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Volumn 12, Issue , 2011, Pages

TAFFEL: Independent Enrichment Analysis of gene sets

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL FUNCTIONS; BIOLOGICAL PATHWAYS; BIOLOGICAL PHENOMENA; BIOLOGICAL PROCESS; DIFFERENTIALLY EXPRESSED GENE; GENE SET ENRICHMENT ANALYSIS; REGULATORY MECHANISM; TRANSCRIPTIONAL REGULATOR;

EID: 79955991962     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-171     Document Type: Article
Times cited : (2)

References (52)
  • 2
    • 24644470505 scopus 로고    scopus 로고
    • Ontological analysis of gene expression data: current tools, limitations, and open problems
    • 10.1093/bioinformatics/bti565, 2435250, 15994189
    • Khatri P, Draghici S. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 2005, 21(18):3587-3595. 10.1093/bioinformatics/bti565, 2435250, 15994189.
    • (2005) Bioinformatics , vol.21 , Issue.18 , pp. 3587-3595
    • Khatri, P.1    Draghici, S.2
  • 3
    • 25444482341 scopus 로고    scopus 로고
    • Theme discovery from gene lists for identification and viewing of multiple functional groups
    • 10.1186/1471-2105-6-162, 1190153, 15987504
    • Pehkonen P, Wong G, Toronen P. Theme discovery from gene lists for identification and viewing of multiple functional groups. BMC Bioinformatics 2005, 6:162. 10.1186/1471-2105-6-162, 1190153, 15987504.
    • (2005) BMC Bioinformatics , vol.6 , pp. 162
    • Pehkonen, P.1    Wong, G.2    Toronen, P.3
  • 4
    • 0038005018 scopus 로고    scopus 로고
    • DAVID: Database for Annotation, Visualization, and Integrated Discovery
    • 10.1186/gb-2003-4-5-p3, 12734009
    • Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003, 4(5):P3. 10.1186/gb-2003-4-5-p3, 12734009.
    • (2003) Genome Biol , vol.4 , Issue.5
    • Dennis, G.1    Sherman, B.T.2    Hosack, D.A.3    Yang, J.4    Gao, W.5    Lane, H.C.6    Lempicki, R.A.7
  • 5
    • 1542399989 scopus 로고    scopus 로고
    • FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes
    • 10.1093/bioinformatics/btg455, 14990455
    • Al-Shahrour F, Diaz-Uriarte R, Dopazo J. FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 2004, 20(4):578-580. 10.1093/bioinformatics/btg455, 14990455.
    • (2004) Bioinformatics , vol.20 , Issue.4 , pp. 578-580
    • Al-Shahrour, F.1    Diaz-Uriarte, R.2    Dopazo, J.3
  • 6
    • 20444365683 scopus 로고    scopus 로고
    • GOToolBox: functional analysis of gene datasets based on Gene Ontology
    • 10.1186/gb-2004-5-12-r101, 545796, 15575967
    • Martin D, Brun C, Remy E, Mouren P, Thieffry D, Jacq B. GOToolBox: functional analysis of gene datasets based on Gene Ontology. Genome Biol 2004, 5(12):R101. 10.1186/gb-2004-5-12-r101, 545796, 15575967.
    • (2004) Genome Biol , vol.5 , Issue.12
    • Martin, D.1    Brun, C.2    Remy, E.3    Mouren, P.4    Thieffry, D.5    Jacq, B.6
  • 7
    • 0036578644 scopus 로고    scopus 로고
    • GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways
    • 10.1038/ng0502-19, 11984561
    • Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet 2002, 31(1):19-20. 10.1038/ng0502-19, 11984561.
    • (2002) Nat Genet , vol.31 , Issue.1 , pp. 19-20
    • Dahlquist, K.D.1    Salomonis, N.2    Vranizan, K.3    Lawlor, S.C.4    Conklin, B.R.5
  • 9
    • 3142665525 scopus 로고    scopus 로고
    • GOstat: find statistically overrepresented Gene Ontologies within a group of genes
    • 10.1093/bioinformatics/bth088, 14962934
    • Beissbarth T, Speed TP. GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 2004, 20(9):1464-1465. 10.1093/bioinformatics/bth088, 14962934.
