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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.


Quantitative inference of dynamic regulatory pathways via microarray data.

Chang WC, Li CW, Chen BS.

BMC Bioinformatics. 2005 Mar 7;6:44.


Regulator of G-protein signalling 2 mRNA is differentially expressed in mammary epithelial subpopulations and over-expressed in the majority of breast cancers.

Smalley MJ, Iravani M, Leao M, Grigoriadis A, Kendrick H, Dexter T, Fenwick K, Regan JL, Britt K, McDonald S, Lord CJ, Mackay A, Ashworth A.

Breast Cancer Res. 2007;9(6):R85.


Origin of co-expression patterns in E. coli and S. cerevisiae emerging from reverse engineering algorithms.

Zampieri M, Soranzo N, Bianchini D, Altafini C.

PLoS One. 2008 Aug 20;3(8):e2981. doi: 10.1371/journal.pone.0002981.


Metastatic canine mammary carcinomas can be identified by a gene expression profile that partly overlaps with human breast cancer profiles.

Klopfleisch R, Lenze D, Hummel M, Gruber AD.

BMC Cancer. 2010 Nov 9;10:618. doi: 10.1186/1471-2407-10-618.


Signal transduction pathway profiling of individual tumor samples.

Breslin T, Krogh M, Peterson C, Troein C.

BMC Bioinformatics. 2005 Jun 29;6:163.


Transcriptome profiling of a Saccharomyces cerevisiae mutant with a constitutively activated Ras/cAMP pathway.

Jones DL, Petty J, Hoyle DC, Hayes A, Ragni E, Popolo L, Oliver SG, Stateva LI.

Physiol Genomics. 2003 Dec 16;16(1):107-18.


Early dysregulation of cell adhesion and extracellular matrix pathways in breast cancer progression.

Emery LA, Tripathi A, King C, Kavanah M, Mendez J, Stone MD, de las Morenas A, Sebastiani P, Rosenberg CL.

Am J Pathol. 2009 Sep;175(3):1292-302. doi: 10.2353/ajpath.2009.090115. Epub 2009 Aug 21.


Intratumor heterogeneity and precision of microarray-based predictors of breast cancer biology and clinical outcome.

Barry WT, Kernagis DN, Dressman HK, Griffis RJ, Hunter JD, Olson JA, Marks JR, Ginsburg GS, Marcom PK, Nevins JR, Geradts J, Datto MB.

J Clin Oncol. 2010 May 1;28(13):2198-206. doi: 10.1200/JCO.2009.26.7245. Epub 2010 Apr 5.


Semaphorin-plexin signalling genes associated with human breast tumourigenesis.

Gabrovska PN, Smith RA, Tiang T, Weinstein SR, Haupt LM, Griffiths LR.

Gene. 2011 Dec 10;489(2):63-9. doi: 10.1016/j.gene.2011.08.024. Epub 2011 Sep 2.


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.


An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer.

Xu M, Kao MC, Nunez-Iglesias J, Nevins JR, West M, Zhou XJ.

BMC Genomics. 2008;9 Suppl 1:S12. doi: 10.1186/1471-2164-9-S1-S12.


D-Serine exposure resulted in gene expression changes implicated in neurodegenerative disorders and neuronal dysfunction in male Fischer 344 rats.

Davidson ME, Kerepesi LA, Soto A, Chan VT.

Arch Toxicol. 2009 Aug;83(8):747-62. doi: 10.1007/s00204-009-0405-3. Epub 2009 Feb 11.


Average rank-based score to measure deregulation of molecular pathway gene sets.

Yang H, Cheng C, Zhang W.

PLoS One. 2011;6(11):e27579. doi: 10.1371/journal.pone.0027579. Epub 2011 Nov 9.


MicroRNAs dysregulated in breast cancer preferentially target key oncogenic pathways.

Lim WK, Micklem G.

Mol Biosyst. 2011 Sep;7(9):2571-6. doi: 10.1039/c1mb05181d. Epub 2011 Jul 18.


Maximization of negative correlations in time-course gene expression data for enhancing understanding of molecular pathways.

Zeng T, Li J.

Nucleic Acids Res. 2010 Jan;38(1):e1. doi: 10.1093/nar/gkp822. Epub 2009 Oct 23.


Improved detection of differentially expressed genes through incorporation of gene locations.

Xiao G, Reilly C, Khodursky AB.

Biometrics. 2009 Sep;65(3):805-14. doi: 10.1111/j.1541-0420.2008.01161.x. Epub 2009 Jan 23.


Gene expression patterns and profile changes pre- and post-erlotinib treatment in patients with metastatic breast cancer.

Yang SX, Simon RM, Tan AR, Nguyen D, Swain SM.

Clin Cancer Res. 2005 Sep 1;11(17):6226-32.

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