65, (no. 9), pp.3509-3512, May 2005.
    • (2005) Cancer Res , vol.65 , Issue.9 , pp. 3509-3512
    • Gregory, R.I.1    Shiekhattar, R.2
  • 21
    • 33750370444 scopus 로고    scopus 로고
    • MicroRNA signatures in human cancers
    • Nov
    • G. A. Calin, and C. M. Croce, "MicroRNA signatures in human cancers," Nat Rev Cancer. vol. 6, (no.11), pp.857-866, Nov 2006.
    • (2006) Nat Rev Cancer , vol.6 , Issue.11 , pp. 857-866
    • Calin, G.A.1    Croce, C.M.2
  • 22
    • 33645294070 scopus 로고    scopus 로고
    • Oncomirs - MicroRNAs with a role in cancer
    • Apr
    • A. Esquela-Kerscher, and F. J. Slack, "Oncomirs - microRNAs with a role in cancer," Nat Rev Cancer. vol. 6, (no. 4), pp.259-269, Apr 2006.
    • (2006) Nat Rev Cancer , vol.6 , Issue.4 , pp. 259-269
    • Esquela-Kerscher, A.1    Slack, F.J.2
  • 23
    • 77349125856 scopus 로고    scopus 로고
    • MicroRNA-21 inhibitor sensitizes human glioblastoma cells U251 (PTEN-mutant) and LN229 (PTEN-wild type) to taxol
    • Jan
    • Y. Ren, X. Zhou, M. Mei, X. B. Yuan, L. Han, G. X. Wang, et al., "MicroRNA-21 inhibitor sensitizes human glioblastoma cells U251 (PTEN-mutant) and LN229 (PTEN-wild type) to taxol," BMC Cancer, vol. 10, pp. 27, Jan 2010.
    • (2010) BMC Cancer , vol.10 , pp. 27
    • Ren, Y.1    Zhou, X.2    Mei, M.3    Yuan, X.B.4    Han, L.5    Wang, G.X.6
  • 25
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • Oct
    • M. Rehmsmeier, P. Steffen, M. Hochsmann, and R. Giegerich, "Fast and effective prediction of microRNA/target duplexes," RNA, vol. 10, (no. 10), pp. 1507-17, Oct 2004.
    • (2004) RNA , vol.10 , Issue.10 , pp. 1507-1517
    • Rehmsmeier, M.1    Steffen, P.2    Hochsmann, M.3    Giegerich, R.4
  • 26
    • 77952671774 scopus 로고    scopus 로고
    • TargetSpy: A supervised machine learning approach for microRNA target prediction
    • May
    • M. Sturm, M. Hackenberg, D. Langenberger, and D. Frishman, "TargetSpy: a supervised machine learning approach for microRNA target prediction," BMC Bioinformatics, vol. 11, pp. 292, May 2010.
    • (2010) BMC Bioinformatics , vol.11 , pp. 292
    • Sturm, M.1    Hackenberg, M.2    Langenberger, D.3    Frishman, D.4
  • 27
    • 84864956117 scopus 로고    scopus 로고
    • Normalization, bias correction, and peak calling for ChIP-seq
    • Mar
    • A. Diaz, K. Park, D. A. Lim, and J. S. Song, "Normalization, bias correction, and peak calling for ChIP-seq," Stat Appl Genet Mol Biol, vol. 11, (no. 3), Mar 2012.
    • (2012) Stat Appl Genet Mol Biol , vol.11 , Issue.3
    • Diaz, A.1    Park, K.2    Lim, D.A.3    Song, J.S.4
  • 28
    • 34250159524 scopus 로고    scopus 로고
    • Genomewide mapping of in vivo protein-DNA interactions
    • Jun
    • D. S. Johnson, A. Mortazavi, R. M. Myers, and B. Wold, "Genomewide mapping of in vivo protein-DNA interactions," Science, 316, pp.1497-1502, Jun 2007.
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 29
    • 78650857350 scopus 로고    scopus 로고
    • The SOX2 response program in glioblastoma multiforme: An integrated ChIP-seq, expression microarray, and microRNA analysis
    • Jan
    • X. F. Fang, J. G. Yoon, L. S. Li, W. Yu, J. F. Shao, D. S. Hua, et al., "The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis," BMC Genomics, vol. 12, pp. 11, Jan 2011.
    • (2011) BMC Genomics , vol.12 , pp. 11
    • Fang, X.F.1    Yoon, J.G.2    Li, L.S.3    Yu, W.4    Shao, J.F.5    Hua, D.S.6
  • 31
    • 52649132425 scopus 로고    scopus 로고
    • Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
    • R. Jothi, S. Cuddapah, A. Barski, K. Cui, K. Zhao, "Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data," Nucleic Acids Res, vol. 36, (no. 16), pp. 5221-31, 2008.
    • (2008) Nucleic Acids Res , vol.36 , Issue.16 , pp. 5221-5231
    • Jothi, R.1    Cuddapah, S.2    Barski, A.3    Cui, K.4    Zhao, K.5
  • 32
    • 84868286477 scopus 로고    scopus 로고
    • Comparative microarray data analysis for the expression of genes in the pathway of glioma
    • Jun
    • P. Katara, S. Neeru, S. Sugandha, K. Indu, K. Akansha, K. Lalima, and S. Vinay, "Comparative microarray data analysis for the expression of genes in the pathway of glioma," Bioinformation, vol. 5, (no. 1), pp. 31-4, Jun 2010.
