메뉴 건너뛰기




Volumn 9, Issue 11, 2008, Pages

ArrayPlex: Distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ANALYTIC METHOD; ARTICLE; COMPUTER INTERFACE; COMPUTER LANGUAGE; COMPUTER PROGRAM; DATA ANALYSIS; GENE SEQUENCE; GENETICS; GENOMICS; INFORMATION STORAGE; INTERNET; MICROARRAY ANALYSIS; MOLECULAR BIOLOGY; QUALITY CONTROL; METHODOLOGY;

EID: 57249105133     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2008-9-11-r159     Document Type: Article
Times cited : (1)

References (47)
  • 4
    • 0037099005 scopus 로고    scopus 로고
    • BioArray Software Environment (BASE): A platform for comprehensive management and analysis of microarray data
    • SOFTWARE0003. 139402 12186655 10.1186/gb-2002-3-8-software0003
    • Saal L Troein C Vallon-Christersson J Gruvberger S Borg A Peterson C BioArray Software Environment (BASE): A platform for comprehensive management and analysis of microarray data. Genome Biol 2002, 3:SOFTWARE0003. 139402 12186655 10.1186/gb-2002-3-8-software0003
    • (2002) Genome Biol , vol.3
    • Saal, L.1    Troein, C.2    Vallon-Christersson, J.3    Gruvberger, S.4    Borg, A.5    Peterson, C.6
  • 5
    • 0642340504 scopus 로고    scopus 로고
    • The Longhorn Array Database (LAD): An open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD)
    • 194174 12930545 10.1186/1471-2105-4-32
    • Killion PJ Sherlock G Iyer VR The Longhorn Array Database (LAD): An open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD). BMC Bioinformatics 2003, 4:32. 194174 12930545 10.1186/ 1471-2105-4-32
    • (2003) BMC Bioinformatics , vol.4 , pp. 32
    • Killion, P.J.1    Sherlock, G.2    Iyer, V.R.3
  • 7
    • 57249110950 scopus 로고    scopus 로고
    • Linux http://www.linux.org/
    • Linux
  • 8
  • 9
    • 84885380243 scopus 로고    scopus 로고
    • PostgreSQL http://www.postgresql.org/
    • PostgreSQL
  • 12
    • 84875617816 scopus 로고    scopus 로고
    • FASTA Format http://www.ncbi.nlm.nih.gov/blast/fasta.shtml
    • FASTA Format
  • 13
    • 0037270315 scopus 로고    scopus 로고
    • AVID: A global alignment program
    • 430967 12529311 10.1101/gr.789803
    • Bray N Dubchak I Pachter L AVID: A global alignment program. Genome Res 2003, 13:97-102. 430967 12529311 10.1101/gr.789803
    • (2003) Genome Res , vol.13 , pp. 97-102
    • Bray, N.1    Dubchak, I.2    Pachter, L.3
  • 14
    • 0036105591 scopus 로고    scopus 로고
    • rVista for comparative sequence-based discovery of functional transcription factor binding sites
    • 186580 11997350
    • Loots GG Ovcharenko I Pachter L Dubchak I Rubin EM rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res 2002, 12:832-839. 186580 11997350
    • (2002) Genome Res , vol.12 , pp. 832-839
    • Loots, G.G.1    Ovcharenko, I.2    Pachter, L.3    Dubchak, I.4    Rubin, E.M.5
  • 15
    • 0034628901 scopus 로고    scopus 로고
    • Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
    • 10.1006/jmbi.2000.3519 10698627
    • Hughes J Estep P Tavazoie S Church G Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 2000, 296:1205-1214. 10.1006/jmbi.2000.3519 10698627
    • (2000) J Mol Biol , vol.296 , pp. 1205-1214
    • Hughes, J.1    Estep, P.2    Tavazoie, S.3    Church, G.4
  • 16
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • 308517 7984417 10.1093/nar/22.22.4673
    • Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680. 308517 7984417 10.1093/nar/22.22.4673
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 19
