-
1
-
-
0038054341
-
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
-
Mootha VK, et al. PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003;34(3):267-73.
-
(2003)
Nat Genet
, vol.34
, Issue.3
, pp. 267-273
-
-
Mootha, V.K.1
-
2
-
-
63449107173
-
A general modular framework for gene set enrichment analysis
-
Ackermann M, Strimmer K. A general modular framework for gene set enrichment analysis. BMC Bioinformatics. 2009;10:47.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 47
-
-
Ackermann, M.1
Strimmer, K.2
-
3
-
-
79958152651
-
Pathway analysis of expression data: deciphering functional building blocks of complex diseases
-
Emmert-Streib F, Glazko GV. Pathway analysis of expression data: deciphering functional building blocks of complex diseases. PLoS Comput Biol. 2011;7(5):e1002053.
-
(2011)
PLoS Comput Biol
, vol.7
, Issue.5
-
-
Emmert-Streib, F.1
Glazko, G.V.2
-
4
-
-
84876544061
-
Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential
-
Tripathi S, Glazko GV, Emmert-Streib F. Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential. Nucleic Acids Res. 2013;41(7):e82.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.7
-
-
Tripathi, S.1
Glazko, G.V.2
Emmert-Streib, F.3
-
5
-
-
84971667844
-
Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline
-
Rahmatallah Y, Emmert-Streib F, Glazko G. Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline. Brief Bioinform. 2016;17(3):393-407.
-
(2016)
Brief Bioinform
, vol.17
, Issue.3
, pp. 393-407
-
-
Rahmatallah, Y.1
Emmert-Streib, F.2
Glazko, G.3
-
6
-
-
77955889132
-
ROAST: rotation gene set tests for complex microarray experiments
-
Wu D, et al. ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics. 2010;26(17):2176-82.
-
(2010)
Bioinformatics
, vol.26
, Issue.17
, pp. 2176-2182
-
-
Wu, D.1
-
7
-
-
34547483895
-
Improving gene set analysis of microarray data by SAM-GS
-
Dinu I, et al. Improving gene set analysis of microarray data by SAM-GS. BMC Bioinformatics. 2007;8:242.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 242
-
-
Dinu, I.1
-
8
-
-
0346973088
-
On a new multivariate two-sample test
-
Baringhaus L, Franz C. On a new multivariate two-sample test. J Multivar Anal. 2004;88:190-206.
-
(2004)
J Multivar Anal
, vol.88
, pp. 190-206
-
-
Baringhaus, L.1
Franz, C.2
-
9
-
-
84923922737
-
Comparative evaluation of gene set analysis approaches for RNA-Seq data
-
Rahmatallah Y, Emmert-Streib F, Glazko G. Comparative evaluation of gene set analysis approaches for RNA-Seq data. BMC Bioinformatics. 2014;15:397.
-
(2014)
BMC Bioinformatics
, vol.15
, pp. 397
-
-
Rahmatallah, Y.1
Emmert-Streib, F.2
Glazko, G.3
-
10
-
-
84870441671
-
Gene set analysis for self-contained tests: complex null and specific alternative hypotheses
-
Rahmatallah Y, Emmert-Streib F, Glazko G. Gene set analysis for self-contained tests: complex null and specific alternative hypotheses. Bioinformatics. 2012;28(23):3073-80.
-
(2012)
Bioinformatics
, vol.28
, Issue.23
, pp. 3073-3080
-
-
Rahmatallah, Y.1
Emmert-Streib, F.2
Glazko, G.3
-
11
-
-
84867342942
-
Identifying the stem cell of the intestinal crypt: strategies and pitfalls
-
Barker N, van Oudenaarden A, Clevers H. Identifying the stem cell of the intestinal crypt: strategies and pitfalls. Cell Stem Cell. 2012;11(4):452-60.
-
(2012)
Cell Stem Cell
, vol.11
, Issue.4
, pp. 452-460
-
-
Barker, N.1
Oudenaarden, A.2
Clevers, H.3
-
12
-
-
46249103142
-
Differential variability analysis of gene expression and its application to human diseases
-
Ho JW, et al. Differential variability analysis of gene expression and its application to human diseases. Bioinformatics. 2008;24(13):i390-8.
-
(2008)
Bioinformatics
, vol.24
, Issue.13
, pp. i390-i398
-
-
Ho, J.W.1
-
13
-
-
84871819437
-
Genetic variants contribute to gene expression variability in humans
-
Hulse AM, Cai JJ. Genetic variants contribute to gene expression variability in humans. Genetics. 2013;193(1):95-108.
-
(2013)
Genetics
, vol.193
, Issue.1
, pp. 95-108
-
-
Hulse, A.M.1
Cai, J.J.2
-
14
-
-
80052308980
-
Variance of gene expression identifies altered network constraints in neurological disease
-
Mar JC, et al. Variance of gene expression identifies altered network constraints in neurological disease. PLoS Genet. 2011;7(8).
-
(2011)
PLoS Genet.
