ArticleOncotarget2014
Signaling pathways activation profiles make better markers of cancer than expression of individual genes.
Article in Oncotarget, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 79 citations in OpenAlex.
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- Personalized targeted therapy prescription in colorectal cancer using algorithmic analysis of RNA sequencing data.BMC cancer · 2022Article
- Transcriptomic Portraits and Molecular Pathway Activation Features of Adult Spinal Intramedullary Astrocytomas.Frontiers in oncology · 2022Article
- Key radioresistance regulation models and marker genes identified by integrated transcriptome analysis in nasopharyngeal carcinoma.Cancer medicine · 2021Article
- Algorithmic Annotation of Functional Roles for Components of 3,044 Human Molecular Pathways.Frontiers in genetics · 2021Article
- Machine Learning Applicability for Classification of PAD/VCD Chemotherapy Response Using 53 Multiple Myeloma RNA Sequencing Profiles.Frontiers in oncology · 2021Article
- Cancer gene expression profiles associated with clinical outcomes to chemotherapy treatments.BMC medical genomics · 2020Article
- RNA Sequencing in Comparison to Immunohistochemistry for Measuring Cancer Biomarkers in Breast Cancer and Lung Cancer Specimens.Biomedicines · 2020Article
- RNA sequencing profiles and diagnostic signatures linked with response to ramucirumab in gastric cancer.Cold Spring Harbor molecular case studies · 2020Article
- Gene signatures associated with genomic aberrations predict prognosis in neuroblastoma.Cancer communications (London, England) · 2020Article
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- Mutation Enrichment and Transcriptomic Activation Signatures of 419 Molecular Pathways in Cancer.Cancers · 2020Article
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- Pathway Based Analysis of Mutation Data Is Efficient for Scoring Target Cancer Drugs.Frontiers in pharmacology · 2019Article
- Use of deep neural network ensembles to identify embryonic-fetal transition markers: repression ofOncotarget · 2018Article
- Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers.Frontiers in oncology · 2018Article
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- Gene expression and molecular pathway activation signatures ofOncotarget · 2017Article
- Data aggregation at the level of molecular pathways improves stability of experimental transcriptomic and proteomic data.Cell cycle (Georgetown, Tex.) · 2017Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identification of reliable and accurate molecular markers remains one of the major challenges of contemporary biomedicine. We developed a new bioinformatic technique termed OncoFinder that for the first time enables to quantatively measure activation of intracellular signaling pathways basing on transcriptomic data. Signaling pathways regulate all major cellular events in health and disease. Here, we showed that the Pathway Activation Strength (PAS) value itself may serve as the biomarker for cancer, and compared it with the "traditional" molecular markers based on the expression of individual genes. We applied OncoFinder to profile gene expression datasets for the nine human cancer types including bladder cancer, basal cell carcinoma, glioblastoma, hepatocellular carcinoma, lung adenocarcinoma, oral tongue squamous cell carcinoma, primary melanoma, prostate cancer and renal cancer, totally 292 cancer and 128 normal tissue samples taken from the Gene expression omnibus (GEO) repository. We profiled activation of 82 signaling pathways that involve ~2700 gene products. For 9/9 of the cancer types tested, the PAS values showed better area-under-the-curve (AUC) scores compared to the individual genes enclosing each of the pathways. These results evidence that the PAS values can be used as a new type of cancer biomarkers, superior to the traditional gene expression biomarkers.
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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.