메뉴 건너뛰기




Volumn 35, Issue 3, 2015, Pages 237-244

Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes

Author keywords

Clinical outcomes; Gene regulation; Predictions; SNP

Indexed keywords

BONE MORPHOGENETIC PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

EID: 84937975666     PISSN: 02709295     EISSN: 15584488     Source Type: Journal    
DOI: 10.1016/j.semnephrol.2015.04.003     Document Type: Review
Times cited : (1)

References (35)
  • 1
    • 52949110955 scopus 로고    scopus 로고
    • MYH9 is a major-effect risk gene for focal segmental glomerulosclerosis
    • Kopp J.B., Smith M.W., Nelson G.W., et al. MYH9 is a major-effect risk gene for focal segmental glomerulosclerosis. Nat Genet 2008, 40:1175-1184.
    • (2008) Nat Genet , vol.40 , pp. 1175-1184
    • Kopp, J.B.1    Smith, M.W.2    Nelson, G.W.3
  • 2
    • 52949092735 scopus 로고    scopus 로고
    • MYH9 is associated with nondiabetic end-stage renal disease in African Americans
    • Kao W.H., Klag M.J., Meoni L.A., et al. MYH9 is associated with nondiabetic end-stage renal disease in African Americans. Nat Genet 2008, 40:1185-1192.
    • (2008) Nat Genet , vol.40 , pp. 1185-1192
    • Kao, W.H.1    Klag, M.J.2    Meoni, L.A.3
  • 3
    • 77955646179 scopus 로고    scopus 로고
    • Association of trypanolytic ApoL1 variants with kidney disease in African Americans
    • Genovese G., Friedman D.J., Ross M.D., et al. Association of trypanolytic ApoL1 variants with kidney disease in African Americans. Science 2010, 329:841-845.
    • (2010) Science , vol.329 , pp. 841-845
    • Genovese, G.1    Friedman, D.J.2    Ross, M.D.3
  • 4
    • 66649089156 scopus 로고    scopus 로고
    • Genome-wide association scan for diabetic nephropathy susceptibility genes in type 1 diabetes
    • Pezzolesi M.G., Poznik G.D., Mychaleckyj J.C., et al. Genome-wide association scan for diabetic nephropathy susceptibility genes in type 1 diabetes. Diabetes 2009, 58:1403-1410.
    • (2009) Diabetes , vol.58 , pp. 1403-1410
    • Pezzolesi, M.G.1    Poznik, G.D.2    Mychaleckyj, J.C.3
  • 5
    • 84872170007 scopus 로고    scopus 로고
    • Searching for transcription factor binding sites in vector spaces
    • Lee C., Huang C.H. Searching for transcription factor binding sites in vector spaces. BMC Bioinformatics 2012, 13:215.
    • (2012) BMC Bioinformatics , vol.13 , pp. 215
    • Lee, C.1    Huang, C.H.2
  • 6
    • 0041853625 scopus 로고    scopus 로고
    • MATCH: a tool for searching transcription factor binding sites in DNA sequences
    • Kel A.E., Gossling E., Reuter I., et al. MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 2003, 31:3576-3579.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3576-3579
    • Kel, A.E.1    Gossling, E.2    Reuter, I.3
  • 7
    • 0032919364 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • Ogata H., Goto S., Sato K., et al. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 1999, 27:29-34.
    • (1999) Nucleic Acids Res , vol.27 , pp. 29-34
    • Ogata, H.1    Goto, S.2    Sato, K.3
  • 8
    • 84891774001 scopus 로고    scopus 로고
    • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
    • Caspi R., Altman T., Billington R., et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 2014, 42:D459-D471.
    • (2014) Nucleic Acids Res , vol.42 , pp. D459-D471
    • Caspi, R.1    Altman, T.2    Billington, R.3
  • 9
    • 84866931187 scopus 로고    scopus 로고
    • Tissue-specific functional networks for prioritizing phenotype and disease genes
    • Guan Y., Gorenshteyn D., Burmeister M., et al. Tissue-specific functional networks for prioritizing phenotype and disease genes. PLoS Comput Biol 2012, 8:e1002694.
    • (2012) PLoS Comput Biol , vol.8
    • Guan, Y.1    Gorenshteyn, D.2    Burmeister, M.3
  • 10
    • 84864455716 scopus 로고    scopus 로고
    • IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks
    • Wong A.K., Park C.Y., Greene C.S., et al. IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res 2012, 40:W484-W490.
    • (2012) Nucleic Acids Res , vol.40 , pp. W484-W490
    • Wong, A.K.1    Park, C.Y.2    Greene, C.S.3
  • 11