, vol.7
, Issue.8
-
-
Mar, J.C.1
-
15
-
-
79951801979
-
Antisense expression increases gene expression variability and locus interdependency
-
Xu Z, et al. Antisense expression increases gene expression variability and locus interdependency. Mol Syst Biol. 2011;7:468.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 468
-
-
Xu, Z.1
-
16
-
-
76549135113
-
Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease
-
Feinberg AP, Irizarry RA. Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc Natl Acad Sci U S A. 2010;107 Suppl 1:1757-64.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 1757-1764
-
-
Feinberg, A.P.1
Irizarry, R.A.2
-
17
-
-
79960927422
-
Increased methylation variation in epigenetic domains across cancer types
-
Hansen KD, et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet. 2011;43(8):768-75.
-
(2011)
Nat Genet
, vol.43
, Issue.8
, pp. 768-775
-
-
Hansen, K.D.1
-
18
-
-
84867637986
-
Gene expression anti-profiles as a basis for accurate universal cancer signatures
-
Bravo HC, et al. Gene expression anti-profiles as a basis for accurate universal cancer signatures. BMC Bioinformatics. 2012;13:272.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 272
-
-
Bravo, H.C.1
-
19
-
-
84930643211
-
Gene expression signatures based on variability can robustly predict tumor progression and prognosis
-
Dinalankara W, Bravo HC. Gene expression signatures based on variability can robustly predict tumor progression and prognosis. Cancer Inform. 2015;14:71-81.
-
(2015)
Cancer Inform
, vol.14
, pp. 71-81
-
-
Dinalankara, W.1
Bravo, H.C.2
-
20
-
-
84893275855
-
Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets
-
Rahmatallah Y, Emmert-Streib F, Glazko G. Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets. Bioinformatics. 2014;30(3):360-8.
-
(2014)
Bioinformatics
, vol.30
, Issue.3
, pp. 360-368
-
-
Rahmatallah, Y.1
Emmert-Streib, F.2
Glazko, G.3
-
21
-
-
70350682038
-
Statistical methods for gene set co-expression analysis
-
Choi Y, Kendziorski C. Statistical methods for gene set co-expression analysis. Bioinformatics. 2009;25(21):2780-6.
-
(2009)
Bioinformatics
, vol.25
, Issue.21
, pp. 2780-2786
-
-
Choi, Y.1
Kendziorski, C.2
-
22
-
-
65549155929
-
Identifying set-wise differential co-expression in gene expression microarray data
-
Cho SB, Kim J, Kim JH. Identifying set-wise differential co-expression in gene expression microarray data. BMC Bioinformatics. 2009;10:109.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 109
-
-
Cho, S.B.1
Kim, J.2
Kim, J.H.3
-
23
-
-
77951944123
-
A semi-parametric Bayesian model for unsupervised differential co-expression analysis
-
Freudenberg JM, et al. A semi-parametric Bayesian model for unsupervised differential co-expression analysis. BMC Bioinformatics. 2010;11:234.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 234
-
-
Freudenberg, J.M.1
-
24
-
-
81955161934
-
Capturing changes in gene expression dynamics by gene set differential coordination analysis
-
Yu T, Bai Y. Capturing changes in gene expression dynamics by gene set differential coordination analysis. Genomics. 2011;98(6):469-77.
-
(2011)
Genomics
, vol.98
, Issue.6
, pp. 469-477
-
-
Yu, T.1
Bai, Y.2
-
25
-
-
84943303297
-
CoGA: An R package to identify differentially co-expressed gene sets by analyzing the graph spectra
-
Santos SS, et al. CoGA: An R package to identify differentially co-expressed gene sets by analyzing the graph spectra. PLoS One. 2015;10(8):e0135831.
-
(2015)
PLoS One
, vol.10
, Issue.8
-
-
Santos, S.S.1
-
26
-
-
84871334644
-
Discriminating different classes of biological networks by analyzing the graphs spectra distribution
-
Takahashi DY, et al. Discriminating different classes of biological networks by analyzing the graphs spectra distribution. PLoS One. 2012;7(12):e49949.
-
(2012)
PLoS One
, vol.7
, Issue.12
-
-
Takahashi, D.Y.1
-
27
-
-
28744458859
-
Bioconductor: open software development for computational biology and bioinformatics
-
Gentleman RC, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):R80.
-
(2004)
Genome Biol
, vol.5
, Issue.10
, pp. R80
-
-
Gentleman, R.C.1
-
28
-
-
43349094507
-
The igraph software package for complex network research
-
Complex Systems
-
Scardi G, Nepusz T. The igraph software package for complex network research. InterJournal. 2006;Complex Systems:1695.
-
(2006)
InterJournal.
, pp. 1695
-
-
Scardi, G.1
Nepusz, T.2
-
29
-
-
0000673504
-
Multivariate generalization of the Wald-Wolfowitz and Smirnov two-sample tests
-
Friedman J, Rafsky L. Multivariate generalization of the Wald-Wolfowitz and Smirnov two-sample tests. Ann Stat. 1979;7:697-717.
