-
1
-
-
63449107173
-
A general modular framework for gene set enrichment analysis
-
Ackermann,M. and Strimmer,K. (2009) A general modular framework for gene set enrichment analysis. BMC Bioinformatics, 10, 47.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 47
-
-
Ackermann, M.1
Strimmer, K.2
-
2
-
-
1542399989
-
FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes
-
Al-Shahrour,F. et al. (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
-
3
-
-
21444445084
-
BABELOMICS: A suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments
-
Al-Shahrour,F. et al. (2005) BABELOMICS: A suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res., 33, W460-W464.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Al-Shahrour, F.1
-
4
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner,M. et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
-
(2000)
Nat. Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
-
5
-
-
34547602163
-
GeneTrail-advanced gene set enrichment analysis
-
Backes,C. et al. (2007) GeneTrail-advanced gene set enrichment analysis. Nucleic Acids Res., 35, W186-W192.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Backes, C.1
-
6
-
-
33747884345
-
Gene Expression Omnibus: Microarray data storage, submission, retrieval, and analysis
-
Barrett,T. and Edgar,R. (2006) Gene Expression Omnibus: Microarray data storage, submission, retrieval, and analysis. Meth. Enzymol., 411, 352-369.
-
(2006)
Meth. Enzymol
, vol.411
, pp. 352-369
-
-
Barrett, T.1
Edgar, R.2
-
7
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. B, 57, 289-300.
-
(1995)
J. R. Stat. Soc. B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
8
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
Bolstad,B.M. et al. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193.
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
-
9
-
-
20844450402
-
Differential network expression during drug and stress response
-
Cabusora,L. et al. (2005) Differential network expression during drug and stress response. Bioinformatics, 21, 2898-2905.
-
(2005)
Bioinformatics
, vol.21
, pp. 2898-2905
-
-
Cabusora, L.1
-
10
-
-
0037097325
-
PKC, p42/44MAPK and p38MAPK regulate hepatocyte growth factor secretion from human astrocytoma cells
-
Chattopadhyay,N. et al. (2002) PKC, p42/44MAPK and p38MAPK regulate hepatocyte growth factor secretion from human astrocytoma cells. Brain Res. Mol. Brain Res., 102, 73-82.
-
(2002)
Brain Res. Mol. Brain Res
, vol.102
, pp. 73-82
-
-
Chattopadhyay, N.1
-
11
-
-
35348891430
-
Network-based classification of breast cancer metastasis
-
Chuang,H.Y. et al. (2007) Network-based classification of breast cancer metastasis. Mol. Syst. Biol., 3, 140.
-
(2007)
Mol. Syst. Biol
, vol.3
, pp. 140
-
-
Chuang, H.Y.1
-
12
-
-
33748374441
-
Dobesilate diminishes activation of the mitogen-activated protein kinase ERK1/2 in glioma cells
-
Cuevas,P. et al. (2006) Dobesilate diminishes activation of the mitogen-activated protein kinase ERK1/2 in glioma cells. J. Cell. Mol. Med., 10, 225-230.
-
(2006)
J. Cell. Mol. Med
, vol.10
, pp. 225-230
-
-
Cuevas, P.1
-
13
-
-
0036578644
-
GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways
-
Dahlquist,K. et al. (2002) GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat. Genet., 31, 19-20.
-
(2002)
Nat. Genet
, vol.31
, pp. 19-20
-
-
Dahlquist, K.1
-
14
-
-
46249128543
-
Identifying functional modules in protein-protein interaction networks: An integrated exact approach
-
Dittrich,M. et al. (2008) Identifying functional modules in protein-protein interaction networks: An integrated exact approach. Bioinformatics, 24, i223-i231.
-
(2008)
Bioinformatics
, vol.24
-
-
Dittrich, M.1
-
15
-
-
0036081355
-
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
-
Edgar,R. et al. (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30, 207-210.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 207-210
-
-
Edgar, R.1
-
17
-
-
37849009181
-
Emerging applications of network and pathway analysis in drug discovery and development
-
Ganter,B. and Giroux,C. (2008) Emerging applications of network and pathway analysis in drug discovery and development. Curr. Opin. Drug Discov. Dev., 11, 86-94.
-
(2008)
Curr. Opin. Drug Discov. Dev
, vol.11
, pp. 86-94
-
-
Ganter, B.1
Giroux, C.2
-
18
-
-
33645762226
-
A sharper bonferroni procedure for multiple tests of significance
-
Hochberg,Y. (1988) A sharper bonferroni procedure for multiple tests of significance. Biometrika, 75, 800-802.
-
(1988)
Biometrika
, vol.75
, pp. 800-802
-
-
Hochberg, Y.1
-
19
-
-
56649097558
-
GSEA-SNP: Applying gene set enrichment analysis to SNP data from genome-wide association studies
-
Holden,M. et al. (2008) GSEA-SNP: Applying gene set enrichment analysis to SNP data from genome-wide association studies. Bioinformatics, 24, 2784-2785.
