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Pathway correlation profile of gene-gene co-expression for identifying pathway perturbation.

Tegge AN, Caldwell CW, Xu D.

PLoS One. 2012;7(12):e52127. doi: 10.1371/journal.pone.0052127. Epub 2012 Dec 20.


Biological and functional analysis of statistically significant pathways deregulated in colon cancer by using gene expression profiles.

Distaso A, Abatangelo L, Maglietta R, Creanza TM, Piepoli A, Carella M, D'Addabbo A, Ancona N.

Int J Biol Sci. 2008;4(6):368-78. Epub 2008 Oct 14.


Evaluation of biological pathways involved in chemotherapy response in breast cancer.

Tordai A, Wang J, Andre F, Liedtke C, Yan K, Sotiriou C, Hortobagyi GN, Symmans WF, Pusztai L.

Breast Cancer Res. 2008;10(2):R37. doi: 10.1186/bcr2088. Epub 2008 Apr 29.


Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models.

Hirose O, Yoshida R, Imoto S, Yamaguchi R, Higuchi T, Charnock-Jones DS, Print C, Miyano S.

Bioinformatics. 2008 Apr 1;24(7):932-42. doi: 10.1093/bioinformatics/btm639. Epub 2008 Feb 21.


Gene expression profiling reveals new aspects of PIK3CA mutation in ERalpha-positive breast cancer: major implication of the Wnt signaling pathway.

Cizkova M, Cizeron-Clairac G, Vacher S, Susini A, Andrieu C, Lidereau R, Bièche I.

PLoS One. 2010 Dec 30;5(12):e15647. doi: 10.1371/journal.pone.0015647.


Using pathway signatures as means of identifying similarities among microarray experiments.

Beltrame L, Rizzetto L, Paola R, Rocca-Serra P, Gambineri L, Battaglia C, Cavalieri D.

PLoS One. 2009;4(1):e4128. doi: 10.1371/journal.pone.0004128. Epub 2009 Jan 6.


Transient over-expression of estrogen receptor-α in breast cancer cells promotes cell survival and estrogen-independent growth.

Tolhurst RS, Thomas RS, Kyle FJ, Patel H, Periyasamy M, Photiou A, Thiruchelvam PT, Lai CF, Al-Sabbagh M, Fisher RA, Barry S, Crnogorac-Jurcevic T, Martin LA, Dowsett M, Charles Coombes R, Kamalati T, Ali S, Buluwela L.

Breast Cancer Res Treat. 2011 Jul;128(2):357-68. doi: 10.1007/s10549-010-1122-6. Epub 2010 Aug 22.


Identification of single- and multiple-class specific signature genes from gene expression profiles by group marker index.

Tsai YS, Aguan K, Pal NR, Chung IF.

PLoS One. 2011;6(9):e24259. doi: 10.1371/journal.pone.0024259. Epub 2011 Sep 1.


Quantitative inference of dynamic regulatory pathways via microarray data.

Chang WC, Li CW, Chen BS.

BMC Bioinformatics. 2005 Mar 7;6:44.


A microarray approach to translational medicine in breast cancer: how representative are cell line models of clinical conditions?

Mehta JP, O'Driscoll L, Barron N, Clynes M, Doolan P.

Anticancer Res. 2007 May-Jun;27(3A):1295-300.


Gene Set/Pathway enrichment analysis.

Hung JH.

Methods Mol Biol. 2013;939:201-13. doi: 10.1007/978-1-62703-107-3_13.


Identifying neighborhoods of coordinated gene expression and metabolite profiles.

Hancock T, Wicker N, Takigawa I, Mamitsuka H.

PLoS One. 2012;7(2):e31345. doi: 10.1371/journal.pone.0031345. Epub 2012 Feb 15.


Bayesian network expansion identifies new ROS and biofilm regulators.

Hodges AP, Dai D, Xiang Z, Woolf P, Xi C, He Y.

PLoS One. 2010 Mar 3;5(3):e9513. doi: 10.1371/journal.pone.0009513.


The gene expression response of breast cancer to growth regulators: patterns and correlation with tumor expression profiles.

Cunliffe HE, Ringnér M, Bilke S, Walker RL, Cheung JM, Chen Y, Meltzer PS.

Cancer Res. 2003 Nov 1;63(21):7158-66.


Analysis of tumor environmental response and oncogenic pathway activation identifies distinct basal and luminal features in HER2-related breast tumor subtypes.

Gatza ML, Kung HN, Blackwell KL, Dewhirst MW, Marks JR, Chi JT.

Breast Cancer Res. 2011 Jun 7;13(3):R62. doi: 10.1186/bcr2899.


Genes dysregulated to different extent or oppositely in estrogen receptor-positive and estrogen receptor-negative breast cancers.

Zhou X, Shi T, Li B, Zhang Y, Shen X, Li H, Hong G, Liu C, Guo Z.

PLoS One. 2013 Jul 18;8(7):e70017. doi: 10.1371/journal.pone.0070017. Print 2013.


iTAP: integrated transcriptomics and phenotype database for stress response of Escherichia coli and Saccharomyces cerevisiae.

Sundararaman N, Ash C, Guo W, Button R, Singh J, Feng X.

BMC Res Notes. 2015 Dec 12;8:771. doi: 10.1186/s13104-015-1759-7.

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