-
(1979)
Ann Stat
, vol.7
, pp. 697-717
-
-
Friedman, J.1
Rafsky, L.2
-
30
-
-
0036258111
-
The IARC TP53 database: new online mutation analysis and recommendations to users
-
Olivier M, et al. The IARC TP53 database: new online mutation analysis and recommendations to users. Hum Mutat. 2002;19(6):607-14.
-
(2002)
Hum Mutat
, vol.19
, Issue.6
, pp. 607-614
-
-
Olivier, M.1
-
31
-
-
70449091786
-
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1
-
Barbie DA, et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature. 2009;462(7269):108-12.
-
(2009)
Nature
, vol.462
, Issue.7269
, pp. 108-112
-
-
Barbie, D.A.1
-
32
-
-
23844524767
-
Gene signatures of progression and metastasis in renal cell cancer
-
Jones J, et al. Gene signatures of progression and metastasis in renal cell cancer. Clin Cancer Res. 2005;11(16):5730-9.
-
(2005)
Clin Cancer Res
, vol.11
, Issue.16
, pp. 5730-5739
-
-
Jones, J.1
-
33
-
-
0033982936
-
KEGG: kyoto encyclopedia of genes and genomes
-
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27-30.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
34
-
-
27344435774
-
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian A, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545-50.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, Issue.43
, pp. 15545-15550
-
-
Subramanian, A.1
-
35
-
-
77958614226
-
Self-contained gene-set analysis of expression data: an evaluation of existing and novel methods
-
Fridley BL, Jenkins GD, Biernacka JM. Self-contained gene-set analysis of expression data: an evaluation of existing and novel methods. PLoS One. 2010;5:9.
-
(2010)
PLoS One
, vol.5
, pp. 9
-
-
Fridley, B.L.1
Jenkins, G.D.2
Biernacka, J.M.3
-
36
-
-
0003493777
-
Statistical methods for research workers
-
Edinburgh: Oliver and Boyd
-
Fisher RA. Statistical methods for research workers. Edinburgh: Oliver and Boyd; 1925.
-
(1925)
-
-
Fisher, R.A.1
-
37
-
-
33847735810
-
Gene alterations identified by expression profiling in tumor-associated endothelial cells from invasive ovarian carcinoma
-
Lu C, et al. Gene alterations identified by expression profiling in tumor-associated endothelial cells from invasive ovarian carcinoma. Cancer Res. 2007;67(4):1757-68.
-
(2007)
Cancer Res
, vol.67
, Issue.4
, pp. 1757-1768
-
-
Lu, C.1
-
38
-
-
73449095467
-
Versican overexpression in human breast cancer lesions: known and new isoforms for stromal tumor targeting
-
Kischel P, et al. Versican overexpression in human breast cancer lesions: known and new isoforms for stromal tumor targeting. Int J Cancer. 2010;126(3):640-50.
-
(2010)
Int J Cancer
, vol.126
, Issue.3
, pp. 640-650
-
-
Kischel, P.1
-
39
-
-
0029874902
-
Differential expression of versican isoforms in brain tumors
-
Paulus W, et al. Differential expression of versican isoforms in brain tumors. J Neuropathol Exp Neurol. 1996;55(5):528-33.
-
(1996)
J Neuropathol Exp Neurol
, vol.55
, Issue.5
, pp. 528-533
-
-
Paulus, W.1
-
40
-
-
0037180503
-
Gene expression profiling of isogenic cells with different TP53 gene dosage reveals numerous genes that are affected by TP53 dosage and identifies CSPG2 as a direct target of p53
-
Yoon H, et al. Gene expression profiling of isogenic cells with different TP53 gene dosage reveals numerous genes that are affected by TP53 dosage and identifies CSPG2 as a direct target of p53. Proc Natl Acad Sci U S A. 2002;99(24):15632-7.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, Issue.24
, pp. 15632-15637
-
-
Yoon, H.1
-
41
-
-
84963960008
-
Protein-protein interaction analysis for functional characterization of helicases
-
Zybailov BL, et al. Protein-protein interaction analysis for functional characterization of helicases. Methods. 2016;108(1):56-64.
-
(2016)
Methods
, vol.108
, Issue.1
, pp. 56-64
-
-
Zybailov, B.L.1
-
42
-
-
84862160806
-
PINA v2.0: mining interactome modules
-
Cowley MJ, et al. PINA v2.0: mining interactome modules. Nucleic Acids Res. 2012;40(Database issue):D862-5.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.DATABASE ISSUE
, pp. D862-D865
-
-
Cowley, M.J.1
-
43
-
-
84941051170
-
STRING v10: protein-protein interaction networks, integrated over the tree of life
-
Szklarczyk D, et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015;43(Database issue):D447-52.
-
(2015)
Nucleic Acids Res
, vol.43
, Issue.DATABASE ISSUE
, pp. D447-D452
-
-
Szklarczyk, D.1
|