    • (2004) Bioinformatics , vol.20 , Issue.9 , pp. 1464-1465
    • Beissbarth, T.1    Speed, T.P.2
  • 10
    • 0042121055 scopus 로고    scopus 로고
    • Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate
    • 10.1093/nar/gkg624, 169030, 12824416
    • Draghici S, Khatri P, Bhavsar P, Shah A, Krawetz SA, Tainsky MA. Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res 2003, 31(13):3775-3781. 10.1093/nar/gkg624, 169030, 12824416.
    • (2003) Nucleic Acids Res , vol.31 , Issue.13 , pp. 3775-3781
    • Draghici, S.1    Khatri, P.2    Bhavsar, P.3    Shah, A.4    Krawetz, S.A.5    Tainsky, M.A.6
  • 12
    • 3142673366 scopus 로고    scopus 로고
    • Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex
    • Pavlidis P, Qin J, Arango V, Mann JJ, Sibille E. Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex. Neurochem Res 2004, 29(6):1213-1222.
    • (2004) Neurochem Res , vol.29 , Issue.6 , pp. 1213-1222
    • Pavlidis, P.1    Qin, J.2    Arango, V.3    Mann, J.J.4    Sibille, E.5
  • 14
    • 33846373607 scopus 로고    scopus 로고
    • Subarachnoid haemorrhage
    • 10.1016/S0140-6736(07)60153-6, 17258671
    • Van Gijn J, Kerr RS, Rinkel GJ. Subarachnoid haemorrhage. Lancet 2007, 369(9558):306-318. 10.1016/S0140-6736(07)60153-6, 17258671.
    • (2007) Lancet , vol.369 , Issue.9558 , pp. 306-318
    • Van Gijn, J.1    Kerr, R.S.2    Rinkel, G.J.3
  • 15
    • 4744352163 scopus 로고    scopus 로고
    • Remodeling of saccular cerebral artery aneurysm wall is associated with rupture: histological analysis of 24 unruptured and 42 ruptured cases
    • 10.1161/01.STR.0000140636.30204.da, 15322297
    • Frösen J, Piippo A, Paetau A, Kangasniemi M, Niemelä M, Hernesniemi J, Jääskelainen J. Remodeling of saccular cerebral artery aneurysm wall is associated with rupture: histological analysis of 24 unruptured and 42 ruptured cases. Stroke 2004, 35(10):2287-2293. 10.1161/01.STR.0000140636.30204.da, 15322297.
    • (2004) Stroke , vol.35 , Issue.10 , pp. 2287-2293
    • Frösen, J.1    Piippo, A.2    Paetau, A.3    Kangasniemi, M.4    Niemelä, M.5    Hernesniemi, J.6    Jääskelainen, J.7
  • 16
    • 33746793810 scopus 로고    scopus 로고
    • Growth factor receptor expression and remodeling of saccular cerebral artery aneurysm walls: implications for biological therapy preventing rupture
    • discussion 534-41
    • Frösen J, Piippo A, Paetau A, Kangasniemi M, Niemela M, Hernesniemi J, Jaaskelainen J. Growth factor receptor expression and remodeling of saccular cerebral artery aneurysm walls: implications for biological therapy preventing rupture. Neurosurgery 2006, 58(3):534-41. discussion 534-41.
    • (2006) Neurosurgery , vol.58 , Issue.3 , pp. 534-541
    • Frösen, J.1    Piippo, A.2    Paetau, A.3    Kangasniemi, M.4    Niemela, M.5    Hernesniemi, J.6    Jaaskelainen, J.7
  • 18
    • 41249087240 scopus 로고    scopus 로고
    • Involvement of mitogen-activated protein kinase signaling in growth and rupture of human intracranial aneurysms
    • 10.1161/STROKEAHA.107.497875, 18239167
    • Laaksamo E, Tulamo R, Baumann M, Dashti R, Hernesniemi J, Juvela S, Niemela M, Laakso A. Involvement of mitogen-activated protein kinase signaling in growth and rupture of human intracranial aneurysms. Stroke 2008, 39(3):886-892. 10.1161/STROKEAHA.107.497875, 18239167.
