Triple negative breast cancer: A multi-omics network discovery strategy for candidate targets and driving pathways

OMICS A Journal of Integrative Biology

Volumn 19, Issue 2, 2015, Pages 115-130

  Karagoz, Kubra ^a   Sinha, Raghu ^b   Arga, Kazim Yalcin ^a  

^a MARMARA UNIVERSITY   (Turkey)

^b PENN STATE COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

B LYMPHOCYTE RECEPTOR; HEPATOCYTE NUCLEAR FACTOR 3ALPHA; JANUS KINASE; MYC PROTEIN; STAT PROTEIN; T LYMPHOCYTE RECEPTOR; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR GATA 3; TUMOR NECROSIS FACTOR; PROTEOME; TRANSCRIPTOME;

APOPTOSIS; ARTICLE; CELL PROLIFERATION; CELL SURVIVAL; DOWN REGULATION; FEMALE; GENE; GENE EXPRESSION; GENE IDENTIFICATION; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN TISSUE; MLPH GENE; MOLECULAR THERAPY; MOLECULARLY TARGETED THERAPY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; TISSUE DIFFERENTIATION; TRANSCRIPTOMICS; TRIPLE NEGATIVE BREAST CANCER; UPREGULATION; BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION; GENETICS; INFORMATION PROCESSING; METABOLISM; PROTEIN ANALYSIS; PROTEOMICS;

COMPUTATIONAL BIOLOGY; DATASETS AS TOPIC; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; HUMANS; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; PROTEOME; PROTEOMICS; SIGNAL TRANSDUCTION; TRANSCRIPTION, GENETIC; TRANSCRIPTOME; TRIPLE NEGATIVE BREAST NEOPLASMS;

EID: 84923167998     PISSN: 15362310     EISSN: 15578100     Source Type: Journal    
DOI: 10.1089/omi.2014.0135     Document Type: Article

References (138)

1. Abba MC, Sun H, Hawkins KA, et al. (2007). Breast cancer molecular signatures as determined by SAGE: Correlation with lymph node status. Mol Cancer Res 5, 881-890.
2. Abramovitz M, Barwick BG, Willis S, et al. (2011). Molecular characterisation of formalin-fixed paraffin-embedded (FFPE) breast tumour specimens using a custom 512-gene breast cancer bead array-based platform. Br J Cancer 105, 1574-1581.
3. Adnane J, Muro-Cacho C, Mathews L, Sebti SM, and Munoz-Antonia T. (2002). Suppression of rho B expression in invasive carcinoma from head and neck cancer patients. Clin Cancer Res 8, 2225-2232.
4. Alles MC, Gardiner-Garden M, Nott DJ, et al. (2009). Metaanalysis and gene set enrichment relative to er status reveal elevated activity of MYC and E2F in the basal breast cancer subgroup. PLoS One 4, e4710.
5. Amberger J, Bocchini C, and Hamosh A. (2011). A new face and new challenges for Online Mendelian Inheritance in Man (OMIM(R)). Hum Mutat 32, 564-567.
6. Bailey CM, Khalkhali-Ellis Z, Kondo S, et al. (2005). Mammary serine protease inhibitor (Maspin) binds directly to interferon regulatory factor 6: Identification of a novel serpin partnership. J Biol Chem 280, 34210-34217.
7. Barrett T, Wilhite SE, Ledoux P, et al. (2013). NCBI GEO: Archive for functional genomics data sets-update. Nucleic Acids Res 41, D991-995.
8. Bartek J, and Lukas J. (2003). Chk1 and Chk2 kinases in checkpoint control and cancer. Cancer Cell 3, 421-429.
9. Baselga J, Segalla JG, Roche H, et al. (2012). Sorafenib in combination with capecitabine: An oral regimen for patients with HER2-negative locally advanced or metastatic breast cancer. J Clin Oncol 30, 1484-1491.
10. Becker KG, Barnes KC, Bright TJ, and Wang SA. (2004) the genetic association database. Nature Genet 36, 431-432.
11. Bender RJ, and Mac Gabhann F. (2013). Expression of VEGF and semaphorin genes define subgroups of triple negative breast cancer. PLoS One 8, e61788.
12. Ben-Porath I, Thomson MW, Carey VJ, et al. (2008). An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nature Genet 40, 499-507.
