Coexpression and coregulation analysis of time-series gene expression data in estrogen-induced breast cancer cell

[1]  Ujjwal Maulik,et al.  Coexpression and coregulation analysis of time-series gene expression data in estrogen-induced breast cancer cell , 2013, Algorithms for Molecular Biology.

[2]  A E Giuliano,et al.  FOXC1 regulates the functions of human basal-like breast cancer cells by activating NF-κB signaling , 2012, Oncogene.

[3]  Ujjwal Maulik,et al.  δ-TRIMAX: Extracting Triclusters and Analysing Coregulation in Time Series Gene Expression Data , 2012, WABI.

[4]  Benjamin J. Raphael,et al.  Algorithms in Bioinformatics: 12th International Workshop, WABI 2012, Ljubljana, Slovenia, September 10-12, 2012 , 2012 .

[5]  W. Ye,et al.  CCL2 mediates cross-talk between cancer cells and stromal fibroblasts that regulates breast cancer stem cells. , 2012, Cancer research.

[6]  Matej Oresic,et al.  15‐Hydroxyprostaglandin dehydrogenase associates with poor prognosis in breast cancer, induces epithelial–mesenchymal transition, and promotes cell migration in cultured breast cancer cells , 2012, The Journal of pathology.

[7]  R. Aft,et al.  Targeting New Pathways and Cell Death in Breast Cancer , 2012 .

[8]  Mark Kester,et al.  The ATF/CREB Family of Transcription Factors in Breast Cancer , 2012 .

[9]  Wonshik Han,et al.  NFIB is a potential target for estrogen receptor‐negative breast cancers , 2011, Molecular oncology.

[10]  Eric A. Ariazi,et al.  Estrogen induces apoptosis in estrogen deprivation-resistant breast cancer through stress responses as identified by global gene expression across time , 2011, Proceedings of the National Academy of Sciences.

[11]  Simon Lord,et al.  Gene expression and hypoxia in breast cancer , 2011, Genome Medicine.

[12]  Alan Mackay,et al.  Functional viability profiles of breast cancer. , 2011, Cancer discovery.

[13]  Sheng Ding,et al.  Pretreatment with phosphatase and tensin homolog deleted on chromosome 10 (PTEN) inhibitor SF1670 augments the efficacy of granulocyte transfusion in a clinically relevant mouse model. , 2011, Blood.

[14]  Matthew Freeman,et al.  Mammalian EGF receptor activation by the rhomboid protease RHBDL2 , 2011, EMBO reports.

[15]  Daniel Birnbaum,et al.  High-Resolution Comparative Genomic Hybridization of Inflammatory Breast Cancer and Identification of Candidate Genes , 2011, PloS one.

[16]  Sridhar Ramaswamy,et al.  CK1ε Is Required for Breast Cancers Dependent on β-Catenin Activity , 2010, PloS one.

[17]  Kristina B. Emdal,et al.  Breast cancer cells can switch between estrogen receptor α and ErbB signaling and combined treatment against both signaling pathways postpones development of resistance , 2010, Breast Cancer Research and Treatment.

[18]  Matthias B. Stope,et al.  Estrogen receptor α attenuates transforming growth factor-β signaling in breast cancer cells independent from agonistic and antagonistic ligands , 2010, Breast Cancer Research and Treatment.

[19]  Piero Portincasa,et al.  New insights into the molecular mechanisms underlying effects of estrogen on cholesterol gallstone formation. , 2009, Biochimica et biophysica acta.

[20]  A. Toker,et al.  NFAT proteins: emerging roles in cancer progression , 2009, Nature Reviews Cancer.

[21]  Ujjwal Maulik,et al.  Finding Multiple Coherent Biclusters in Microarray Data Using Variable String Length Multiobjective Genetic Algorithm , 2009, IEEE Transactions on Information Technology in Biomedicine.

[22]  Ujjwal Maulik,et al.  A Novel Coherence Measure for Discovering Scaling Biclusters from Gene Expression Data , 2009, J. Bioinform. Comput. Biol..

[23]  Said Kamel,et al.  Extracellular Signal-Regulated Kinases 1 and 2 and TRPC1 Channels are Required for Calcium-Sensing Receptor-Stimulated MCF-7 Breast Cancer Cell Proliferation , 2009, Cellular Physiology and Biochemistry.