    • (2008) Stroke , vol.39 , Issue.3 , pp. 886-892
    • Laaksamo, E.1    Tulamo, R.2    Baumann, M.3    Dashti, R.4    Hernesniemi, J.5    Juvela, S.6    Niemela, M.7    Laakso, A.8
  • 20
    • 33847205295 scopus 로고    scopus 로고
    • GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists
    • 10.1186/gb-2007-8-1-r3, 1839127, 17204154
    • Carmona-Saez P, Chagoyen M, Tirado F, Carazo JM, Pascual-Montano A. GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists. Genome Biol 2007, 8(1):R3. 10.1186/gb-2007-8-1-r3, 1839127, 17204154.
    • (2007) Genome Biol , vol.8 , Issue.1
    • Carmona-Saez, P.1    Chagoyen, M.2    Tirado, F.3    Carazo, J.M.4    Pascual-Montano, A.5
  • 23
    • 0035282835 scopus 로고    scopus 로고
    • Repression of cytochrome P450 1A1 gene expression by oxidative stress: mechanisms and biological implications
    • 10.1016/S0006-2952(00)00543-8, 11239493
    • Barouki R, Morel Y. Repression of cytochrome P450 1A1 gene expression by oxidative stress: mechanisms and biological implications. Biochem Pharmacol 2001, 61(5):511-516. 10.1016/S0006-2952(00)00543-8, 11239493.
    • (2001) Biochem Pharmacol , vol.61 , Issue.5 , pp. 511-516
    • Barouki, R.1    Morel, Y.2
  • 28
    • 3042745465 scopus 로고    scopus 로고
    • Statistical concerns about the GSEA procedure
    • author reply 663
    • Damian D, Gorfine M. Statistical concerns about the GSEA procedure. Nat Genet 2004, 36(7):663. author reply 663.
    • (2004) Nat Genet , vol.36 , Issue.7 , pp. 663
    • Damian, D.1    Gorfine, M.2
  • 29
    • 33747835614 scopus 로고    scopus 로고
    • POXO: a web-enabled tool series to discover transcription factor binding sites
    • 1538773, 16845065
    • Kankainen M, Pehkonen P, Rosenstom P, Toronen P, Wong G, Holm L. POXO: a web-enabled tool series to discover transcription factor binding sites. Nucleic Acids Res 2006, 34(Web Server issue):W534-40. 1538773, 16845065.
    • (2006) Nucleic Acids Res , vol.34
    • Kankainen, M.1    Pehkonen, P.2    Rosenstom, P.3    Toronen, P.4    Wong, G.5    Holm, L.6
  • 30
    • 20144370200 scopus 로고    scopus 로고
    • OPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes
    • 10.1093/nar/gki624, 1142402, 15933209
    • Ho Sui SJ, Mortimer JR, Arenillas DJ, Brumm J, Walsh CJ, Kennedy BP, Wasserman WW. oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes. Nucl Acids Res 2005, 33(10):3154-3164. 10.1093/nar/gki624, 1142402, 15933209.
    • (2005) Nucl Acids Res , vol.33 , Issue.10 , pp. 3154-3164
    • Ho Sui, S.J.1    Mortimer, J.R.2    Arenillas, D.J.3    Brumm, J.4    Walsh, C.J.5    Kennedy, B.P.6    Wasserman, W.W.7
  • 31
    • 45549107329 scopus 로고    scopus 로고
    • Use and misuse of the gene ontology annotations
    • 10.1038/nrg2363, 18475267
    • Rhee SY, Wood V, Dolinski K, Draghici S. Use and misuse of the gene ontology annotations. Nat Rev Genet 2008, 9(7):509-515. 10.1038/nrg2363, 18475267.
    • (2008) Nat Rev Genet , vol.9 , Issue.7 , pp. 509-515
    • Rhee, S.Y.1    Wood, V.2    Dolinski, K.3    Draghici, S.4
  • 32
    • 44349109637 scopus 로고    scopus 로고
    • Eukaryotic transcription factor binding sites--modeling and integrative search methods
    • 10.1093/bioinformatics/btn198, 18426806
    • Hannenhalli S. Eukaryotic transcription factor binding sites--modeling and integrative search methods. Bioinformatics 2008, 24(11):1325-1331. 10.1093/bioinformatics/btn198, 18426806.
