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Volumn 30, Issue 5, 2010, Pages 477-486

Pathways and promoter networks analysis provides systems topology for systems biology approaches

Author keywords

Bioinformatics; Promoter modeling; Systems biology; Systems topology

Indexed keywords

IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERFERON REGULATORY FACTOR 1; PROTEIN ZO1; STEROL REGULATORY ELEMENT BINDING PROTEIN 1; TUMOR NECROSIS FACTOR; WNT PROTEIN;

EID: 78049429128     PISSN: 02709295     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.semnephrol.2010.07.005     Document Type: Article
Times cited : (4)

References (29)
  • 1
    • 53049110295 scopus 로고    scopus 로고
    • Genomic analysis in nephrology-towards systems biology and systematic medicine?
    • Neusser M.A., Lindenmeyer M.T., Kretzler M., Cohen C.D. Genomic analysis in nephrology-towards systems biology and systematic medicine?. Nephrol Ther 2008, 4:306-311.
    • (2008) Nephrol Ther , vol.4 , pp. 306-311
    • Neusser, M.A.1    Lindenmeyer, M.T.2    Kretzler, M.3    Cohen, C.D.4
  • 2
    • 33846064113 scopus 로고    scopus 로고
    • NCBI GEO: mining tens of millions of expression profiles-database and tools update
    • Barrett T., Troup D.B., Wilhite S.E., Ledoux P., Rudnev D., Evangelista C., et al. NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res 2007, 35(database issue):D760-D765.
    • (2007) Nucleic Acids Res , vol.35 , Issue.DATABASE ISSUE
    • Barrett, T.1    Troup, D.B.2    Wilhite, S.E.3    Ledoux, P.4    Rudnev, D.5    Evangelista, C.6
  • 4
    • 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., Botstein D., Butler H., Cherry J.M., 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    Botstein, D.4    Butler, H.5    Cherry, J.M.6
  • 5
    • 0037805574 scopus 로고    scopus 로고
    • On ontologies for biologists: the Gene Ontology-untangling the web
    • 244-52
    • Ashburner M., Lewis S. On ontologies for biologists: the Gene Ontology-untangling the web. Novartis Found Symp 2002, 247:66-90. 244-52.
    • (2002) Novartis Found Symp , vol.247 , pp. 66-90
    • Ashburner, M.1    Lewis, S.2
  • 6
    • 51849115165 scopus 로고    scopus 로고
    • Improved elucidation of biological processes linked to diabetic nephropathy by single probe-based microarray data analysis
    • Cohen C.D., Lindenmeyer M.T., Eichinger F., Hahn A., Seifert M., Moll A.G., et al. Improved elucidation of biological processes linked to diabetic nephropathy by single probe-based microarray data analysis. PLoS One 2008, 3:e2937.
    • (2008) PLoS One , vol.3
    • Cohen, C.D.1    Lindenmeyer, M.T.2    Eichinger, F.3    Hahn, A.4    Seifert, M.5    Moll, A.G.6
  • 7
    • 65249134946 scopus 로고    scopus 로고
    • Wnt/beta-catenin signaling promotes renal interstitial fibrosis
    • He W., Dai C., Li Y., Zeng G., Monga S.P., Liu Y. Wnt/beta-catenin signaling promotes renal interstitial fibrosis. J Am Soc Nephrol 2009, 20:765-776.
    • (2009) J Am Soc Nephrol , vol.20 , pp. 765-776
    • He, W.1    Dai, C.2    Li, Y.3    Zeng, G.4    Monga, S.P.5    Liu, Y.6
  • 8
    • 48749101937 scopus 로고    scopus 로고
    • WNT signalling in the immune system: WNT is spreading its wings
    • Staal F.J., Luis T.C., Tiemessen M.M. WNT signalling in the immune system: WNT is spreading its wings. Nat Rev Immunol 2008, 8:581-593.
    • (2008) Nat Rev Immunol , vol.8 , pp. 581-593
    • Staal, F.J.1    Luis, T.C.2    Tiemessen, M.M.3
  • 10
    • 33847701747 scopus 로고    scopus 로고
    • Beneficial effects of CCR1 blockade on the progression of chronic renal allograft damage
