-
1
-
-
41349096445
-
Gene regulation by transcription factors and micrornas
-
Hobert, O. (2008) Gene regulation by transcription factors and microRNAs. Science, 319, 1785-1786.
-
(2008)
Science
, vol.319
, pp. 1785-1786
-
-
Hobert, O.1
-
2
-
-
0034056133
-
Online mendelian inheritance in man (OMIM) as a knowledgebase for human developmental disorders
-
Boyadjiev, S.A. and Jabs, E.W. (2000) Online Mendelian Inheritance in Man (OMIM) as a knowledgebase for human developmental disorders. Clin Genet, 57, 253-266.
-
(2000)
Clin Genet
, vol.57
, pp. 253-266
-
-
Boyadjiev, S.A.1
Jabs, E.W.2
-
3
-
-
54849408182
-
An analysis of human microrna and disease associations
-
Lu, M., Zhang, Q., Deng, M., Miao, J., Guo, Y., Gao, W. and Cui, Q. (2008) An analysis of human microRNA and disease associations. PLoS ONE, 3, e3420.
-
(2008)
PLoS ONE
, vol.3
-
-
Lu, M.1
Zhang, Q.2
Deng, M.3
Miao, J.4
Guo, Y.5
Gao, W.6
Cui, Q.7
-
4
-
-
33144462258
-
Structural and functional properties of genes involved in human cancer
-
Furney, S.J., Higgins, D.G., Ouzounis, C.A. and Lopez-Bigas, N. (2006) Structural and functional properties of genes involved in human cancer. BMC Genomics, 7, 3.
-
(2006)
BMC Genomics
, vol.7
, pp. 3
-
-
Furney, S.J.1
Higgins, D.G.2
Ouzounis, C.A.3
Lopez-Bigas, N.4
-
5
-
-
1542399989
-
Fatigo: A web tool for finding significant associations of gene ontology terms with groups of genes
-
Al-Shahrour, F., Diaz-Uriarte, R. and Dopazo, J. (2004) FatiGO: a web tool for finding significant associations of gene ontology terms with groups of genes. Bioinformatics, 20, 578-580.
-
(2004)
Bioinformatics
, vol.20
, pp. 578-580
-
-
Al-Shahrour, F.1
Diaz-Uriarte, R.2
Dopazo, J.3
-
6
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S. et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA, 102, 15545-15550.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
-
7
-
-
78651275182
-
Reactome: A database of reactions, pathways and biological processes
-
Croft, D., O'Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B. et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res, 39, D691-D697.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Croft, D.1
O'Kelly, G.2
Wu, G.3
Haw, R.4
Gillespie, M.5
Matthews, L.6
Caudy, M.7
Garapati, P.8
Gopinath, G.9
Jassal, B.10
-
8
-
-
0035733108
-
The control of false discovery rate in multiple testing under dependency
-
Benjamini, Y. and Yekutieli, D. (2001) The control of false discovery rate in multiple testing under dependency. Ann Statist, 29, 1165-1188.
-
(2001)
Ann Statist
, vol.29
, pp. 1165-1188
-
-
Benjamini, Y.1
Yekutieli, D.2
-
9
-
-
84858221706
-
Ensembl 2012
-
Flicek, P., Amode, M.R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S. et al. (2012) Ensembl 2012. Nucleic Acids Res, 40, D84-D90.
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Brent, S.5
Carvalho-Silva, D.6
Clapham, P.7
Coates, G.8
Fairley, S.9
Fitzgerald, S.10
-
10
-
-
33644750115
-
MiRBase: MicroRNA sequences, targets and gene nomenclature
-
Griffiths-Jones, S., Grocock, R.J., van Dongen, S., Bateman, A. and Enright, A.J. (2006) miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res, 34, D140-D144.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Griffiths-Jones, S.1
Grocock, R.J.2
Van Dongen, S.3
Bateman, A.4
Enright, A.J.5
-
11
-
-
60149095444
-
Most mammalian mrnas are conserved targets of micrornas
-
Friedman, R.C., Farh, K.K., Burge, C.B. and Bartel, D.P. (2009) Most mammalian mrnas are conserved targets of micrornas. Genome Res, 19, 92-105.
-
(2009)
Genome Res
, vol.19
, pp. 92-105
-
-
Friedman, R.C.1
Farh, K.K.2
Burge, C.B.3
Bartel, D.P.4
-
12
-
-
58149186499
-
Mirecords: An integrated resource for microrna-target interactions
-
Xiao, F., Zuo, Z., Cai, G., Kang, S., Gao, X. and Li, T. (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res, 37, D105-D110.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Xiao, F.1
Zuo, Z.2
Cai, G.3
Kang, S.4
Gao, X.5
Li, T.6
-
13
-
-
78651266827
-
Mirtarbase: A database curates experimentally validated microrna-target interactions
-
Hsu, S.D., Lin, F.M., Wu, W.Y., Liang, C., Huang, W.C., Chan, W.L., Tsai, W.T., Chen, G.Z., Lee, C.J., Chiu, C.M. et al. (2011) miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res, 39, D163-D169.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Hsu, S.D.1
Lin, F.M.2
Wu, W.Y.3
Liang, C.4
Huang, W.C.5
Chan, W.L.6
Tsai, W.T.7
Chen, G.Z.8
Lee, C.J.9
Chiu, C.M.10
-
14
-
-
84855955378
-
Phenomir: Micrornas in human diseases and biological processes
-
Ruepp, A., Kowarsch, A. and Theis, F. (2012) PhenomiR: microRNAs in human diseases and biological processes. Methods Mol Biol, 822, 249-260.