    • (2008) Bioinformatics , vol.24 , Issue.11 , pp. 1325-1331
    • Hannenhalli, S.1
  • 35
    • 59149097969 scopus 로고    scopus 로고
    • The aryl hydrocarbon receptor cross-talks with multiple signal transduction pathways
    • 10.1016/j.bcp.2008.08.031, 2657192, 18817753
    • Puga A, Ma C, Marlowe JL. The aryl hydrocarbon receptor cross-talks with multiple signal transduction pathways. Biochem Pharmacol 2009, 77(4):713-722. 10.1016/j.bcp.2008.08.031, 2657192, 18817753.
    • (2009) Biochem Pharmacol , vol.77 , Issue.4 , pp. 713-722
    • Puga, A.1    Ma, C.2    Marlowe, J.L.3
  • 36
    • 0036711207 scopus 로고    scopus 로고
    • Activation of mitogen-activated protein kinases (MAPKs) by aromatic hydrocarbons: role in the regulation of aryl hydrocarbon receptor (AHR) function
    • 10.1016/S0006-2952(02)01138-3, 12213569
    • Tan Z, Chang X, Puga A, Xia Y. Activation of mitogen-activated protein kinases (MAPKs) by aromatic hydrocarbons: role in the regulation of aryl hydrocarbon receptor (AHR) function. Biochem Pharmacol 2002, 64(5-6):771-780. 10.1016/S0006-2952(02)01138-3, 12213569.
    • (2002) Biochem Pharmacol , vol.64 , Issue.5-6 , pp. 771-780
    • Tan, Z.1    Chang, X.2    Puga, A.3    Xia, Y.4
  • 37
    • 59149102150 scopus 로고    scopus 로고
    • Role of cAMP in mediating AHR signaling
    • 10.1016/j.bcp.2008.10.017, 19013136
    • Oesch-Bartlomowicz B, Oesch F. Role of cAMP in mediating AHR signaling. Biochem Pharmacol 2009, 77(4):627-641. 10.1016/j.bcp.2008.10.017, 19013136.
    • (2009) Biochem Pharmacol , vol.77 , Issue.4 , pp. 627-641
    • Oesch-Bartlomowicz, B.1    Oesch, F.2
  • 38
    • 1642495627 scopus 로고    scopus 로고
    • HES-1, a novel target gene for the aryl hydrocarbon receptor
    • 10.1124/mol.65.1.165, 14722248
    • Thomsen JS, Kietz S, Strom A, Gustafsson JA. HES-1, a novel target gene for the aryl hydrocarbon receptor. Mol Pharmacol 2004, 65(1):165-171. 10.1124/mol.65.1.165, 14722248.
    • (2004) Mol Pharmacol , vol.65 , Issue.1 , pp. 165-171
    • Thomsen, J.S.1    Kietz, S.2    Strom, A.3    Gustafsson, J.A.4
  • 39
    • 0030888748 scopus 로고    scopus 로고
    • Aryl hydrocarbon receptor-mediated signal transduction
    • 10.3109/10408449709021615, 9099515
    • Rowlands JC, Gustafsson JA. Aryl hydrocarbon receptor-mediated signal transduction. Crit Rev Toxicol 1997, 27(2):109-134. 10.3109/10408449709021615, 9099515.
    • (1997) Crit Rev Toxicol , vol.27 , Issue.2 , pp. 109-134
    • Rowlands, J.C.1    Gustafsson, J.A.2
  • 40
    • 56549091431 scopus 로고    scopus 로고
    • The complexity of mitogen-activated protein kinases (MAPKs) made simple
    • 10.1007/s00018-008-8170-7, 18668205
    • Krishna M, Narang H. The complexity of mitogen-activated protein kinases (MAPKs) made simple. Cell Mol Life Sci 2008, 65(22):3525-3544. 10.1007/s00018-008-8170-7, 18668205.