    • Bedke J., Kiss E., Schaefer L., Behnes C.L., Bonrouhi M., Gretz N., et al. Beneficial effects of CCR1 blockade on the progression of chronic renal allograft damage. Am J Transplant 2007, 7:527-537.
    • (2007) Am J Transplant , vol.7 , pp. 527-537
    • Bedke, J.1    Kiss, E.2    Schaefer, L.3    Behnes, C.L.4    Bonrouhi, M.5    Gretz, N.6
  • 11
    • 21244473728 scopus 로고    scopus 로고
    • 13-cis retinoic acid inhibits development and progression of chronic allograft nephropathy
    • Adams J., Kiss E., Arroyo A.B., Bonrouhi M., Sun Q., Li Z., et al. 13-cis retinoic acid inhibits development and progression of chronic allograft nephropathy. Am J Pathol 2005, 167:285-298.
    • (2005) Am J Pathol , vol.167 , pp. 285-298
    • Adams, J.1    Kiss, E.2    Arroyo, A.B.3    Bonrouhi, M.4    Sun, Q.5    Li, Z.6
  • 12
    • 36549002108 scopus 로고    scopus 로고
    • Gene annotation and pathway mapping in KEGG
    • Aoki-Kinoshita K.F., Kanehisa M. Gene annotation and pathway mapping in KEGG. Methods Mol Biol 2007, 396:71-91.
    • (2007) Methods Mol Biol , vol.396 , pp. 71-91
    • Aoki-Kinoshita, K.F.1    Kanehisa, M.2
  • 14
    • 0037785111 scopus 로고    scopus 로고
    • Computer modeling of promoter organization as a tool to study transcriptional coregulation
    • Werner T., Fessele S., Maier H., Nelson P.J. Computer modeling of promoter organization as a tool to study transcriptional coregulation. FASEB J 2003, 17:1228-1237.
    • (2003) FASEB J , vol.17 , pp. 1228-1237
    • Werner, T.1    Fessele, S.2    Maier, H.3    Nelson, P.J.4
  • 15
    • 0038444122 scopus 로고    scopus 로고
    • Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells
    • Elkon R., Linhart C., Sharan R., Shamir R., Shiloh Y. Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res 2003, 13:773-780.
    • (2003) Genome Res , vol.13 , pp. 773-780
    • Elkon, R.1    Linhart, C.2    Sharan, R.3    Shamir, R.4    Shiloh, Y.5
  • 16
    • 0032948782 scopus 로고    scopus 로고
    • Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity
    • Klingenhoff A., Frech K., Quandt K., Werner T. Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity. Bioinformatics 1999, 15:180-186.
    • (1999) Bioinformatics , vol.15 , pp. 180-186
    • Klingenhoff, A.1    Frech, K.2    Quandt, K.3    Werner, T.4
  • 17
    • 33645807621 scopus 로고    scopus 로고
    • Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins
    • Cohen C.D., Klingenhoff A., Boucherot A., Nitsche A., Henger A., Brunner B., et al. Comparative promoter analysis allows de novo identification of specialized cell junction-associated proteins. Proc Natl Acad Sci U S A 2006, 103:5682-5687.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 5682-5687
    • Cohen, C.D.1    Klingenhoff, A.2    Boucherot, A.3    Nitsche, A.4    Henger, A.5    Brunner, B.6
  • 18
    • 0035291240 scopus 로고    scopus 로고
    • Molecular and in silico characterization of a promoter module and C/EBP element that mediate LPS-induced RANTES/CCL5 expression in monocytic cells
    • Fessele S., Boehlk S., Mojaat A., Miyamoto N.G., Werner T., Nelson E.L., et al. Molecular and in silico characterization of a promoter module and C/EBP element that mediate LPS-induced RANTES/CCL5 expression in monocytic cells. FASEB J 2001, 15:577-579.
    • (2001) FASEB J , vol.15 , pp. 577-579
    • Fessele, S.1    Boehlk, S.2    Mojaat, A.3    Miyamoto, N.G.4    Werner, T.5    Nelson, E.L.6
  • 19
    • 2342568371 scopus 로고    scopus 로고
    • Nuclear factor-kappaB motif and interferon-alpha-stimulated response element co-operate in the activation of guanylate-binding protein-1 expression by inflammatory cytokines in endothelial cells