    • 57249110947 scopus 로고    scopus 로고
    • MEME http://meme.nbcr.net/downloads/
    • MEME
  • 20
    • 57249109385 scopus 로고    scopus 로고
    • MDSCAN http://motif.stanford.edu/distributions/mdscan/
    • MDSCAN
  • 21
    • 34247629588 scopus 로고    scopus 로고
    • Genetic reconstruction of a functional transcriptional regulatory network
    • 10.1038/ng2012 17417638
    • Hu Z Killion PJ Iyer VR Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet 2007, 39:683-687. 10.1038/ ng2012 17417638
    • (2007) Nat Genet , vol.39 , pp. 683-687
    • Hu, Z.1    Killion, P.J.2    Iyer, V.R.3
  • 22
    • 0242333835 scopus 로고    scopus 로고
    • Normalization of cDNA microarray data
    • 10.1016/S1046-2023(03)00155-5 14597310
    • Smyth G Speed T Normalization of cDNA microarray data. Methods 2003, 31:265-273. 10.1016/S1046-2023(03)00155-5 14597310
    • (2003) Methods , vol.31 , pp. 265-273
    • Smyth, G.1    Speed, T.2
  • 23
    • 2942598422 scopus 로고    scopus 로고
    • Genome-wide analysis of the biology of stress responses through heat shock transcription factor
    • 419887 15169889 10.1128/MCB.24.12.5249-5256.2004
    • Hahn JS Hu Z Thiele DJ Iyer VR Genome-wide analysis of the biology of stress responses through heat shock transcription factor. Mol Cell Biol 2004, 24:5249-5256. 419887 15169889 10.1128/MCB.24.12.5249-5256.2004
    • (2004) Mol Cell Biol , vol.24 , pp. 5249-5256
    • Hahn, J.S.1    Hu, Z.2    Thiele, D.J.3    Iyer, V.R.4
  • 24
    • 0037811432 scopus 로고    scopus 로고
    • Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
    • 193630 12844359 10.1186/gb-2003-4-7-r43
    • Chiang DY Moses AM Kellis M Lander ES Eisen MB Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts. Genome Biol 2003, 4:R43. 193630 12844359 10.1186/ gb-2003-4-7-r43
    • (2003) Genome Biol , vol.4
    • Chiang, D.Y.1    Moses, A.M.2    Kellis, M.3    Lander, E.S.4    Eisen, M.B.5
  • 26
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • 10.1038/nature01644 12748633
    • Kellis M Patterson N Endrizzi M Birren B Lander ES Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423:241-254. 10.1038/nature01644 12748633
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 27
    • 0032861774 scopus 로고    scopus 로고
    • SCPD: A promoter database of the yeast Saccharomyces cerevisiae
    • 10.1093/bioinformatics/15.7.607 10487868
    • Zhu J Zhang MQ SCPD: A promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 1999, 15:607-611. 10.1093/bioinformatics/ 15.7.607 10487868
    • (1999) Bioinformatics , vol.15 , pp. 607-611
    • Zhu, J.1    Zhang, M.Q.2
  • 28
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software environment for integrated models of biomolecular interaction network
    • 14597658 403769 10.1101/gr.1239303
    • Shannon P Markiel A Ozier O Baliga N Wang J Ramage D Amin N Schwikowski B Ideker T Cytoscape: A software environment for integrated models of biomolecular interaction networks Genome Res 2003, 13:2498-2504. 14597658 403769 10.1101/gr.1239303
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1    Markiel, A.2    Ozier, O.3    Baliga, N.4    Wang, J.5    Ramage, D.6    Amin, N.7    Schwikowski, B.8    Ideker, T.9
  • 29
    • 0026267950 scopus 로고
    • A new role for MCM1 in yeast: Cell cycle regulation of SW15 transcription
    • 10.1101/gad.5.12b.2405 1752436
    • Lydall D Ammerer G Nasmyth K A new role for MCM1 in yeast: Cell cycle regulation of SW15 transcription. Genes Dev 1991, 5:2405-2419. 10.1101/ gad.5.12b.2405 1752436