13. Bieche I, Girault I, Urbain E, Tozlu S, and Lidereau R. (2004). Relationship between intratumoral expression of genes coding for xenobiotic-metabolizing enzymes and benefit from adjuvant tamoxifen in estrogen receptor alpha-positive postmenopausal breast carcinoma. Breast Cancer Res 6, R252-263.
14. Blakely CM, Sintasath L, D'Cruz CM, et al. (2005). Developmental stage determines the effects of MYC in the mammary epithelium. Development 132, 1147-1160.
15. Bolstad BM, Irizarry RA, Astrand M, and Speed TP. (2003). A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193.
16. Bosch A, Eroles P, Zaragoza R, Vina JR, and Lluch A. (2010). Triple-negative breast cancer: Molecular features, pathogenesis, treatment and current lines of research. Cancer Treat Rev 36, 206-215.
17. Bovolenta LA, Acencio ML, and Lemke N. (2012). HTRIdb: An open-Access database for experimentally verified human transcriptional regulation interactions. BMC Genomics, 13, 405.
18. Boyle EI, Weng S, Gollub J, et al. (2004). GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20, 3710-3715.
19. Braun S, Hepp F, Kentenich CR, et al. (1999). Monoclonal antibody therapy with edrecolomab in breast cancer patients: Monitoring of elimination of disseminated cytokeratinpositive tumor cells in bone marrow. Clin Cancer Res 5, 3999-4004.
20. Braun S, Pantel K, Muller P, et al. (2000). Cytokeratin-positive cells in the bone marrow and survival of patients with stage I, II, or III breast cancer. New Eng J Med 342, 525-533.
21. Britschgi A, Andraos R, Brinkhaus H, et al. (2012). JAK2/STAT5 inhibition circumvents resistance to PI3K/mTOR blockade: A rationale for cotargeting these pathways in metastatic breast cancer. Cancer Cell 22, 796-811.
22. Cascione L, Gasparini P, Lovat F, et al. (2013). Integrated microRNA and mRNA signatures associated with survival in triple negative breast cancer. PLoS One 8, e55910.
23. Chandriani S, Frengen E, Cowling VH, et al. (2009). A core MYC gene expression signature is prominent in basal-like breast cancer but only partially overlaps the core serum response. Plos One 4, e6693.
24. Charpentier AH, Bednarek AK, Daniel RL, et al. (2000). Effects of estrogen on global gene expression: Identification of novel targets of estrogen action. Cancer Res 60, 5977-5983.
25. Cho HJ, Baek KE, Park SM, et al. (2009). RhoGDI2 expression is associated with tumor growth and malignant progression of gastric cancer. Clin Cancer Res 15, 2612-2619.
26. Chu IM, Michalowski AM, Hoenerhoff M, et al. (2012). GATA3 inhibits lysyl oxidase-mediated metastases of human basal triple-negative breast cancer cells. Oncogene 31, 2017-2027.
27. Cimino-Mathews A, Subhawong AP, Illei PB, et al. (2013). GATA3 expression in breast carcinoma: Utility in triplenegative, sarcomatoid, and metastatic carcinomas. Hum Pathol 44, 1341-1349.
28. Couderc B, Pradines A, Rafii A, et al. (2008). In vivo restoration of RhoB expression leads to ovarian tumor regression. Cancer Gene Therapy 15, 456-464.
29. Coughlin SS, and Ekwueme DU. (2009). Breast cancer as a global health concern. Cancer Epidemiol 33, 315-318.
30. Croft D, O'Kelly G, Wu G, et al. (2011). Reactome: A database of reactions, pathways and biological processes. Nucleic Acids Res 39 (Database issue), D691-697.
31. Dang CV. (1999). c-MYC target genes involved in cell growth, apoptosis and metabolism. Mol Cell Biol 19, 1-11.
32. Datta D, Flaxenburg JA, Laxmanan S, et al. (2006). Rasinduced modulation of CXCL10 and its receptor splice variant CXCR3-B in MDA-MB-435 and MCF-7 cells: Relevance for the development of human breast cancer. Cancer Res 66, 9509-9518.
33. De Santi M, Galluzzi L, Lucarini S, et al. (2011) the indole-3-carbinol cyclic tetrameric derivative CTet inhibits cell proliferation via overexpression of p21/CDKN1A in both estrogen receptor-positive and triple-negative breast cancer cell lines. Breast Cancer Res 13, R33.
