ArticlePloS one2013
Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
25 citing papers in PubMed, 41 citations in OpenAlex.
- Unraveling the molecular landscape: an overview on gene expression, epigenetic alterations, and therapeutic challenges in head and neck squamous cell carcinoma.Molecular genetics and genomics : MGG · 2026Review
- NeMO Analytics: a compendium of transcriptomic data for the exploration of neocortical development.Nature neuroscience · 2026Article
- Building digital histology models of transcriptional tumor programs with generative deep learning for pathology-based precision medicine.Genome medicine · 2025Article
- Inferring cellular and molecular processes in single-cell data with non-negative matrix factorization using Python, R and GenePattern Notebook implementations of CoGAPS.Nature protocols · 2023Review
- Review
- Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma.Epigenetics · 2020Article
- DeepMF: deciphering the latent patterns in omics profiles with a deep learning method.BMC bioinformatics · 2019Article
- Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer.Scientific reports · 2019Article
- Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species.Cell systems · 2019Article
- 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
- Article
- Epigenetic regulation of gene expression in cancer: techniques, resources and analysis.Briefings in functional genomics · 2018Article
- NSD1 inactivation defines an immune cold, DNA hypomethylated subtype in squamous cell carcinoma.Scientific reports · 2017Article
- PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.Bioinformatics (Oxford, England) · 2017Article
- Prognostic significance of the methylation of Wnt pathway antagonists-CXXC4, DACT2, and the inhibitors of sonic hedgehog signaling-ZIC1, ZIC4, and HHIP in head and neck squamous cell carcinomas.Clinical oral investigations · 2017Article
- Identification of an atypical etiological head and neck squamous carcinoma subtype featuring the CpG island methylator phenotype.EBioMedicine · 2017Article
- Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC.Oncotarget · 2017Article
- Smoking status regulates a novel panel of PIWI-interacting RNAs in head and neck squamous cell carcinoma.Oral oncology · 2017Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 4 institutions in 1 country.
Funding
Abstract
Head and neck squamous cell carcinoma (HNSCC) is largely divided into two groups based on their etiology, human papillomavirus (HPV)-positive and -negative. Global DNA methylation changes are known to drive oncogene and tumor suppressor expression in primary HNSCC of both types. However, significant heterogeneity in DNA methylation within the groups results in different transcriptional profiles and clinical outcomes. We applied a meta-pathway analysis to link gene expression changes to DNA methylation in distinguishing HNSCC subtypes. This approach isolated specific epigenetic changes controlling expression in HPV- HNSCC that distinguish it from HPV+ HNSCC. Analysis of genes identified Hedgehog pathway activation specific to HPV- HNSCC. We confirmed that GLI1, the primary Hedgehog target, showed higher expression in tumors compared to normal samples with HPV- tumors having the highest GLI1 expression, suggesting that increased expression of GLI1 is a potential driver in HPV- HNSCC. Our algorithm for integration of DNA methylation and gene expression can infer biologically significant molecular pathways that may be exploited as therapeutics targets. Our results suggest that therapeutics targeting the Hedgehog pathway may be of benefit in HPV- HNSCC. Similar integrative analysis of high-throughput coupled DNA methylation and expression datasets may yield novel insights into deregulated pathways in other cancers.
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Registered trials
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.