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Volumn 11, Issue , 2010, Pages

ProbFAST: Probabilistic Functional Analysis System Tool

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN INFERENCE; BIOLOGICAL CONDITIONS; BIOLOGICAL PROCESS; DIFFERENTIAL EXPRESSIONS; FUNCTIONAL INFORMATION; METHODOLOGICAL APPROACH; TISSUE DIFFERENTIATION; WEB-BASED APPLICATIONS;

EID: 77950400520     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-161     Document Type: Article
Times cited : (1)

References (41)
  • 1
    • 0028789793 scopus 로고
    • Serial analysis of gene expression
    • 10.1126/science.270.5235.484, 7570003
    • Velculescu V, Zhang L, Vogelstein B, Kinzler K. Serial analysis of gene expression. Science 1995, 270:484-487. 10.1126/science.270.5235.484, 7570003.
    • (1995) Science , vol.270 , pp. 484-487
    • Velculescu, V.1    Zhang, L.2    Vogelstein, B.3    Kinzler, K.4
  • 3
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • 10.1126/science.270.5235.467, 7569999
    • Schena M, Shalon D, Davis R, Brown P. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270:467-470. 10.1126/science.270.5235.467, 7569999.
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.3    Brown, P.4
  • 4
    • 34547759761 scopus 로고    scopus 로고
    • Gene expression analysis goes digital
    • 10.1038/nbt0807-878, 17687366
    • Velculescu V, Kinzler K. Gene expression analysis goes digital. Nat Biotechnol 2007, 25:878-880. 10.1038/nbt0807-878, 17687366.
    • (2007) Nat Biotechnol , vol.25 , pp. 878-880
    • Velculescu, V.1    Kinzler, K.2
  • 5
    • 46249122034 scopus 로고    scopus 로고
    • Molecular biology: power sequencing
    • 10.1038/4531197b, 18580940
    • Graveley B. Molecular biology: power sequencing. Nature 2008, 453:1197-1198. 10.1038/4531197b, 18580940.
    • (2008) Nature , vol.453 , pp. 1197-1198
    • Graveley, B.1
  • 6
    • 0034772104 scopus 로고    scopus 로고
    • Detecting differentially expressed genes in multiple tag sampling experiments: comparative evaluation of statistical tests
    • 10.1093/hmg/10.19.2133, 11590130
    • Romualdi C, Bortoluzzi S, Danieli G. Detecting differentially expressed genes in multiple tag sampling experiments: comparative evaluation of statistical tests. Hum Mol Genet 2001, 10:2133-2141. 10.1093/hmg/10.19.2133, 11590130.
    • (2001) Hum Mol Genet , vol.10 , pp. 2133-2141
    • Romualdi, C.1    Bortoluzzi, S.2    Danieli, G.3
  • 7
    • 0037276175 scopus 로고    scopus 로고
    • Statistical tests for differential expression in cDNA microarray experiments
    • 10.1186/gb-2003-4-4-210, 154570, 12702200
    • Cui X, Churchill G. Statistical tests for differential expression in cDNA microarray experiments. Genome Biol 2003, 4:210. 10.1186/gb-2003-4-4-210, 154570, 12702200.
    • (2003) Genome Biol , vol.4 , pp. 210
    • Cui, X.1    Churchill, G.2
  • 8
    • 0037440150 scopus 로고    scopus 로고
    • IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments
    • Romualdi C, Bortoluzzi S, D'Alessi F, Danieli G. IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments. Physiol Genomics 2003, 12:159-162.
    • (2003) Physiol Genomics , vol.12 , pp. 159-162
    • Romualdi, C.1    Bortoluzzi, S.2    D'Alessi, F.3    Danieli, G.4
  • 9
    • 34548529255 scopus 로고    scopus 로고
    • In silico gene expression analysis - an overview
    • 10.1186/1476-4598-6-50, 1964762, 17683638
    • Murray D, Doran P, MacMathuna P, Moss AC. In silico gene expression analysis - an overview. Molecular Cancer 2007, 6:50-59. 10.1186/1476-4598-6-50, 1964762, 17683638.
    • (2007) Molecular Cancer , vol.6 , pp. 50-59
    • Murray, D.1    Doran, P.2    MacMathuna, P.3    Moss, A.C.4
  • 11
    • 23144447446 scopus 로고    scopus 로고
    • WEB-SAGE: a web tool for visual analysis of differentially expressed human SAGE tags
    • 10.1093/nar/gki444, 1160205, 15980565
    • Pylouster J, Sénamaud-Beaufort C, Saison-Behmoaras T. WEB-SAGE: a web tool for visual analysis of differentially expressed human SAGE tags. Nucleic Acids Res 2005, 33:W693-695. 10.1093/nar/gki444, 1160205, 15980565.