34. Dey N, Barwick BG, Moreno CS, et al. (2013). Wnt signaling in triple negative breast cancer is associated with metastasis. BMC Cancer 13, 537.
35. Dluzen D, Li G, Tacelosky D, Moreau M, and Liu DX. (2011). BCL-2 is a downstream target of ATF5 that mediates the prosurvival function of ATF5 in a cell type-dependent manner. J Biol Chem 286, 7705-7713.
36. Drabsch Y, Hugo H, Zhang R, et al. (2007). Mechanism of and requirement for estrogen-regulated MYB expression in estrogen-receptor-positive breast cancer cells. Proc Natl Acad Sci USA 104, 13762-13767.
37. Drabsch Y, Robert RG, and Gonda TJ. (2010). MYB suppresses differentiation and apoptosis of human breast cancer cells. Breast Cancer Res 12, R55.
38. Dydensborg AB, Rose AA, Wilson BJ, et al. (2009). GATA3 inhibits breast cancer growth and pulmonary breast cancer metastasis. Oncogene 28, 2634-2642.
39. Eilers M, and Eisenman RN. (2008). Myc's broad reach. Genes Devel 22, 2755-2766.
40. El Baroudi M, La Sala D, Cinti C, and Capobianco E. (2013). DAC-driven integrative network regulation and pathway coordination in breast cancer. IWBBIO Proc 413-425.
41. Ell B, and Kang Y. (2013). Transcriptional control of cancer metastasis. Trends Cell Biol 23, 603-611.
42. Esseghir S, Kennedy A, Seedhar P, et al. (2007). Identification of NTN4, TRA1, and STC2 as prognostic markers in breast cancer in a screen for signal sequence encoding proteins. Clin Cancer Res 13, 3164-3173.
43. Ferrandina G, Lauriola L, Zannoni GF, et al. (2002). Increased cyclooxygenase-2 (COX-2) expression is associated with chemotherapy resistance and outcome in ovarian cancer patients. Ann Oncol 13, 1205-1211.
44. Fountzilas G, Dafni U, Gogas H, et al. (2008). Postoperative dose-dense sequential chemotherapy with epirubicin, paclitaxel and CMF in patients with high-risk breast cancer: Safety analysis of the Hellenic Cooperative Oncology Group randomized phase III trial HE 10/00. Ann Oncol 19, 853-860.
45. Galluzzi L, De Santi M, Crinelli R, et al. (2012). Induction of endoplasmic reticulum stress response by the indole-3-carbinol cyclic tetrameric derivative CTet in human breast cancer cell lines. PLoS One 7, e43249.
46. Galus R, and Wlodarski K. (2007). Cytokeratin detection as a diagnostic tool in oncology. Pol Merkur Lekarski 23, 209-211.
47. Gatza ML, Lucas JE, Barry WT, et al. (2010). A pathway-based classification of human breast cancer. Proc Natl Acad Sci USA 107, 6994-6999.
48. Gautier L, Cope L, Bolstad BM, and Irizarry RA. (2004). Affyanalysis of Affymetrix GeneChip data at the probe level. Bioinformatics 20, 307-315.
49. Gentleman RC, Carey VJ, Bates DM, et al. (2004). Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol 5, R80.
50. Gira AK, Kowalczyk AP, Feng Y, and Swerlick RA. (2009). Iron chelators and hypoxia mimetics inhibit IFNgammamediated Jak-STAT signaling. J Invest Dermatol 129, 723-729.
51. Girvan M, and Newman ME. (2002). Community structure in social and biological networks. Proc Natl Acad Sci USA 99, 7821-7826.
52. Gomis RR, Alarcon C, Nadal C, Van Poznak C, and Massague J. (2006). C/EBPbeta at the core of the TGFbeta cytostatic response and its evasion in metastatic breast cancer cells. Cancer Cell 10, 203-214.
53. Griffiths CL, and Olin JL. (2012). Triple negative breast cancer: A brief review of its characteristics and treatment options. J Res Pharmacy Pract 25, 319-323.
54. Guilluy C, Garcia-Mata R, and Burridge K. (2011). Rho protein crosstalk: Another social network? Trends Cell Biol 21, 718-726.