    • (1991) Genes Dev , vol.5 , pp. 2405-2419
    • Lydall, D.1    Ammerer, G.2    Nasmyth, K.3
  • 30
    • 0028265881 scopus 로고
    • Induction of pseudohyphal growth by overexpression of PHD1, a Saccharomyces cerevisiae gene related to transcriptional regulators of fungal development
    • 358570 8114741
    • Gimeno C Fink G Induction of pseudohyphal growth by overexpression of PHD1, a Saccharomyces cerevisiae gene related to transcriptional regulators of fungal development. Mol Cell Biol 1994, 14:2100-2112. 358570 8114741
    • (1994) Mol Cell Biol , vol.14 , pp. 2100-2112
    • Gimeno, C.1    Fink, G.2
  • 31
    • 0031762569 scopus 로고    scopus 로고
    • Regulators of pseudohyphal differentiation in Saccharomyces cerevisiae identified through multicopy suppressor analysis in ammonium permease mutant strains
    • 1460428 9832522
    • Lorenz M Heitman J Regulators of pseudohyphal differentiation in Saccharomyces cerevisiae identified through multicopy suppressor analysis in ammonium permease mutant strains. Genetics 1998, 150:1443-1457. 1460428 9832522
    • (1998) Genetics , vol.150 , pp. 1443-1457
    • Lorenz, M.1    Heitman, J.2
  • 32
    • 0033756154 scopus 로고    scopus 로고
    • Sok2 regulates yeast pseudohyphal differentiation via a transcription factor cascade that regulates cell-cell adhesion
    • 102143 11046133 10.1128/MCB.20.22.8364-8372.2000
    • Pan X Heitman J Sok2 regulates yeast pseudohyphal differentiation via a transcription factor cascade that regulates cell-cell adhesion. Mol Cell Biol 2000, 20:8364-8372. 102143 11046133 10.1128/MCB.20.22.8364-8372.2000
    • (2000) Mol Cell Biol , vol.20 , pp. 8364-8372
    • Pan, X.1    Heitman, J.2
  • 33
    • 33645804408 scopus 로고    scopus 로고
    • Mayday - A microarray data analysis workbench
    • 10.1093/bioinformatics/btl070 16500939
    • Dietzsch J Gehlenborg N Nieselt K Mayday - a microarray data analysis workbench. Bioinformatics 2006, 22:1010-1012. 10.1093/bioinformatics/ btl070 16500939
    • (2006) Bioinformatics , vol.22 , pp. 1010-1012
    • Dietzsch, J.1    Gehlenborg, N.2    Nieselt, K.3
  • 35
  • 37
    • 0012787398 scopus 로고    scopus 로고
    • SeqHound: Biological Sequence and Structure Database as a Platform for Bioinformatics Research
    • 138791 12401134 10.1186/1471-2105-3-32
    • Michalickova K Bader GD Dumontier M Lieu H Betel D Isserlin R Hogue CW SeqHound: Biological Sequence and Structure Database as a Platform for Bioinformatics Research. BMC Bioinformatics 2002, 3:32. 138791 12401134 10.1186/1471-2105-3-32
    • (2002) BMC Bioinformatics , vol.3 , pp. 32
    • Michalickova, K.1    Bader, G.D.2    Dumontier, M.3    Lieu, H.4    Betel, D.5    Isserlin, R.6    Hogue, C.W.7
  • 39
    • 22044453632 scopus 로고    scopus 로고
    • Atlas - A Data Warehouse for Integrative Bioinformatics
    • 554782 15723693 10.1186/1471-2105-6-34
    • Shah SP Huang Y Xu T Yuen MM Ling J Ouellette BF Atlas - a Data Warehouse for Integrative Bioinformatics. BMC Bioinformatics 2005, 6:34. 554782 15723693 10.1186/1471-2105-6-34
    • (2005) BMC Bioinformatics , vol.6 , pp. 34
    • Shah, S.P.1    Huang, Y.2    Xu, T.3    Yuen, M.M.4    Ling, J.5    Ouellette, B.F.6
  • 43
    • 57249116599 scopus 로고    scopus 로고
    • Fedora Linux http://www.fedoraproject.org/
    • Fedora Linux
  • 44
  • 45
  • 46


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.