Comparative gene expression analysis in mouse models for identifying critical pathways in mammary gland development

Breast Cancer Research and Treatment

Volumn 132, Issue 3, 2012, Pages 969-977

  Zhao, Hongbo ^b   Huang, Mini ^a   Chen, Qiang ^a,c   Wang, Qishan ^a,c   Pan, Yuchun ^a,c  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b KUNMING MEDICAL UNIVERSITY   (China)

^c Key Lab for Animal Bio technology   (China)

Author keywords

Gene set enrichment analysis; Mammary gland; Microarray; Pathways

Indexed keywords

ADIPOCYTOKINE; CYTOKINE RECEPTOR;

ARACHIDONIC ACID METABOLISM; ARTICLE; BILE SECRETION; BREAST DEVELOPMENT; CELL COMMUNICATION; CELL METABOLISM; CELL PHAGOCYTOSIS; CONTROLLED STUDY; DNA REPLICATION; DOWN REGULATION; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; HEART CONTRACTION; INVOLUTION; LACTATION; LIPID ABSORPTION; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; OSTEOCLASTOGENESIS; PANCREAS SECRETION; PREGNANCY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PUBERTY; PYRIMIDINE METABOLISM; RHEUMATOID ARTHRITIS; SALIVATION; SIGNAL TRANSDUCTION; STAPHYLOCOCCUS INFECTION; UPREGULATION; AGING; ANIMAL; BAGG ALBINO MOUSE; C57BL MOUSE; COMPARATIVE STUDY; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; UDDER;

AGING; ANIMALS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; LACTATION; MAMMARY GLANDS, ANIMAL; METABOLIC NETWORKS AND PATHWAYS; MICE; MICE, INBRED BALB C; MICE, INBRED C57BL; PREGNANCY;

EID: 84865155189     PISSN: 01676806     EISSN: 15737217     Source Type: Journal    
DOI: 10.1007/s10549-011-1650-8     Document Type: Article

References (33)