    • Naschberger E., Werner T., Vicente A.B., Guenzi E., Topolt K., Leubert R., et al. Nuclear factor-kappaB motif and interferon-alpha-stimulated response element co-operate in the activation of guanylate-binding protein-1 expression by inflammatory cytokines in endothelial cells. Biochem J 2004, 379:409-420.
    • (2004) Biochem J , vol.379 , pp. 409-420
    • Naschberger, E.1    Werner, T.2    Vicente, A.B.3    Guenzi, E.4    Topolt, K.5    Leubert, R.6
  • 20
    • 21444443478 scopus 로고    scopus 로고
    • MatInspector and beyond: promoter analysis based on transcription factor binding sites
    • Cartharius K., Frech K., Grote K., Klocke B., Haltmeier M., Klingenhoff A., et al. MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 2005, 21:2933-2942.
    • (2005) Bioinformatics , vol.21 , pp. 2933-2942
    • Cartharius, K.1    Frech, K.2    Grote, K.3    Klocke, B.4    Haltmeier, M.5    Klingenhoff, A.6
  • 21
    • 68749092181 scopus 로고    scopus 로고
    • Slit diaphragm dysfunction in proteinuric states: identification of novel therapeutic targets for nephrotic syndrome
    • Kawachi H., Suzuki K., Miyauchi N., Hashimoto T., Otaki Y., Shimizu F. Slit diaphragm dysfunction in proteinuric states: identification of novel therapeutic targets for nephrotic syndrome. Clin Exp Nephrol 2009, 13:275-280.
    • (2009) Clin Exp Nephrol , vol.13 , pp. 275-280
    • Kawachi, H.1    Suzuki, K.2    Miyauchi, N.3    Hashimoto, T.4    Otaki, Y.5    Shimizu, F.6
  • 22
    • 58149361842 scopus 로고    scopus 로고
    • Signaling in regulation of podocyte phenotypes
    • Chuang P.Y., He J.C. Signaling in regulation of podocyte phenotypes. Nephron Physiol 2009, 111:p9-p15.
    • (2009) Nephron Physiol , vol.111
    • Chuang, P.Y.1    He, J.C.2
  • 23
    • 16644374992 scopus 로고    scopus 로고
    • WT1 activates a glomerular-specific enhancer identified from the human nephrin gene
    • Guo G., Morrison D.J., Licht J.D., Quaggin S.E. WT1 activates a glomerular-specific enhancer identified from the human nephrin gene. J Am Soc Nephrol 2004, 15:2851-2856.
    • (2004) J Am Soc Nephrol , vol.15 , pp. 2851-2856
    • Guo, G.1    Morrison, D.J.2    Licht, J.D.3    Quaggin, S.E.4
  • 25
    • 33845526226 scopus 로고    scopus 로고
    • Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy
    • Schmid H., Boucherot A., Yasuda Y., Henger A., Brunner B., Eichinger F., et al. Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes 2006, 55:2993-3003.
    • (2006) Diabetes , vol.55 , pp. 2993-3003
    • Schmid, H.1    Boucherot, A.2    Yasuda, Y.3    Henger, A.4    Brunner, B.5    Eichinger, F.6
  • 26
    • 0027957398 scopus 로고
    • HLA class I heavy-chain gene promoter elements mediating synergy between tumor necrosis factor and interferons
    • Johnson D.R., Pober J.S. HLA class I heavy-chain gene promoter elements mediating synergy between tumor necrosis factor and interferons. Mol Cell Biol 1994, 14:1322-1332.
    • (1994) Mol Cell Biol , vol.14 , pp. 1322-1332
    • Johnson, D.R.1    Pober, J.S.2
  • 27
  • 28
    • 67650064593 scopus 로고    scopus 로고
    • Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes
    • Hormozdiari F., Alkan C., Eichler E.E., Sahinalp S.C. Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res 2009, 19:1270-1278.
    • (2009) Genome Res , vol.19 , pp. 1270-1278
    • Hormozdiari, F.1    Alkan, C.2    Eichler, E.E.3    Sahinalp, S.C.4
  • 29
    • 70349312354 scopus 로고    scopus 로고
    • ChIP-seq: advantages and challenges of a maturing technology
    • Park P.J. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 2009, 10:669-680.
    • (2009) Nat Rev Genet , vol.10 , pp. 669-680
    • Park, P.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.