-
(2008)
Bioinformatics
, vol.24
, pp. 2784-2785
-
-
Holden, M.1
-
20
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
Ideker,T. et al. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18 (Suppl. 1), S233-S240.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Ideker, T.1
-
21
-
-
34548418574
-
Formyl peptide receptor like 1 differentially requires mitogen-activated protein kinases for the induction of glial fibrillary acidic protein and interleukin-1alpha in human U87 astrocytoma cells
-
Kam,A. et al. (2007) Formyl peptide receptor like 1 differentially requires mitogen-activated protein kinases for the induction of glial fibrillary acidic protein and interleukin-1alpha in human U87 astrocytoma cells. Cell. Signal., 19, 2106-2117.
-
(2007)
Cell. Signal
, vol.19
, pp. 2106-2117
-
-
Kam, A.1
-
22
-
-
0037805576
-
The KEGG database
-
Kanehisa,M. (2002) The KEGG database. Novartis Found. Symp., 247, 91-101.
-
(2002)
Novartis Found. Symp
, vol.247
, pp. 91-101
-
-
Kanehisa, M.1
-
23
-
-
33644874819
-
From genomics to chemical genomics: New developments in KEGG
-
Kanehisa,M. et al. (2006) From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Res., 34, D354-D357.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kanehisa, M.1
-
24
-
-
35548988505
-
Computation of significance scores of unweighted Gene Set Enrichment Analyses
-
Keller,A. et al. (2007) Computation of significance scores of unweighted Gene Set Enrichment Analyses. BMC Bioinformatics, 8 290.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 290
-
-
Keller, A.1
-
25
-
-
33644877426
-
TRANSPATH: An information resource for storing and visualizing signaling pathways and their pathological aberrations
-
Krull,M. et al. (2006) TRANSPATH: An information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Res., 34, D546-D551.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Krull, M.1
-
26
-
-
0033670135
-
Pathway analysis in metabolic databases via differential metabolic display (DMD)
-
Kueffner,R. et al. (2000) Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics, 16 825-836.
-
(2000)
Bioinformatics
, vol.16
, pp. 825-836
-
-
Kueffner, R.1
-
27
-
-
36349035305
-
BN++ - a biological information system
-
Kuentzer,J. et al. (2006) BN++ - a biological information system. J. Integr. Bioinform., 3, 34.
-
(2006)
J. Integr. Bioinform
, vol.3
, pp. 34
-
-
Kuentzer, J.1
-
28
-
-
36349018852
-
BNDB - the biochemical network database
-
Kuentzer,J. et al. (2007) BNDB - the biochemical network database. BMC Bioinformatics, 8, 367.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 367
-
-
Kuentzer, J.1
-
29
-
-
0036369840
-
Genome-wide pathway analysis and visualization using gene expression data
-
Kurhekar,M. et al. (2002) Genome-wide pathway analysis and visualization using gene expression data. Pac. Symp. Biocomput., 462-473.
-
(2002)
Pac. Symp. Biocomput
, pp. 462-473
-
-
Kurhekar, M.1
-
30
-
-
0042354669
-
A mechanism of cyclin d1 action encoded in the patterns of gene expression in human cancer
-
Lamb,J. et al. (2003) A mechanism of cyclin d1 action encoded in the patterns of gene expression in human cancer. Cell, 114, 323-332.
-
(2003)
Cell
, vol.114
, pp. 323-332
-
-
Lamb, J.1
-
31
-
-
27944474776
-
ErmineJ: Tool for functional analysis of gene expression data sets
-
Lee,H. et al. (2005) ErmineJ: Tool for functional analysis of gene expression data sets. BMC Bioinformatics, 6, 269.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 269
-
-
Lee, H.1
-
32
-
-
60849088565
-
Gene set enrichment analysis for non-monotone association and multiple experimental categories
-
Lin,R. et al. (2008) Gene set enrichment analysis for non-monotone association and multiple experimental categories. BMC Bioinformatics 9, 481.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 481
-
-
Lin, R.1
-
33
-
-
33748554850
-
Topology-based cancer classification and related pathway mining using microarray data
-
Liu,C. et al. (2006) Topology-based cancer classification and related pathway mining using microarray data. Nucleic Acids Res., 34, 4069-4080.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 4069-4080
-
-
Liu, C.1
-
34
-
-
34347326247
-
Network-based analysis of affected biological processes in type 2 diabetes models
-
Liu,M. et al. (2007) Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet., 3, e96.
-
(2007)
PLoS Genet
, vol.3
-
-
Liu, M.1
-
35
-
-
54549108740
-
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
-
McLendon,R. et al. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455 1061-1068.