1. Masso-Welch PA, Darcy KM, Stangle-Castor NC, Ip MM (2000) A developmental atlas of rat mammary gland histology. J Mammary Gland Biol Neoplasia 5:165-185
2. Richert MM, Schwertfeger KL, Ryder JW, Anderson SM (2000) An atlas of mouse mammary gland development. J Mammary Gland Biol Neoplasia 5:227-241
3. Rudolph MC, McManaman JL, Hunter L, Phang T, Neville MC (2003) Functional development of the mammary gland: use of expression profiling and trajectory clustering to reveal changes in gene expression during pregnancy, lactation, and involution. J Mammary Gland Biol Neoplasia 8:287-307
4. Clarkson RW, Wayland MT, Lee J, Freeman T, Watson CJ (2004) Gene expression profiling of mammary gland development reveals putative roles for death receptors and immune mediators in post-lactational regression. Breast Cancer Res 6:R92-R109
5. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP (2005) Gene set enrichment analysis: a knowledgebased approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102:15545-15550
6. Visvader JE, Venter D, Hahm K, Santamaria M, Sum EY, O'Reilly L, White D, Williams R, Armes J, Lindeman GJ (2001) The LIM domain gene LMO4 inhibits differentiation of mammary epithelial cells in vitro and is overexpressed in breast cancer. Proc Natl Acad Sci USA 98:14452-14457
7. Porter DA, Krop IE, Nasser S, Sgroi D, Kaelin CM, Marks JR, Riggins G, Polyak K (2001) A SAGE (serial analysis of gene expression) view of breast tumor progression. Cancer Res 61:5697-5702
8. Stein T, Morris JS, Davies CR, Weber-Hall SJ, Duffy MA, Heath VJ, Bell AK, Ferrier RK, Sandilands GP, Gusterson BA (2004) Involution of the mouse mammary gland is associated with an immune cascade and an acute-phase response, involving LBP, CD14 and STAT3. Breast Cancer Res 6:R75-R91
9. Ron M, Israeli G, Seroussi E, Weller JI, Gregg JP, Shani M, Medrano JF (2007) Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle. BMC Genomics 8:183
10. Anderson SM, Rudolph MC, McManaman JL, and Neville MC (2007) Key stages in mammary gland development. Secretory activation in the mammary gland: it's not just about milk protein synthesis! Breast Cancer Res 9:204
11. Mootha VK, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstrale M, Laurila E, Houstis N, Daly MJ, Patterson N, Mesirov JP, Golub TR, Tamayo P, Spiegelman B, Lander ES, Hirschhorn JN, Altshuler D, Groop LC (2003) PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34:267-273
12. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80
13. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4:249-264
14. Gautier L, Cope L, Bolstad BM, Irizarry RA (2004) Affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20:307-315
15. Gentleman R (2011). Using Categories to Analyze Microarray Data. http://www.bioconductor.org/packages/2.8/bioc/vignettes/Category/inst/doc/ Category.pdf
16. Manoli T, Gretz N, Grone HJ, Kenzelmann M, Eils R, Brors B (2006) Group testing for pathway analysis improves comparability of different microarray datasets. Bioinformatics 22:2500-2506
17. Robinson GW, Hennighausen L, Johnson PF (2000) Sidebranching in the mammary gland: the progesterone-Wnt connection. Genes Dev 14:889-894
18. Li M, Hu J, Heermeier K, Hennighausen L, Furth PA (1996) Expression of a viral oncoprotein during mammary gland development alters cell fate and function: induction of p53-independent apoptosis is followed by impaired milk protein production in surviving cells. Cell Growth Differ 7:3-11
19. Singer KL, Stevenson BR, Woo PL, Firestone GL (1994) Relationship of serine/threonine phosphorylation/dephosphorylation signaling to glucocorticoid regulation of tight junction permeability and ZO-1 distribution in nontransformed mammary epithelial cells. J Biol Chem 269:16108-16115
20. Buse P, Woo PL, Alexander DB, Reza A, Firestone GL (1995) Glucocorticoid-induced functional polarity of growth factor responsiveness regulates tight junction dynamics in transformed mammary epithelial tumor cells. J Biol Chem 270:28223-28227
21. Nguyen D-AD, Neville MC (1998) Tight junction regulation in the mammary gland. J Mammary Gland Biol Neoplasia 3:233-246
22. Mellenberger RW, Bauman DE (1974) Metabolic adaptations during lactogenesis fatty acid synthesis in rabbit mammary tissue during pregnancy and lactation. Biochem J 138:373-379
23. Barcellos-Hoff MH, Derynck R, Tsang ML, Weatherbee JA (1994) Transforming growth factor-beta activation in irradiated murine mammary gland. J Clin Invest 93:892-899
24. Soriano JV, Pepper MS, Orci L, Montesano R (1998) Roles of hepatocyte growth factor/scatter factor and transforming growth factor-β1 in mammary gland ductal morphogenesis. J Mammary Gland Biol Neoplasia 3:133-150
25. Wakefield LM, Piek E, Bottinger EP (2001) TGF-beta signaling in mammary gland development and tumorigenesis. J Mammary Gland Biol Neoplasia 6:67-82
26. Robinson SD, Silberstein GB, Roberts AB, Flanders KC, Daniel CW (1991) Regulated expression and growth inhibitory effects of transforming growth factor-beta isoforms in mouse mammary gland development. Development 113:867-878
27. Sordillo LM, Shafer-Weaver K, De Rosa D (1997) Immunobiology of the mammary gland. J Dairy Sci 80:1851-1865
28. Weisz-Carrington P, Roux ME, McWilliams M, Phillips-Quagliata JM, Lamm ME (1978) Hormonal induction of the secretory immune system in the mammary gland. Proc Natl Acad Sci USA 75:2928-2932
29. Wiseman BS, Werb Z (2002) Stromal effects on mammary gland development and breast cancer. Science 296:1046-1049
30. Schorr K, Li M, Krajewski S, Reed JC, Furth PA (1999) Bcl-2 gene family and related proteins in mammary gland involution and breast cancer. J Mammary Gland Biol Neoplasia 4:153-164
31. Cao Y, Karin M (2003) NF-κB in mammary gland development and breast cancer. J Mammary Gland Biol Neoplasia 8:215-223
32. Politi K, Feirt N, Kitajewski J (2004) Notch in mammary gland development and breast cancer. Semin Cancer Biol 14:341-347
33. Russo J, Hu YF, Silva ID, Russo IH (2001) Cancer risk related to mammary gland structure and development. Microsc Res Tech 52:204-223