    • (2005) Nucleic Acids Res , vol.33
    • Pylouster, J.1    Sénamaud-Beaufort, C.2    Saison-Behmoaras, T.3
  • 13
    • 33749223143 scopus 로고    scopus 로고
    • The Kyoto encyclopedia of genes and genomes-KEGG
    • 10.1002/(SICI)1097-0061(200004)17:1<48::AID-YEA2>3.0.CO;2-H, 2447041, 10928937
    • Wixon J, Kell D. The Kyoto encyclopedia of genes and genomes-KEGG. Yeast 2000, 17:48-55. 10.1002/(SICI)1097-0061(200004)17:1<48::AID-YEA2>3.0.CO;2-H, 2447041, 10928937.
    • (2000) Yeast , vol.17 , pp. 48-55
    • Wixon, J.1    Kell, D.2
  • 14
    • 84888274293 scopus 로고    scopus 로고
    • The BioCarta databases
    • The BioCarta databases. , http://cgap.nci.nih.gov/Pathways/BioCarta_Pathways
  • 15
    • 84888283372 scopus 로고    scopus 로고
    • The Mysql databases
    • The Mysql databases. , http://www.mysql.com
  • 16
    • 33747884345 scopus 로고    scopus 로고
    • Gene expression omnibus: microarray data storage, submission, retrieval, and analysis
    • 10.1016/S0076-6879(06)11019-8, 1619900, 16939800
    • Barrett T, Edgar R. Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Meth Enzymol 2006, 411:352-369. 10.1016/S0076-6879(06)11019-8, 1619900, 16939800.
    • (2006) Meth Enzymol , vol.411 , pp. 352-369
    • Barrett, T.1    Edgar, R.2
  • 17
    • 0348143189 scopus 로고    scopus 로고
    • Using credibility intervals instead of hypothesis tests in SAGE analysis
    • 10.1093/bioinformatics/btg357, 14668232
    • Vêncio R, Brentani H, Pereira C. Using credibility intervals instead of hypothesis tests in SAGE analysis. Bioinformatics 2003, 19:2461-2464. 10.1093/bioinformatics/btg357, 14668232.
    • (2003) Bioinformatics , vol.19 , pp. 2461-2464
    • Vêncio, R.1    Brentani, H.2    Pereira, C.3
  • 18
    • 13244287798 scopus 로고    scopus 로고
    • Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE)
    • 10.1186/1471-2105-5-119, 517707, 15339345
    • Vêncio R, Brentani H, Patrão D, Pereira C. Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE). BMC Bioinformatics 2004, 5:119. 10.1186/1471-2105-5-119, 517707, 15339345.
    • (2004) BMC Bioinformatics , vol.5 , pp. 119
    • Vêncio, R.1    Brentani, H.2    Patrão, D.3    Pereira, C.4
  • 19
    • 25444469952 scopus 로고    scopus 로고
    • Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach
    • 10.1186/1471-2105-6-165, 1189357, 15987513
    • Lu J, Tomfohr J, Kepler T. Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach. BMC Bioinformatics 2005, 6:165. 10.1186/1471-2105-6-165, 1189357, 15987513.
    • (2005) BMC Bioinformatics , vol.6 , pp. 165
    • Lu, J.1    Tomfohr, J.2    Kepler, T.3
  • 20
    • 0043009767 scopus 로고    scopus 로고
    • Differential expression in SAGE: accounting for normal between-library variation
    • 10.1093/bioinformatics/btg173, 12912827
    • Baggerly K, Deng L, Morris J, Aldaz C. Differential expression in SAGE: accounting for normal between-library variation. Bioinformatics 2003, 19:1477-1483. 10.1093/bioinformatics/btg173, 12912827.
    • (2003) Bioinformatics , vol.19 , pp. 1477-1483
    • Baggerly, K.1    Deng, L.2    Morris, J.3    Aldaz, C.4
  • 21
    • 33646023117 scopus 로고    scopus 로고
    • An introduction to ROC analysis
    • Fawcett T. An introduction to ROC analysis. Pattern Recogn Lett 2006, 27(8):861-874.
    • (2006) Pattern Recogn Lett , vol.27 , Issue.8 , pp. 861-874
    • Fawcett, T.1
  • 22
    • 84888283827 scopus 로고    scopus 로고
    • The probMDE algorithm
    • The probMDE algorithm. , http://gdm.fmrp.usp.br/probfast/src/
  • 23
    • 37549065883 scopus 로고    scopus 로고
    • ProbCD: enrichment analysis accounting for categorization uncertainty
    • 10.1186/1471-2105-8-383, 2169266, 17935624
    • Vêncio R, Shmulevich I. ProbCD: enrichment analysis accounting for categorization uncertainty. BMC Bioinformatics 2007, 8:383. 10.1186/1471-2105-8-383, 2169266, 17935624.