55. Hasko G, Linden J, Cronstein B, and Pacher P. (2008). Adenosine receptors: Therapeutic aspects for inflammatory and immune diseases. Nature Rev Drug Discov 7, 759-770.
56. Hicks C, Kumar R, Pannuti A, et al. (2013). An integrative genomics approach for associating GWAS information with triple-negative breast cancer. Cancer Informatics 12, 1-20.
57. Holm K, Hegardt C, Staaf J, et al. (2010). Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns. Breast Cancer Res 12, R36.
58. Horiuchi D, Kusdra L, Huskey NE, et al. (2012). MYC pathway activation in triple-negative breast cancer is synthetic lethal with CDK inhibition. J Exp Med 209, 679-696.
59. Howe EN, Cochrane DR, Cittelly DM, and Richer JK. (2012). miR-200c targets a NF-kappaB up-regulated TrkB/NTF3 autocrine signaling loop to enhance anoikis sensitivity in triple negative breast cancer. PLoS One 7, e49987.
60. Hsia TC, Tu CY, Chen YJ, et al. (2013). Lapatinib-mediated cyclooxygenase-2 expression via epidermal growth factor receptor/HuR interaction enhances the aggressiveness of triple-negative breast cancer cells. Mol Pharmacol 83, 857-869.
61. Huang da W, Sherman BT, and Lempicki RA. (2009). Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 7, 1-13.
62. Huang L, He Z, Guo L, and Wang H. (2008). Improvement of cognitive deficit and neuronal damage in rats with chronic cerebral ischemia via relative long-Term inhibition of rhokinase. Cell Mol Neurobiol 28, 757-768.
63. Idowu MO, Kmieciak M, Dumur C, et al. (2012). CD44( + )/ CD24(-/low) cancer stem/progenitor cells are more abundant in triple-negative invasive breast carcinoma phenotype and are associated with poor outcome. Hum Pathol 43, 364-373.
64. Ismail-Khan R, and Bui MM. (2010). A review of triplenegative breast cancer. Cancer Control 17, 173-176.
65. Iwaya K, and Mukai K. (2005). Accumulation of ubiquitinconjugated cytokeratin fragments in tumor cells. Sem Cancer Biol 15, 309-318.
66. Jiang C, Xuan Z, Zhao F, and Zhang MQ. (2007). TRED: A transcriptional regulatory element database, new entries and other development. Nucleic Acids Res 35 (Database issue), D137-140.
67. Kanehisa M, Goto S, Sato Y, Furumichi M, and Tanabe M. (2012). KEGG for integration and interpretation of largescale molecular data sets. Nucleic Acids Res 40 (Database issue), D109-114.
68. Kazerounian S, Gerald D, Huang M, et al. (2013). RhoB differentially controls Akt function in tumor cells and stromal endothelial cells during breast tumorigenesis. Cancer Res 73, 50-61.
69. Kessler O, Shraga-Heled N, Lange T, et al. (2004). Semaphorin-3F is an inhibitor of tumor angiogenesis. Cancer Res 64, 1008-1015.
70. Knopfova L, Benes P, Pekarcikova L, et al. (2012). c-Myb regulates matrix metalloproteinases 1/9, and cathepsin D: Implications for matrix-dependent breast cancer cell invasion and metastasis. Mol Cancer 11, 1-15.
71. Komatsu M, Yoshimaru T, Matsuo T, et al. (2013). Molecular features of triple negative breast cancer cells by genome-wide gene expression profiling analysis. Intl J Oncol 42, 478-506.
72. Kramer A, Green J, Pollard J, and Tugendreich S. (2014). Causal analysis approaches in Ingenuity Pathway Analysis. Bioinformatics 30, 523-530.
73. Kuo WH, Chang YY, Lai LC, et al. (2012). Molecular characteristics and metastasis predictor genes of triple-negative breast cancer: A clinical study of triple-negative breast carcinomas. PLoS One 7, e45831.
74. Lee ST, Feng M, Wei Y, et al. (2013). Protein tyrosine phosphatase UBASH3B is overexpressed in triple-negative breast cancer and promotes invasion and metastasis. Proc Natl Acad Sci USA 110, 11121-11126.
75. Lee U, Frankenberger C, Yun J, et al. (2013). A prognostic gene signature for metastasis-free survival of triple negative breast cancer patients. PLoS One 8, e82125.