-
(2008)
Nature
, vol.455
, pp. 1061-1068
-
-
McLendon, R.1
-
36
-
-
0038054341
-
Pgc-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
-
Mootha,V. et al. (2003) Pgc-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat. Genet., 34, 267-273.
-
(2003)
Nat. Genet
, vol.34
, pp. 267-273
-
-
Mootha, V.1
-
37
-
-
43149116763
-
Gene-set approach for expression pattern analysis
-
Nam,D. and Kim,S. (2008) Gene-set approach for expression pattern analysis. Brief. Bioinform., 9, 189-197.
-
(2008)
Brief. Bioinform
, vol.9
, pp. 189-197
-
-
Nam, D.1
Kim, S.2
-
38
-
-
52949127312
-
An integrated genomic analysis of human glioblastoma multiforme
-
Parsons,D.W. et al. (2008) An integrated genomic analysis of human glioblastoma multiforme. Science, 321, 1807-1812.
-
(2008)
Science
, vol.321
, pp. 1807-1812
-
-
Parsons, D.W.1
-
39
-
-
33644820339
-
Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis
-
Phillips,H. et al. (2006) Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell, 9, 157-173.
-
(2006)
Cancer Cell
, vol.9
, pp. 157-173
-
-
Phillips, H.1
-
40
-
-
14644430468
-
-
Rahnenfuehrer,J. et al. (2004) Calculating the statistical significance of changes in pathway activity from gene expression data. Stat. Appl. Genet. Mol. Biol., 3, Article16.
-
Rahnenfuehrer,J. et al. (2004) Calculating the statistical significance of changes in pathway activity from gene expression data. Stat. Appl. Genet. Mol. Biol., 3, Article16.
-
-
-
-
41
-
-
34447640967
-
GenMAPP 2: New features and resources for pathway analysis
-
Salomonis,N. et al. (2007) GenMAPP 2: New features and resources for pathway analysis. BMC Bioinformatics, 8, 217.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 217
-
-
Salomonis, N.1
-
42
-
-
0034730944
-
TheAkt/protein kinase B-dependent anti-apoptotic pathway and the mitogen-activated protein kinase cascade are alternatively activated in human glioblastoma multiforme
-
Schlegel,J. et al. (2000) TheAkt/protein kinase B-dependent anti-apoptotic pathway and the mitogen-activated protein kinase cascade are alternatively activated in human glioblastoma multiforme. Cancer Lett., 158, 103-108.
-
(2000)
Cancer Lett
, vol.158
, pp. 103-108
-
-
Schlegel, J.1
-
43
-
-
84856043672
-
A mathematical theory of communication
-
Shannon (1984) A mathematical theory of communication. Bell Syst. Tech. J., 27, 623-656.
-
(1984)
Bell Syst. Tech. J
, vol.27
, pp. 623-656
-
-
Shannon1
-
44
-
-
2942533792
-
BioMiner-modeling, analyzing, and visualizing biochemical pathways and networks
-
Sirava,M. et al. (2002) BioMiner-modeling, analyzing, and visualizing biochemical pathways and networks. Bioinformatics, 18 (Suppl. 2), S219-S230.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 2
-
-
Sirava, M.1
-
45
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes
-
Su,A. et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA, 101 6062-6067.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 6062-6067
-
-
Su, A.1
-
46
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian,A. 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
-
47
-
-
47249120912
-
Detecting disease-specific dysregulated pathways via analysis of clinical expression profiles
-
Springer, Berlin, pp
-
Ulitsky,I. et al. (2008) Detecting disease-specific dysregulated pathways via analysis of clinical expression profiles. In Proceedings of Research in Computational Molecular Biology (RECOMB), Springer, Berlin, pp. 347-359.
-
(2008)
Proceedings of Research in Computational Molecular Biology (RECOMB)
, pp. 347-359
-
-
Ulitsky, I.1
-
48
-
-
4544276777
-
Network-based regulatory pathways analysis
-
Xiong,M. et al. (2004) Network-based regulatory pathways analysis. Bioinformatics, 20, 2056-2066.
-
(2004)
Bioinformatics
, vol.20
, pp. 2056-2066
-
-
Xiong, M.1
-
49
-
-
23144464901
-
WebGestalt: An integrated system for exploring gene sets in various biological contexts
-
Zhang,B. et al. (2005) WebGestalt: An integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res., 33, W741-W748.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Zhang, B.1
-
50
-
-
0034564487
-
Analysis of gene expression data with pathway scores
-
Zien,A. et al. (2000) Analysis of gene expression data with pathway scores. Proc. Int. Conf. Intell. Syst. Mol. Biol., 8 407-417.
-
(2000)
Proc. Int. Conf. Intell. Syst. Mol. Biol
, vol.8
, pp. 407-417
-
-
Zien, A.1
|