    • (2010) Bioinformation , vol.5 , Issue.1 , pp. 31-34
    • Katara, P.1    Neeru, S.2    Sugandha, S.3    Indu, K.4    Akansha, K.5    Lalima, K.6    Vinay, S.7
  • 33
    • 84857801483 scopus 로고    scopus 로고
    • cDNA microarray analysis of gene expression in parthenotes and in vitro produced buffalo embryos
    • Apr
    • A. S. Abdoon, N. Ghanem, O. M. Kandil, A. Gad, K. Schellander, and D. Tesfaye, "cDNA microarray analysis of gene expression in parthenotes and in vitro produced buffalo embryos," Theriogenology, vol. 77, (no. 6), pp. 1240-51, Apr 2012.
    • (2012) Theriogenology , vol.77 , Issue.6 , pp. 1240-1251
    • Abdoon, A.S.1    Ghanem, N.2    Kandil, O.M.3    Gad, A.4    Schellander, K.5    Tesfaye, D.6
  • 34
    • 71549126830 scopus 로고    scopus 로고
    • Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology
    • Dec
    • L. A. M. Gravendeel, M. C. M. Kouwenhoven, O. Gevaert, J. J. de Rooi, A. P. Stubbs, J. E. Duijm, et al., "Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology," Cancer Res, vol. 69, (no. 23), pp. 9065-72, Dec 2009.
    • (2009) Cancer Res , vol.69 , Issue.23 , pp. 9065-9072
    • Gravendeel, L.A.M.1    Kouwenhoven, M.C.M.2    Gevaert, O.3    De Rooi, J.J.4    Stubbs, A.P.5    Duijm, J.E.6
  • 35
    • 70350099256 scopus 로고    scopus 로고
    • Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers
    • Sep
    • J. M. Dreyfuss, M. D. Johnson, and P. J. Park, "Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers," Mol Cancer, vol. 8, pp. 71, Sep 2009.
    • (2009) Mol Cancer , vol.8 , pp. 71
    • Dreyfuss, J.M.1    Johnson, M.D.2    Park, P.J.3
  • 36
    • 77950461380 scopus 로고    scopus 로고
    • Identification of the role of Smad interacting protein 1 (SIP1) in glioma
    • Apr
    • M. Xia, M. H. Hu, J. Wang, Y. J. Xu, X. B. Chen, Y. D. Ma, et al., "Identification of the role of Smad interacting protein 1 (SIP1) in glioma," J Neurooncol, vol. 97, (no. 2), pp. 225-32, Apr 2010.
    • (2010) J Neurooncol , vol.97 , Issue.2 , pp. 225-232
    • Xia, M.1    Hu, M.H.2    Wang, J.3    Xu, Y.J.4    Chen, X.B.5    Ma, Y.D.6
  • 37
    • 63249123273 scopus 로고    scopus 로고
    • TGF-beta increases glioma-initiating cell self-renewal through the induction of LIF in human glioblastoma
    • Apr
    • S. Penuelas, J. Anido, R. M. Prieto-Sanchez, G. Folch, I. Barba, I. Cuartas, et al., "TGF-beta increases glioma-initiating cell self- renewal through the induction of LIF in human glioblastoma," Cancer Cell, vol. 15, (no. 4), pp. 315-27, Apr 2009.
    • (2009) Cancer Cell , vol.15 , Issue.4 , pp. 315-327
    • Penuelas, S.1    Anido, J.2    Prieto-Sanchez, R.M.3    Folch, G.4    Barba, I.5    Cuartas, I.6
  • 38
    • 0029662342 scopus 로고    scopus 로고
    • Rel/NFkappaB/ IkappaB proteins and cancer
    • Oct
    • T. D. Gilmore, M. Koedood, K. A. Piffat, and D. W. White, "Rel/NFkappaB/ IkappaB proteins and cancer," Oncogene, vol. 13, (no. 7), pp. 1367-78, Oct 1996.
    • (1996) Oncogene , vol.13 , Issue.7 , pp. 1367-1378
    • Gilmore, T.D.1    Koedood, M.2    Piffat, K.A.3    White, D.W.4
  • 39
    • 34250898562 scopus 로고    scopus 로고
    • NF-kappaB as a potential molecular target for cancer therapy
    • C. H. Lee, Y. T. Jeon, S. H. Kim, and Y. S. Song, "NF-kappaB as a potential molecular target for cancer therapy," Biofactors, vol. 29, (no. 1), pp. 19-35, 2007.
    • (2007) Biofactors , vol.29 , Issue.1 , pp. 19-35
    • Lee, C.H.1    Jeon, Y.T.2    Kim, S.H.3    Song, Y.S.4
  • 40
  • 41
    • 77954114174 scopus 로고    scopus 로고
    • Overexpression of candidate tumor suppressor ECRG4 inhibits glioma proliferation and invasion
    • Jul
    • W. Li, X. R. Liu, B. Zhang, D. X. Qi, L. H. Zhang, Y. H. Jin, et al., "Overexpression of candidate tumor suppressor ECRG4 inhibits glioma proliferation and invasion," J Exp Clin Cancer Res, vol. 29, pp. 89, Jul 2010.
    • (2010) J Exp Clin Cancer Res , vol.29 , pp. 89
    • Li, W.1    Liu, X.R.2    Zhang, B.3    Qi, D.X.4    Zhang, L.H.5    Jin, Y.H.6


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