Now showing items 1-6 of 6
CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data
(Oxford University Press, 2010)
Coordinated Gene Activity in Pattern Sets (CoGAPS) provides an integrated package for isolating gene expression driven by a biological process, enhancing inference of biological processes from transcriptomic data. CoGAPS ...
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF
(Oxford University Press, 2017)
Non-negative Matrix Factorization (NMF) algorithms associate gene expression with biological processes (e.g. time-course dynamics or disease subtypes). Compared with univariate associations, the relative weights of NMF ...
Activation of the NOTCH Pathway in Head and Neck Cancer
(American Association for Cancer Research, 2014)
NOTCH1 mutations have been reported to occur in 10% to 15% of head and neck squamous cell carcinomas (HNSCC). To determine the significance of these mutations, we embarked upon a comprehensive study of NOTCH signaling in ...
Identifying context-specific transcription factor targets from prior knowledge and gene expression data
(Institute of Electrical and Electronics Engineers, 2013)
Numerous methodologies, assays, and databases presently provide candidate targets of transcription factors (TFs). However, TFs rarely regulate their targets universally. The context of activation of a TF can change the ...
Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer
(Oxford University Press, 2018)
Motivation Current bioinformatics methods to detect changes in gene isoform usage in distinct phenotypes compare the relative expected isoform usage in phenotypes. These statistics model differences in isoform usage in ...
NF‐κB and stat3 transcription factor signatures differentiate HPV‐positive and HPV‐negative head and neck squamous cell carcinoma
Using high-throughput analyses and the TRANSFAC database, we characterized TF signatures of head and neck squamous cell carcinoma (HNSCC) subgroups by inferential analysis of target gene expression, correcting for the ...