-
(2012)
Methods Mol Biol
, vol.822
, pp. 249-260
-
-
Ruepp, A.1
Kowarsch, A.2
Theis, F.3
-
15
-
-
0034072450
-
DNA binding sites: Representation and discovery
-
Stormo, G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
-
(2000)
Bioinformatics
, vol.16
, pp. 16-23
-
-
Stormo, G.D.1
-
16
-
-
34547561588
-
+: A functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments
-
+: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res, 35, W91-W96.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Al-Shahrour, F.1
Minguez, P.2
Tarraga, J.3
Medina, I.4
Alloza, E.5
Montaner, D.6
Dopazo, J.7
-
17
-
-
38049148026
-
DAVID knowledgebase: A gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis
-
Sherman, B.T., Huang da, W., Tan, Q., Guo, Y., Bour, S., Liu, D., Stephens, R., Baseler, M.W., Lane, H.C. and Lempicki, R.A. (2007) DAVID knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics, 8, 426.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 426
-
-
Sherman, B.T.1
Huang Da, W.2
Tan, Q.3
Guo, Y.4
Bour, S.5
Liu, D.6
Stephens, R.7
Baseler, M.W.8
Lane, H.C.9
Lempicki, R.A.10
-
18
-
-
33750946376
-
Functional interpretation of microarray experiments
-
Dopazo, J. (2006) Functional interpretation of microarray experiments. Omics, 10, 398-410.
-
(2006)
Omics
, vol.10
, pp. 398-410
-
-
Dopazo, J.1
-
19
-
-
67849114236
-
Pscan: Finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes
-
Zambelli, F., Pesole, G. and Pavesi, G. (2009) Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes. Nucleic Acids Res, 37, W247-252.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Zambelli, F.1
Pesole, G.2
Pavesi, G.3
-
20
-
-
77954288773
-
Transfind-Predicting transcriptional regulators for gene sets
-
Kielbasa, S.M., Klein, H., Roider, H.G., Vingron, M. and Bluthgen, N. (2010) TransFind-predicting transcriptional regulators for gene sets. Nucleic Acids Res, 38, W275-W280.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Kielbasa, S.M.1
Klein, H.2
Roider, H.G.3
Vingron, M.4
Bluthgen, N.5
-
21
-
-
34547560557
-
Opossum: Integrated tools for analysis of regulatory motif over-representation
-
Ho Sui, S.J., Fulton, D.L., Arenillas, D.J., Kwon, A.T. and Wasserman, W.W. (2007) oPOSSUM: integrated tools for analysis of regulatory motif over-representation. Nucleic Acids Res, 35, W245-W252.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Ho Sui, S.J.1
Fulton, D.L.2
Arenillas, D.J.3
Kwon, A.T.4
Wasserman, W.W.5
-
22
-
-
3242891885
-
CARRIE web service: Automated transcriptional regulatory network inference and interactive analysis
-
Haverty, P.M., Frith, M.C. and Weng, Z. (2004) CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. Nucleic Acids Res, 32, W213-W216.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Haverty, P.M.1
Frith, M.C.2
Weng, Z.3
-
23
-
-
33747835613
-
Composite module analyst: Identification of transcription factor binding site combinations using genetic algorithm
-
Waleev, T., Shtokalo, D., Konovalova, T., Voss, N., Cheremushkin, E., Stegmaier, P., Kel-Margoulis, O., Wingender, E. and Kel, A. (2006) Composite module analyst: identification of transcription factor binding site combinations using genetic algorithm. Nucleic Acids Res, 34, W541-W545.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Waleev, T.1
Shtokalo, D.2
Konovalova, T.3
Voss, N.4
Cheremushkin, E.5
Stegmaier, P.6
Kel-Margoulis, O.7
Wingender, E.8
Kel, A.9
-
24
-
-
67849101186
-
MicroRNA and mRNA integrated analysis (MMIA): A web tool for examining biological functions of microRNA expression
-
Nam, S., Li, M., Choi, K., Balch, C., Kim, S. and Nephew, K.P. (2009) MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res, 37, W356-W362.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Nam, S.1
Li, M.2
Choi, K.3
Balch, C.4
Kim, S.5
Nephew, K.P.6
-
25
-
-
67849126820
-
Geneset2mirna: Finding the signature of cooperative mirna activities in the gene lists
-
Antonov, A.V., Dietmann, S., Wong, P., Lutter, D. and Mewes, H.W. (2009) GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists. Nucleic Acids Res, 37, W323-W328.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Antonov, A.V.1
Dietmann, S.2
Wong, P.3
Lutter, D.4
Mewes, H.W.5
-
26
-
-
79960022362
-
Mirvestigator: Web application to identify mirnas responsible for co-regulated gene expression patterns discovered through transcriptome profiling
-
Plaisier, C.L., Bare, J.C. and Baliga, N.S. (2011) miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling. Nucleic Acids Res, 39, W125-W131.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Plaisier, C.L.1
Bare, J.C.2
Baliga, N.S.3
-
27
-
-
77955043355
-
MiRror: A combinatorial analysis web tool for ensembles of microRNAs and their targets
-
Friedman, Y., Naamati, G. and Linial, M. (2010) MiRror: a combinatorial analysis web tool for ensembles of microRNAs and their targets. Bioinformatics, 26, 1920-1921.