    • (2007) BMC Bioinformatics , vol.8 , pp. 383
    • Vêncio, R.1    Shmulevich, I.2
  • 24
    • 34250790725 scopus 로고    scopus 로고
    • Estimating the annotation error rate of curated GO database sequence annotations
    • 10.1186/1471-2105-8-170, 1892569, 17519041
    • Jones C, Brown A, Baumann U. Estimating the annotation error rate of curated GO database sequence annotations. BMC Bioinformatics 2007, 8:170. 10.1186/1471-2105-8-170, 1892569, 17519041.
    • (2007) BMC Bioinformatics , vol.8 , pp. 170
    • Jones, C.1    Brown, A.2    Baumann, U.3
  • 26
    • 84888284506 scopus 로고    scopus 로고
    • ProbFAST: Probabilistic Functional Analysis System Tool
    • ProbFAST: Probabilistic Functional Analysis System Tool. , http://gdm.fmrp.usp.br/probfast
  • 27
  • 28
    • 34648817252 scopus 로고    scopus 로고
    • Effectiveness of gene expression profiling for response prediction of rectal cancer to preoperative radiotherapy
    • 10.1007/s00535-007-2089-x, 17876542
    • Ojima E, Inoue Y, Miki C, Mori M, Kusunoki M. Effectiveness of gene expression profiling for response prediction of rectal cancer to preoperative radiotherapy. J Gastroenterol 2007, 42:730-736. 10.1007/s00535-007-2089-x, 17876542.
    • (2007) J Gastroenterol , vol.42 , pp. 730-736
    • Ojima, E.1    Inoue, Y.2    Miki, C.3    Mori, M.4    Kusunoki, M.5
  • 32
    • 33646550160 scopus 로고    scopus 로고
    • Transcription Factor IIA tau is associated with undifferentiated cells and its gene expression is repressed in primary neurons at the chromatin level in vivo
    • 10.1089/scd.2006.15.175, 16646664
    • Howe M, Mehmud Z, Saha S, Buratovich M, Stutius E, Schmidt H, Lenon A, Reddicks C, Ivanov G, Przyborski S, Ozer J. Transcription Factor IIA tau is associated with undifferentiated cells and its gene expression is repressed in primary neurons at the chromatin level in vivo. Stem Cells Dev 2006, 15:175-190. 10.1089/scd.2006.15.175, 16646664.
    • (2006) Stem Cells Dev , vol.15 , pp. 175-190
    • Howe, M.1    Mehmud, Z.2    Saha, S.3    Buratovich, M.4    Stutius, E.5    Schmidt, H.6    Lenon, A.7    Reddicks, C.8    Ivanov, G.9    Przyborski, S.10    Ozer, J.11
  • 33
    • 44349148508 scopus 로고    scopus 로고
    • The three SoxC proteins-Sox4, Sox11 and Sox12-exhibit overlapping expression patterns and molecular properties
    • 10.1093/nar/gkn162, 2396431, 18403418
    • Dy P, Penzo-Méndez A, Wang H, Pedraza C, Macklin W, Lefebvre V. The three SoxC proteins-Sox4, Sox11 and Sox12-exhibit overlapping expression patterns and molecular properties. Nucleic Acids Res 2008, 36:3101-3117. 10.1093/nar/gkn162, 2396431, 18403418.
    • (2008) Nucleic Acids Res , vol.36 , pp. 3101-3117
    • Dy, P.1    Penzo-Méndez, A.2    Wang, H.3    Pedraza, C.4    Macklin, W.5    Lefebvre, V.6
  • 34
    • 0037220011 scopus 로고    scopus 로고
    • Breast cancer metastasis suppressor 1: update
    • 10.1023/A:1022542519586, 12650606
    • Meehan W, Welch D. Breast cancer metastasis suppressor 1: update. Clin Exp Metastasis 2003, 20:45-50. 10.1023/A:1022542519586, 12650606.
    • (2003) Clin Exp Metastasis , vol.20 , pp. 45-50
    • Meehan, W.1    Welch, D.2
  • 35
    • 40449094341 scopus 로고    scopus 로고
    • BRMS1 suppresses breast cancer experimental metastasis to multiple organs by inhibiting several steps of the metastatic process
    • 10.2353/ajpath.2008.070772, 2258257, 18276787
    • Phadke P, Vaidya K, Nash K, Hurst D, Welch D. BRMS1 suppresses breast cancer experimental metastasis to multiple organs by inhibiting several steps of the metastatic process. Am J Pathol 2008, 172:809-817. 10.2353/ajpath.2008.070772, 2258257, 18276787.
