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UNLABELLED Network component analysis (NCA) is a method to deduce transcription factor (TF) activities and TF-gene regulation control strengths from gene expression data and a TF-gene binding connectivity network. Previously, this method could analyze a maximum number of regulators equal to the total sample size because of the identifiability limit in data(More)
BACKGROUND One of the primary objectives in cancer research is to identify causal genomic alterations, such as somatic copy number variation (CNV) and somatic mutations, during tumor development. Many valuable studies lack genomic data to detect CNV; therefore, methods that are able to infer CNVs from gene expression data would help maximize the value of(More)
  • Jing Jiao, Antreas Hindoyan, Shunyou Wang, Linh M. Tran, Andrew S. Goldstein, Devon Lawson +9 others
  • 2012
New therapies for late stage and castration resistant prostate cancer (CRPC) depend on defining unique properties and pathways of cell sub-populations capable of sustaining the net growth of the cancer. One of the best enrichment schemes for isolating the putative stem/progenitor cell from the murine prostate gland is Lin(-);Sca1(+);CD49f(hi) (LSC(hi)),(More)
BACKGROUND Network Component Analysis (NCA) has been used to deduce the activities of transcription factors (TFs) from gene expression data and the TF-gene binding relationship. However, the TF-gene interaction varies in different environmental conditions and tissues, but such information is rarely available and cannot be predicted simply by motif analysis.(More)
MOTIVATION Data from DNA microarrays and ChIP-chip binding assays often form the basis of transcriptional regulatory analyses. However, experimental noise in both data types combined with environmental dependence and uncorrelation between binding and regulation in ChIP-chip binding data complicate analyses that utilize these complimentary data sources.(More)
OBJECTIVES Pancreatic cysts are a group of lesions with heterogeneous malignant potential. Currently, there are no reliable biomarkers to aid in cyst diagnosis and classification. The objective of this study was to identify potential microRNA (miR) biomarkers in endoscopically acquired pancreatic cyst fluid that could be used to distinguish between benign,(More)
The modulation of promoter activity by DNA-binding transcription regulators forms a bipartite network between the regulators and genes, in which a smaller number of regulators control a much lager number of genes. To facilitate representation of gene expression data with the simplest possible network structure, we have characterized the ability of bipartite(More)
PTEN-controlled PI3K-AKT-mTOR pathway represents one of the most deregulated signaling pathways in human cancers. With many small molecule inhibitors that target PI3K-AKT-mTOR pathway being exploited clinically, sensitive and reliable ways of stratifying patients according to their PTEN functional status and determining treatment outcomes are urgently(More)
  • Marcus Ruscetti, Eman L. Dadashian, Weilong Guo, Bill Quach, David J. Mulholland, Juw Won Park +6 others
  • 2016
PI3K (phosphoinositide 3-kinase)/AKT and RAS/MAPK (mitogen-activated protein kinase) pathway coactivation in the prostate epithelium promotes both epithelial-mesenchymal transition (EMT) and metastatic castration-resistant prostate cancer (mCRPC), which is currently incurable. To study the dynamic regulation of the EMT process, we developed novel(More)