76. Lehmann BD, Bauer JA, Chen X, et al. (2011). Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J Clin Invest 121, 2750-2767.
77. Li LF, Xu XJ, Zhao Y, et al. (2009). Integrated gene expression profile predicts prognosis of breast cancer patients. Breast Cancer Res Treatment 113, 231-237.
78. Li XL, Xu JH, Nie JH, and Fan SJ. (2012). Exogenous expression of UHRF1 promotes proliferation and metastasis of breast cancer cells. Oncol Rep 28, 375-383.
79. Liu F, Verin AD, Wang P, et al. (2001). Differential regulation of sphingosine-1-phosphate-And VEGF-induced endothelial cell chemotaxis. Involvement of G(ialpha2)-linked Rho kinase activity. Am J Respir Cell Mol Biol 24, 711-719.
80. Liu D, He J, Yuan Z, et al. (2012a). EGFR expression correlates with decreased disease-free survival in triple-negative breast cancer: A retrospective analysis based on a tissue microarray. Med Oncol 29, 401-405.
81. Liu H, Radisky DC, Yang D, et al. (2012b). MYC suppresses cancer metastasis by direct transcriptional silencing of alphav and beta3 integrin subunits. Nature Cell Biol 14, 567-574.
82. Liu LY, Chang LY, Kuo WH, et al. (2012c). Major functional transcriptome of an inferred center regulator of an ER(-)breast cancer model system. Cancer Informat 11, 87-111.
83. Mazieres J, Antonia T, Daste G, et al. (2004). Loss of RhoB expression in human lung cancer progression. Clin Cancer Res 10, 2742-2750.
84. Medale-Giamarchi C, Lajoie-Mazenc I, Malissein E, et al. (2013). RhoB modifies estrogen responses in breast cancer cells by influencing expression of the estrogen receptor. Breast Cancer Res 15, R6.
85. Meding S, Balluff B, Elsner M, et al. (2012). Tissue-based proteomics reveals FXYD3, S100A11 and GSTM3 as novel markers for regional lymph node metastasis in colon cancer. J Pathol 228, 459-470.
86. Mehra R, Varambally S, Ding L, et al. (2005). Identification of GATA3 as a breast cancer prognostic marker by global gene expression meta-Analysis. Cancer Res 65, 11259-11264.
87. Meyer N, and Penn LZ. (2008). Reflecting on 25 years with MYC. Nature Rev Cancer 8, 976-990.
88. Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, and Thomas PD. (2010). PANTHER version 7: Improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res 38 (Database issue), D204-
89. Moll R, Franke WW, Schiller DL, Geiger B, and Krepler R. (1982) the catalog of human cytokeratins: Patterns of expression in normal epithelia, tumors and cultured cells. Cell 31, 11-24.
90. Mudunuri U, Che A, Yi M, and Stephens RM. (2009). bioDBnet: The biological database network. Bioinformatics 25, 555-556.
91. Mulligan AM, Raitman I, Feeley L, et al. (2013). Tumoral lymphocytic infiltration and expression of the chemokine CXCL10 in breast cancers from the Ontario Familial Breast Cancer Registry. Clin Cancer Res 19, 336-346.
92. Nakshatri H, and Badve S. (2009). FOXA1 in breast cancer. Expert Rev Mol Med 11, e8.
93. Ota M, Shimada H, Masui H, et al. (2004). Adjuvant hepatic arterial infusion chemotherapy after curative resection for Dukes C colorectal cancer: A pilot study. Hepatogastroenterology 51, 124-127.
94. Ota T, Maeda M, Suto S, and Tatsuka M. (2004). LyGDI functions in cancer metastasis by anchoring Rho proteins to the cell membrane. Mol Carcinogenesis 39, 206-220.
95. Pan WW, Li JD, Huang S, Papadimos TJ, Pan ZK, and Chen LY. (2010). Synergistic activation of NF-{kappa}B by bacterial chemoattractant and TNF{alpha} is mediated by p38 MAPK-dependent RelA acetylation. J Biol Chem 285, 34348-34354.
96. Pantel K, Cote RJ, and Fodstad O. (1999). Detection and clinical importance of micrometastatic disease. J Natl Cancer Instit 91, 1113-1124.