    • (2008) Am J Pathol , vol.172 , pp. 809-817
    • Phadke, P.1    Vaidya, K.2    Nash, K.3    Hurst, D.4    Welch, D.5
  • 36
    • 21644489751 scopus 로고    scopus 로고
    • GREB 1 is a critical regulator of hormone dependent breast cancer growth
    • 10.1007/s10549-005-1483-4, 15986123
    • Rae J, Johnson M, Scheys J, Cordero K, Larios J, Lippman M. GREB 1 is a critical regulator of hormone dependent breast cancer growth. Breast Cancer Res Treat 2005, 92:141-149. 10.1007/s10549-005-1483-4, 15986123.
    • (2005) Breast Cancer Res Treat , vol.92 , pp. 141-149
    • Rae, J.1    Johnson, M.2    Scheys, J.3    Cordero, K.4    Larios, J.5    Lippman, M.6
  • 37
    • 13844254274 scopus 로고    scopus 로고
    • PRR5 encodes a conserved proline-rich protein predominant in kidney: analysis of genomic organization, expression, and mutation status in breast and colorectal carcinomas
    • 10.1016/j.ygeno.2004.11.002, 15718101
    • Johnstone C, Castellví-Bel S, Chang L, Sung R, Bowser M, Piqué J, Castells A, Rustgi A. PRR5 encodes a conserved proline-rich protein predominant in kidney: analysis of genomic organization, expression, and mutation status in breast and colorectal carcinomas. Genomics 2005, 85:338-351. 10.1016/j.ygeno.2004.11.002, 15718101.
    • (2005) Genomics , vol.85 , pp. 338-351
    • Johnstone, C.1    Castellví-Bel, S.2    Chang, L.3    Sung, R.4    Bowser, M.5    Piqué, J.6    Castells, A.7    Rustgi, A.8
  • 39
    • 33846276209 scopus 로고    scopus 로고
    • 4E-binding protein 1, a cell signaling hallmark in breast cancer that correlates with pathologic grade and prognosis
    • 10.1158/1078-0432.CCR-06-1560, 17200342
    • Rojo F, Najera L, Lirola J, Jiménez J, Guzmán M, Sabadell M, Baselga J, Ramon y Cajal S. 4E-binding protein 1, a cell signaling hallmark in breast cancer that correlates with pathologic grade and prognosis. Clin Cancer Res 2007, 13:81-89. 10.1158/1078-0432.CCR-06-1560, 17200342.
    • (2007) Clin Cancer Res , vol.13 , pp. 81-89
    • Rojo, F.1    Najera, L.2    Lirola, J.3    Jiménez, J.4    Guzmán, M.5    Sabadell, M.6    Baselga, J.7    Ramon y Cajal, S.8
  • 40
    • 21844445823 scopus 로고    scopus 로고
    • Nuclear localization and mitogen-activated protein kinase phosphorylation of the multifunctional protein CAD
    • 10.1074/jbc.M504581200, 15890648
    • Sigoillot F, Kotsis D, Serre V, Sigoillot S, Evans D, Guy H. Nuclear localization and mitogen-activated protein kinase phosphorylation of the multifunctional protein CAD. J Biol Chem 2005, 280:25611-25620. 10.1074/jbc.M504581200, 15890648.
    • (2005) J Biol Chem , vol.280 , pp. 25611-25620
    • Sigoillot, F.1    Kotsis, D.2    Serre, V.3    Sigoillot, S.4    Evans, D.5    Guy, H.6
  • 41
    • 18544372928 scopus 로고    scopus 로고
    • Expression of S100A6 and S100A4 in matched samples of human colorectal mucosa, primary colorectal adenocarcinomas and liver metastases
    • 10.1159/000063812, 12239456
    • Komatsu K, Murata K, Kameyama M, Ayaki M, Mukai M, Ishiguro S, Miyoshi J, Tatsuta M, Inoue M, Nakamura H. Expression of S100A6 and S100A4 in matched samples of human colorectal mucosa, primary colorectal adenocarcinomas and liver metastases. Oncology 2002, 63:192-200. 10.1159/000063812, 12239456.
    • (2002) Oncology , vol.63 , pp. 192-200
    • Komatsu, K.1    Murata, K.2    Kameyama, M.3    Ayaki, M.4    Mukai, M.5    Ishiguro, S.6    Miyoshi, J.7    Tatsuta, M.8    Inoue, M.9    Nakamura, H.10


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