    • 52949087576 scopus 로고    scopus 로고
    • A genomewide functional network for the laboratory mouse
    • Guan Y., Myers C.L., Lu R., et al. A genomewide functional network for the laboratory mouse. PLoS Comput Biol 2008, 4:e1000165.
    • (2008) PLoS Comput Biol , vol.4
    • Guan, Y.1    Myers, C.L.2    Lu, R.3
  • 12
    • 84930731991 scopus 로고    scopus 로고
    • Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation
    • Zhu F., Shi L., Li H., et al. Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation. Bioinformatics 2014, 30:3325-3333.
    • (2014) Bioinformatics , vol.30 , pp. 3325-3333
    • Zhu, F.1    Shi, L.2    Li, H.3
  • 13
    • 84875968177 scopus 로고    scopus 로고
    • Functional knowledge transfer for high-accuracy prediction of under-studied biological processes
    • Park C.Y., Wong A.K., Greene C.S., et al. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes. PLoS Comput Biol 2013, 9:e1002957.
    • (2013) PLoS Comput Biol , vol.9
    • Park, C.Y.1    Wong, A.K.2    Greene, C.S.3
  • 14
    • 84883690005 scopus 로고    scopus 로고
    • From single nucleotide polymorphism to transcriptional mechanism: a model for FRMD3 in diabetic nephropathy
    • Martini S., Nair V., Patel S.R., et al. From single nucleotide polymorphism to transcriptional mechanism: a model for FRMD3 in diabetic nephropathy. Diabetes 2013, 62:2605-2612.
    • (2013) Diabetes , vol.62 , pp. 2605-2612
    • Martini, S.1    Nair, V.2    Patel, S.R.3
  • 15
    • 84924009565 scopus 로고    scopus 로고
    • Integrative biology identifies shared transcriptional networks in CKD
    • Martini S., Nair V., Keller B.J., et al. Integrative biology identifies shared transcriptional networks in CKD. J Am Soc Nephrol 2014, 25:2559-2572.
    • (2014) J Am Soc Nephrol , vol.25 , pp. 2559-2572
    • Martini, S.1    Nair, V.2    Keller, B.J.3
  • 16
    • 78649680792 scopus 로고    scopus 로고
    • Functional genomics complements quantitative genetics in identifying disease-gene associations
    • Guan Y., Ackert-Bicknell C.L., Kell B., Troyanskaya O.G., Hibbs M.A. Functional genomics complements quantitative genetics in identifying disease-gene associations. PLoS Comput Biol 2010, 6:e1000991.
    • (2010) PLoS Comput Biol , vol.6
    • Guan, Y.1    Ackert-Bicknell, C.L.2    Kell, B.3    Troyanskaya, O.G.4    Hibbs, M.A.5
  • 17
    • 67650895858 scopus 로고    scopus 로고
    • Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans
    • Chikina M.D., Huttenhower C., Murphy C.T., Troyanskaya O.G. Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans. PLoS Comput Biol 2009, 5:e1000417.
    • (2009) PLoS Comput Biol , vol.5
    • Chikina, M.D.1    Huttenhower, C.2    Murphy, C.T.3    Troyanskaya, O.G.4
  • 18
    • 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., 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
  • 19
  • 20
    • 84914170768 scopus 로고    scopus 로고
    • Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence
    • Li H.D., Menon R., Omenn G.S., Guan Y. Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence. Proteomics 2014, 14:2709-2718.
    • (2014) Proteomics , vol.14 , pp. 2709-2718
    • Li, H.D.1    Menon, R.2    Omenn, G.S.3    Guan, Y.4
  • 21
    • 84904756759 scopus 로고    scopus 로고
    • The emerging era of genomic data integration for analyzing splice isoform function
    • Li H.D., Menon R., Omenn G.S., Guan Y. The emerging era of genomic data integration for analyzing splice isoform function. Trends Genet 2014, 30:340-347.
    • (2014) Trends Genet , vol.30 , pp. 340-347
    • Li, H.D.1    Menon, R.2    Omenn, G.S.3    Guan, Y.4
  • 22
    • 84904434702 scopus 로고    scopus 로고
    • A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines
    • Omenn G.S., Guan Y., Menon R. A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines. J Proteomics 2014, 107:103-112.
    • (2014) J Proteomics , vol.107 , pp. 103-112
    • Omenn, G.S.1    Guan, Y.2    Menon, R.3
  • 23
    • 84888234617 scopus 로고    scopus 로고
    • Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data
    • Eksi R., Li H.D., Menon R., et al. Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data. PLoS Comput Biol 2013, 9:e1003314.