-
(2010)
Bioinformatics
, vol.26
, pp. 1920-1921
-
-
Friedman, Y.1
Naamati, G.2
Linial, M.3
-
28
-
-
79959997653
-
MirConnX: Condition-specific mRNA-microRNA network integrator
-
Huang, G.T., Athanassiou, C. and Benos, P.V. (2011) mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res, 39, W416-W423.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Huang, G.T.1
Athanassiou, C.2
Benos, P.V.3
-
29
-
-
77956548953
-
Cytoscape web: An interactive web-based network browser
-
Lopes, C.T., Franz, M., Kazi, F., Donaldson, S.L., Morris, Q. and Bader, G.D. (2010) Cytoscape web: an interactive web-based network browser. Bioinformatics, 26, 2347-2348.
-
(2010)
Bioinformatics
, vol.26
, pp. 2347-2348
-
-
Lopes, C.T.1
Franz, M.2
Kazi, F.3
Donaldson, S.L.4
Morris, Q.5
Bader, G.D.6
-
30
-
-
58549112996
-
Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
-
Huang da, W., Sherman, B.T. and Lempicki, R.A. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res, 37, 1-13.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 1-13
-
-
Huang Da, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
31
-
-
33744481750
-
Molecular pathogenesis of fanconi anemia: Recent progress
-
Taniguchi, T. and D'Andrea, A.D. (2006) Molecular pathogenesis of Fanconi anemia: recent progress. Blood, 107, 4223-4233.
-
(2006)
Blood
, vol.107
, pp. 4223-4233
-
-
Taniguchi, T.1
D'Andrea, A.D.2
-
32
-
-
73949118736
-
Tlr8-dependent TNF-(alpha) overexpression in fanconi anemia group C cells
-
Vanderwerf, S.M., Svahn, J., Olson, S., Rathbun, R.K., Harrington, C., Yates, J., Keeble, W., Anderson, D.C., Anur, P., Pereira, N.F. et al. (2009) TLR8-dependent TNF-(alpha) overexpression in Fanconi anemia group C cells. Blood, 114, 5290-5298.
-
(2009)
Blood
, vol.114
, pp. 5290-5298
-
-
Vanderwerf, S.M.1
Svahn, J.2
Olson, S.3
Rathbun, R.K.4
Harrington, C.5
Yates, J.6
Keeble, W.7
Anderson, D.C.8
Anur, P.9
Pereira, N.F.10
-
33
-
-
77954339096
-
Babelomics: An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling
-
Medina, I., Carbonell, J., Pulido, L., Madeira, S.C., Goetz, S., Conesa, A., Tarraga, J., Pascual-Montano, A., Nogales-Cadenas, R., Santoyo, J. et al. (2010) Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res, 38, W210-W213.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Medina, I.1
Carbonell, J.2
Pulido, L.3
Madeira, S.C.4
Goetz, S.5
Conesa, A.6
Tarraga, J.7
Pascual-Montano, A.8
Nogales-Cadenas, R.9
Santoyo, J.10
-
34
-
-
79961040243
-
Fanconi anemia core complex gene promoters harbor conserved transcription regulatory elements
-
Meier, D. and Schindler, D. (2011) Fanconi anemia core complex gene promoters harbor conserved transcription regulatory elements. PLoS ONE, 6, e22911.
-
(2011)
PLoS ONE
, vol.6
-
-
Meier, D.1
Schindler, D.2
-
35
-
-
80053459622
-
Areca nut induces mir-23a and inhibits repair of DNA double-strand breaks by targeting FANCG
-
Tsai, Y.S., Lin, C.S., Chiang, S.L., Lee, C.H., Lee, K.W. and Ko, Y.C. (2011) Areca nut induces miR-23a and inhibits repair of DNA double-strand breaks by targeting FANCG. Toxicol Sci, 123, 480-490.
-
(2011)
Toxicol Sci
, vol.123
, pp. 480-490
-
-
Tsai, Y.S.1
Lin, C.S.2
Chiang, S.L.3
Lee, C.H.4
Lee, K.W.5
Ko, Y.C.6
|