97. Perou CM, Parker JS, Prat A, Ellis MJ, and Bernard PS. (2010). Clinical implementation of the intrinsic subtypes of breast cancer. Lancet Oncol 11, 718-719; 720-711.
98. Prat A, Adamo B, Cheang MC, Anders CK, Carey LA, and Perou CM. (2013). Molecular characterization of basal-like and non-basal-like triple-negative breast cancer. Oncologist 18, 123-133.
99. Prendergast GC. (2001). Actin up: RhoB in cancer and apoptosis. Nature Rev Cancer 1, 162-168.
100. Qi XF, Kim DH, Yoon YS, et al. (2009). Essential involvement of cross-Talk between IFN-gamma and TNF-Alpha in CXCL10 production in human THP-1 monocytes. J Cell Physiol 220, 690-697.
101. Rastelli F, Biancanelli S, Falzetta A, et al. (2010). Triplenegative breast cancer: Current state of the art. Tumori 96, 875-888.
102. Razick S, Magklaras G, and Donaldson IM. (2008). iRefIndex: A consolidated protein interaction database with provenance. BMC Bioinform 9, 405.
103. Rivera Rosado LA, Rodriguez-Canales J, and Zhang B. (2011). Association of D4-GDI expression with breast cancer progression. Cancer Biomarkers 10, 163-173.
104. Roberti MP, Arriaga JM, Bianchini M, et al. (2012). Protein expression changes during human triple negative breast cancer cell line progression to lymph node metastasis in a xenografted model in nude mice. Cancer Biol Therapy 13, 1123-1140.
105. Roll JD, Rivenbark AG, Sandhu R, et al. (2013). Dysregulation of the epigenome in triple-negative breast cancers: Basal-like and claudin-low breast cancers express aberrant DNA hypermethylation. Exp Mol Pathol 95, 276-287.
106. Saxena R, and Dwivedi A. (2012). ErbB family receptor inhibitors as therapeutic agents in breast cancer: Current status and future clinical perspective. Med Res Rev 32, 166-215.
107. Scherle P, Behrens T, and Staudt LM. (1993). Ly-GDI, a GDPdissociation inhibitor of the RhoA GTP-binding protein, is expressed preferentially in lymphocytes. Proc Natl Acad Sci USA 90, 7568-7572.
108. Sevimoglu T, and Arga KY. (2014) the role of protein interaction networks in system medicine. Comput Struct Biotechnol J 11, 22-24.
109. Siegel R, Naishadham D, and Jemal A. (2013). Cancer statistics, 2013. CA Cancer J Clinicians 63, 11-30.
110. Smoot ME, Ono K, Ruscheinski J, Wang PL, and Ideker T. (2011). Cytoscape 2.8: New features for data integration and network visualization. Bioinformatics 27, 431-432.
111. Smyth GK. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol 3 (article 3).
112. Sorlie T, Perou CM, Tibshirani R, et al. (2001). Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 98, 10869-10874.
113. Sparano JA, Goldstein LJ, Childs BH, et al. (2011). Relationship between quantitative GRB7 RNA expression and recurrence after adjuvant anthracycline chemotherapy in triple-negative breast cancer. Clin Cancer Res 17, 7194-7203.
114. Stathopoulou A, Vlachonikolis I, Mavroudis D, et al. (2002). Molecular detection of cytokeratin-19-positive cells in the peripheral blood of patients with operable breast cancer: Evaluation of their prognostic significance. J Clin Oncol 20, 3404-3412.
115. Szarc vel Szic K, Op de Beeck K, Ratman D, et al. (2014). Pharmacological levels of Withaferin A (Withania somnifera) trigger clinically relevant anticancer effects specific to triple negative breast cancer cells. PLoS One 9, e87850.
116. Tapper J, Kettunen E, El-Rifai W, Seppala M, Andersson LC, and Knuutila S. (2001). Changes in gene expression during progression of ovarian carcinoma. Cancer Genetics Cytogenetics 128, 1-6.
117. Tate CR, Rhodes LV, Segar HC, et al. (2012). Targeting triplenegative breast cancer cells with the histone deacetylase inhibitor panobinostat. Breast Cancer Res 14, R79.
118. Tchou J, Kossenkov AV, Chang L, et al. (2012). Human breast cancer associated fibroblasts exhibit subtype specific gene expression profiles. BMC Med Genomics 5, 39.