[24]  Jie Yu,et al.  Two Estrogen Response Element Sequences Near the PCNA Gene Are Not Responsible for Its Estrogen-Enhanced Expression in MCF7 Cells , 2008, PloS one.

[25]  Ujjwal Maulik,et al.  Multiobjective fuzzy biclustering in microarray data: Method and a new performance measure , 2008, 2008 IEEE Congress on Evolutionary Computation (IEEE World Congress on Computational Intelligence).

[26]  N. Crawford,et al.  Bromodomain 4 activation predicts breast cancer survival , 2008, Proceedings of the National Academy of Sciences.

[27]  Monique Chambon,et al.  Role of estrogens and their receptors in adhesion and invasiveness of breast cancer cells. , 2008, Advances in experimental medicine and biology.

[28]  Peter Langfelder,et al.  Eigengene networks for studying the relationships between co-expression modules , 2007, BMC Systems Biology.

[29]  Qian Wu,et al.  Role of specificity protein transcription factors in estrogen-induced gene expression in MCF-7 breast cancer cells. , 2007, Journal of molecular endocrinology.

[30]  Jayoung Kim,et al.  The phosphoinositide kinase PIKfyve mediates epidermal growth factor receptor trafficking to the nucleus. , 2007, Cancer research.

[31]  Yutaka Matsuda,et al.  Autocrine WNT signaling contributes to breast cancer cell proliferation via the canonical WNT pathway and EGFR transactivation , 2007, Breast Cancer Research.

[32]  Barry Komm,et al.  Estrogen-regulated gene networks in human breast cancer cells: involvement of E2F1 in the regulation of cell proliferation. , 2007, Molecular endocrinology.

[33]  Gordon B. Mills,et al.  Src promotes estrogen-dependent estrogen receptor α proteolysis in human breast cancer , 2007 .

[34]  Robert Gentleman,et al.  Using GOstats to test gene lists for GO term association , 2007, Bioinform..

[35]  Clifford A. Meyer,et al.  Genome-wide analysis of estrogen receptor binding sites , 2006, Nature Genetics.

[36]  Lothar Thiele,et al.  A systematic comparison and evaluation of biclustering methods for gene expression data , 2006, Bioinform..

[37]  Mieke Timmermans,et al.  How ADAM-9 and ADAM-11 Differentially From Estrogen Receptor Predict Response to Tamoxifen Treatment in Patients with Recurrent Breast Cancer: a Retrospective Study , 2005, Clinical Cancer Research.

[38]  Shiuan Chen,et al.  Dual Inhibition of mTOR and Estrogen Receptor Signaling In vitro Induces Cell Death in Models of Breast Cancer , 2005, Clinical Cancer Research.

[39]  Mohammed J. Zaki,et al.  TRICLUSTER: an effective algorithm for mining coherent clusters in 3D microarray data , 2005, SIGMOD '05.

[40]  Rola Barhoumi,et al.  Analysis of estrogen receptor alpha-Sp1 interactions in breast cancer cells by fluorescence resonance energy transfer. , 2005, Molecular endocrinology.

[41]  K. Lindblad-Toh,et al.  Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals , 2005, Nature.

[42]  David Botstein,et al.  GO: : TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes , 2004, Bioinform..

[43]  Gordon K Smyth,et al.  Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .

[44]  Partha Pratim Manna,et al.  CD47 Mediates Killing of Breast Tumor Cells via Gi-Dependent Inhibition of Protein Kinase A , 2004, Cancer Research.

[45]  Y. Benjamini,et al.  THE CONTROL OF THE FALSE DISCOVERY RATE IN MULTIPLE TESTING UNDER DEPENDENCY , 2001 .

[46]  Xin Chen,et al.  The TRANSFAC system on gene expression regulation , 2001, Nucleic Acids Res..

[47]  George M. Church,et al.  Biclustering of Expression Data , 2000, ISMB.

[48]  J. Huff,et al.  Breast cancer and environmental risk factors: epidemiological and experimental findings. , 1996, Annual review of pharmacology and toxicology.

[49]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .