ArticleBMC genomics2012
Gene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 30 citations in OpenAlex.
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- Enter the Matrix: Factorization Uncovers Knowledge from Omics.Trends in genetics : TIG · 2018Review
- Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance.Genome medicine · 2018Article
- Perturbation-response genes reveal signaling footprints in cancer gene expression.Nature communications · 2018Article
- PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.Bioinformatics (Oxford, England) · 2017Article
- Article
- Cleaved NOTCH1 Expression Pattern in Head and Neck Squamous Cell Carcinoma Is Associated with NOTCH1 Mutation, HPV Status, and High-Risk Features.Cancer prevention research (Philadelphia, Pa.) · 2015Article
- c-Abl modulates tumor cell sensitivity to antibody-dependent cellular cytotoxicity.Cancer immunology research · 2014Article
- Learning dysregulated pathways in cancers from differential variability analysis.Cancer informatics · 2014Review
- Capturing drug responses by quantitative promoter activity profiling.CPT: pharmacometrics & systems pharmacology · 2013Article
- Identifying context-specific transcription factor targets from prior knowledge and gene expression data.IEEE transactions on nanobioscience · 2013Article
- Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis.PloS one · 2013Article
- A new analysis approach of epidermal growth factor receptor pathway activation patterns provides insights into cetuximab resistance mechanisms in head and neck cancer.BMC medicine · 2012Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundAberrant activation of signaling pathways downstream of epidermal growth factor receptor (EGFR) has been hypothesized to be one of the mechanisms of cetuximab (a monoclonal antibody against EGFR) resistance in head and neck squamous cell carcinoma (HNSCC). To infer relevant and specific pathway activation downstream of EGFR from gene expression in HNSCC, we generated gene expression signatures using immortalized keratinocytes (HaCaT) subjected to ligand stimulation and transfected with EGFR, RELA/p65, or HRASVal12D.
resultsThe gene expression patterns that distinguished the HaCaT variants and conditions were inferred using the Markov chain Monte Carlo (MCMC) matrix factorization algorithm Coordinated Gene Activity in Pattern Sets (CoGAPS). This approach inferred gene expression signatures with greater relevance to cell signaling pathway activation than the expression signatures inferred with standard linear models. Furthermore, the pathway signature generated using HaCaT-HRASVal12D further associated with the cetuximab treatment response in isogenic cetuximab-sensitive (UMSCC1) and -resistant (1CC8) cell lines.
conclusionsOur data suggest that the CoGAPS algorithm can generate gene expression signatures that are pertinent to downstream effects of receptor signaling pathway activation and potentially be useful in modeling resistance mechanisms to targeted therapies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.