    • (2013) PLoS Comput Biol , vol.9
    • Eksi, R.1    Li, H.D.2    Menon, R.3
  • 24
    • 47549108100 scopus 로고    scopus 로고
    • Predicting gene function in a hierarchical context with an ensemble of classifiers
    • Guan Y., Myers C.L., Hess D.C., et al. Predicting gene function in a hierarchical context with an ensemble of classifiers. Genome Biol 2008, 9:S3.
    • (2008) Genome Biol , vol.9
    • Guan, Y.1    Myers, C.L.2    Hess, D.C.3
  • 25
    • 47549116997 scopus 로고    scopus 로고
    • A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
    • Pena-Castillo L., Tasan M., Myers C.L., et al. A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol 2008, 9(Suppl 1):S2.
    • (2008) Genome Biol , vol.9
    • Pena-Castillo, L.1    Tasan, M.2    Myers, C.L.3
  • 26
    • 84937992293 scopus 로고    scopus 로고
    • Available from: (Last accessed 03/17/2015). DREAM CHALLENGES-powered by Sage Bionetworks.
    • Available from: (Last accessed 03/17/2015). DREAM CHALLENGES-powered by Sage Bionetworks. http://dreamchallenges.org/.
  • 27
    • 84937992294 scopus 로고    scopus 로고
    • Rheumatoid arthritis responder challenge
    • Available from: (Last accessed 03/17/2015).
    • Mangravite L, Sieberts S. Rheumatoid arthritis responder challenge. Available from: (Last accessed 03/17/2015). https://www.synapse.org/#!Synapse:syn1734172/wiki/65264.
    • Mangravite, L.1    Sieberts, S.2
  • 28
    • 84937992295 scopus 로고    scopus 로고
    • Alzheimers disease big data DREAM challenge 1.
    • Available from: (Last accessed 03/17/2015).
    • Peters M. Alzheimers disease big data DREAM challenge 1. Available from: (Last accessed 03/17/2015). https://www.synapse.org/#!Synapse:syn2290704/wiki/70719.
    • Peters, M.1
  • 29
    • 84875701332 scopus 로고    scopus 로고
    • Design of the Nephrotic Syndrome Study Network (NEPTUNE) to evaluate primary glomerular nephropathy by a multidisciplinary approach
    • Gadegbeku C.A., Gipson D.S., Holzman L.B., et al. Design of the Nephrotic Syndrome Study Network (NEPTUNE) to evaluate primary glomerular nephropathy by a multidisciplinary approach. Kidney Int 2013, 83:749-756.
    • (2013) Kidney Int , vol.83 , pp. 749-756
    • Gadegbeku, C.A.1    Gipson, D.S.2    Holzman, L.B.3
  • 30
    • 13444272070 scopus 로고    scopus 로고
    • The Biomolecular Interaction Network Database and related tools 2005 update
    • Alfarano C., Andrade C.E., Anthony K., et al. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res 2005, 33:D418-D424.
    • (2005) Nucleic Acids Res , vol.33 , pp. D418-D424
    • Alfarano, C.1    Andrade, C.E.2    Anthony, K.3
  • 31
    • 75549087047 scopus 로고    scopus 로고
    • The IntAct molecular interaction database in 2010
    • Aranda B., Achuthan P., Alam-Faruque Y., et al. The IntAct molecular interaction database in 2010. Nucleic Acids Res 2010, 38:D525-D531.
    • (2010) Nucleic Acids Res , vol.38 , pp. D525-D531
    • Aranda, B.1    Achuthan, P.2    Alam-Faruque, Y.3
  • 32
    • 75549083295 scopus 로고    scopus 로고
    • MINT, the molecular interaction database: 2009 update
    • Ceol A., Chatr Aryamontri A., Licata L., et al. MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 2010, 38. D532-9.
    • (2010) Nucleic Acids Res , vol.38 , pp. D532-D539
    • Ceol, A.1    Chatr Aryamontri, A.2    Licata, L.3
  • 33
    • 33846077413 scopus 로고    scopus 로고
    • Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together
    • Jayapandian M., Chapman A., Tarcea V.G., et al. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res 2007, 35:D566-D571.
    • (2007) Nucleic Acids Res , vol.35 , pp. D566-D571
    • Jayapandian, M.1    Chapman, A.2    Tarcea, V.G.3
  • 35
    • 0036081347 scopus 로고    scopus 로고
    • MIPS: a database for genomes and protein sequences
    • Mewes H.W., Frishman D., Guldener U., et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res 2002, 30:31-34.
    • (2002) Nucleic Acids Res , vol.30 , pp. 31-34
    • Mewes, H.W.1    Frishman, D.2    Guldener, U.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.