119. Thakkar AD, Raj H, Chakrabarti D, et al. (2010). Identification of gene expression signature in estrogen receptor positive breast carcinoma. Biomarkers Cancer 2, 1-15.
120. Thorner AR, Parker JS, Hoadley KA, and Perou CM. (2010). Potential tumor suppressor role for the c-Myb oncogene in luminal breast cancer. PLoS One 5, e13073.
121. Tommiska J, Bartkova J, Heinonen M, et al. (2008) the DNA damage signalling kinase ATM is aberrantly reduced or lost in BRCA1/BRCA2-deficient and ER/PR/ERBB2-Triplenegative breast cancer. Oncogene 27, 2501-2506.
122. Turner NC, and Reis-Filho JS. (2013). Tackling the diversity of triple-negative breast cancer. Clin Cancer Res 19, 6380-6388.
123. UniProt C. (2014). Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res 42, D191-D198.
124. Vaclavicek A, Bermejo JL, Schmutzler RK, et al. (2007). Polymorphisms in the Janus kinase 2 ( JAK)/signal transducer and activator of transcription (STAT) genes: Putative association of the STAT gene region with familial breast cancer. Endocrine Related Cancer 14, 267-277.
125. Voduc D, Cheang M, and Nielsen T. (2008). GATA-3 expression in breast cancer has a strong association with estrogen receptor but lacks independent prognostic value. Cancer Epidemiol Biomarkers Prevent 17, 365-373.
126. Walker SR, Nelson EA, Zou L, Chaudhury M, Signoretti S, Richardson A, and Frank DA. (2009). Reciprocal effects of STAT5 and STAT3 in breast cancer. Mol Cancer Rese 7, 966-976.
127. Walker SR, Xiang M, and Frank DA. (2014). Distinct roles of STAT3 and STAT5 in the pathogenesis and targeted therapy of breast cancer. Mol Cell Endocrinol 382, 616-621.
128. Wang Y, Tang Z, Xue R, Singh GK, Shi K, Lv Y, and Yang L. (2011). Combined effects of TNF-Alpha, IL-1beta, and HIF-1alpha on MMP-2 production in ACL fibroblasts under me-chanical stretch: an in vitro study. J Orthopaedic Re 29, 1008-1014.
129. Wong DJ, Liu H, Ridky TW, Cassarino D, Segal E, and Chang HY. (2008). Module map of stem cell genes guides creation of epithelial cancer stem cells. Cell Stem Cell 2, 333-344.
130. Xiang R, Davalos AR, Hensel CH, Zhou XJ, Tse C, and Naylor SL. (2002). Semaphorin 3F gene from human 3p21.3 suppresses tumor formation in nude mice. Cancer Res 62, 2637-2643.
131. Yang L, Wu X, Wang Y, et al. (2011). FZD7 has a critical role in cell proliferation in triple negative breast cancer. Oncogene 30, 4437-4446.
132. Yarden Y, and Sliwkowski MX. (2001). Untangling the ErbB signalling network. Nature Rev Mol Cell Biol 2, 127-137.
133. Yu KD, Fan L, Di GH, et al. (2010). Genetic variants in GSTM3 gene within GSTM4-GSTM2-GSTM1-GSTM5-GSTM3 cluster influence breast cancer susceptibility depending on GSTM1. Breast Cancer Res Treatment 121, 485-496.
134. Yu YL, Chou RH, Liang JH, et al. (2013). Targeting the EGFR/ PCNA signaling suppresses tumor growth of triple-negative breast cancer cells with cell-penetrating PCNA peptides. PLoS One 8, e61362.
135. Zhang Y, and Zhang B. (2006). D4-GDI, a Rho GTPase regulator, promotes breast cancer cell invasiveness. Cancer Res 66, 5592-5598.
136. Zheng R, and Blobel GA. (2010). GATA transcription factors and cancer. Genes Cancer 1, 1178-1188.
137. Zhou L, Li K, Luo Y, Tian L, Wang M, Li C, and Huang Q. (2013). Novel prognostic markers for patients with triplenegative breast cancer. Hum Pathol 44, 2180-2187.
138. Zhu H, Bhaijee F, Ishaq N, et al. (2013). Correlation of Notch1, pAKT and nuclear NF-kappaB expression in triple negative breast cancer. Am J Cancer Res 3, 230-239.