    • (2008) Cell Mol Life Sci , vol.65 , Issue.22 , pp. 3525-3544
    • Krishna, M.1    Narang, H.2
  • 41
    • 34548833530 scopus 로고    scopus 로고
    • Incidence of subarachnoid haemorrhage: a systematic review with emphasis on region, age, gender and time trends
    • 10.1136/jnnp.2007.117655, 2095631, 17470467
    • de Rooij NK, Linn FH, van der Plas JA, Algra A, Rinkel GJ. Incidence of subarachnoid haemorrhage: a systematic review with emphasis on region, age, gender and time trends. J Neurol Neurosurg Psychiatry 2007, 78(12):1365-1372. 10.1136/jnnp.2007.117655, 2095631, 17470467.
    • (2007) J Neurol Neurosurg Psychiatry , vol.78 , Issue.12 , pp. 1365-1372
    • de Rooij, N.K.1    Linn, F.H.2    van der Plas, J.A.3    Algra, A.4    Rinkel, G.J.5
  • 44
    • 0029960055 scopus 로고    scopus 로고
    • TRANSFAC: a database on transcription factors and their DNA binding sites
    • 10.1093/nar/24.1.238, 145586, 8594589
    • ingender E, Dietze P, Karas H, Knuppel R. TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res 1996, 24(1):238-241. 10.1093/nar/24.1.238, 145586, 8594589.
    • (1996) Nucleic Acids Res , vol.24 , Issue.1 , pp. 238-241
    • ingender, E.1    Dietze, P.2    Karas, H.3    Knuppel, R.4
  • 46
    • 0033592606 scopus 로고    scopus 로고
    • Learning the parts of objects by non-negative matrix factorization
    • 10.1038/44565, 10548103
    • Lee DD, Seung HS. Learning the parts of objects by non-negative matrix factorization. Nature 1999, 401(6755):788-791. 10.1038/44565, 10548103.
    • (1999) Nature , vol.401 , Issue.6755 , pp. 788-791
    • Lee, D.D.1    Seung, H.S.2
  • 47
    • 84888277257 scopus 로고    scopus 로고
    • Proceedings of the Knowledge Discovery in Databases: PKDD 2003: 7th European Conference on Principles and Practice of Knowledge Discovery in Databases
    • Lavrac N, Gamberger D, Todorovski L, Blockeel H. Proceedings of the Knowledge Discovery in Databases: PKDD 2003: 7th European Conference on Principles and Practice of Knowledge Discovery in Databases. Springer-Verlag 2003,
    • (2003) Springer-Verlag
    • Lavrac, N.1    Gamberger, D.2    Todorovski, L.3    Blockeel, H.4
  • 48
    • 0016355478 scopus 로고
    • A new look at the statistical model identification
    • Akaike H. A new look at the statistical model identification. Automatic Control, IEEE Transactions on 1974, 19(6):716-723.
    • (1974) Automatic Control, IEEE Transactions on , vol.19 , Issue.6 , pp. 716-723
    • Akaike, H.1
  • 49
    • 15844414198 scopus 로고    scopus 로고
    • Objective clustering of proteins based on subcellular location patterns
    • 10.1155/JBB.2005.87, 1184054, 16046813
    • Chen X, Murphy RF. Objective clustering of proteins based on subcellular location patterns. J Biomed Biotechnol 2005, 2005(2):87-95. 10.1155/JBB.2005.87, 1184054, 16046813.
    • (2005) J Biomed Biotechnol , vol.2005 , Issue.2 , pp. 87-95
    • Chen, X.1    Murphy, R.F.2
  • 50
    • 67649197963 scopus 로고    scopus 로고
    • Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments
    • 10.1186/1471-2105-10-146, 2696449, 19445669
    • Liu T, Lin N, Shi N, Zhang B. Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments. BMC Bioinformatics 2009, 10:146. 10.1186/1471-2105-10-146, 2696449, 19445669.
    • (2009) BMC Bioinformatics , vol.10 , pp. 146
    • Liu, T.1    Lin, N.2    Shi, N.3    Zhang, B.4
  • 51
    • 0348013431 scopus 로고    scopus 로고
    • Clustering gene expression pattern and extracting relationship in gene network based on artificial neural networks
    • Huang J, Shimizu H, Shioya S. Clustering gene expression pattern and extracting relationship in gene network based on artificial neural networks. J Biosci Bioeng 2003, 96(5):421-428.
    • (2003) J Biosci Bioeng , vol.96 , Issue.5 , pp. 421-428
    • Huang, J.1    Shimizu, H.2    Shioya, S.3


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