ArticleFrontiers in genetics2014
Oncofinder, a new method for the analysis of intracellular signaling pathway activation using transcriptomic data.
Article in Frontiers in genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
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- Algorithmically Reconstructed Molecular Pathways as the New Generation of Prognostic Molecular Biomarkers in Human Solid Cancers.Proteomes · 2023Article
- Uniformly shaped harmonization combines human transcriptomic data from different platforms while retaining their biological properties and differential gene expression patterns.Frontiers in molecular biosciences · 2023Article
- Omics Data and Data Representations for Deep Learning-Based Predictive Modeling.International journal of molecular sciences · 2022Review
- Better Agreement of Human Transcriptomic and Proteomic Cancer Expression Data at the Molecular Pathway Activation Level.International journal of molecular sciences · 2022Article
- Transcriptomic Portraits and Molecular Pathway Activation Features of Adult Spinal Intramedullary Astrocytomas.Frontiers in oncology · 2022Article
- Algorithmic Annotation of Functional Roles for Components of 3,044 Human Molecular Pathways.Frontiers in genetics · 2021Article
- System, Method and Software for Calculation of a Cannabis Drug Efficiency Index for the Reduction of Inflammation.International journal of molecular sciences · 2020Article
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- Disparity between Inter-Patient Molecular Heterogeneity and Repertoires of Target Drugs Used for Different Types of Cancer in Clinical Oncology.International journal of molecular sciences · 2020Article
- Mutation Enrichment and Transcriptomic Activation Signatures of 419 Molecular Pathways in Cancer.Cancers · 2020Article
- Editorial: Next Generation Sequencing Based Diagnostic Approaches in Clinical Oncology.Frontiers in oncology · 2020Article
- Atlas of RNA sequencing profiles for normal human tissues.Scientific data · 2019Article
- Pathway Based Analysis of Mutation Data Is Efficient for Scoring Target Cancer Drugs.Frontiers in pharmacology · 2019Article
- Exploration of the Transcriptional Landscape of ALPPS Reveals the Pathways of Accelerated Liver Regeneration.Frontiers in oncology · 2019Article
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- Acquired resistance to tyrosine kinase inhibitors may be linked with the decreased sensitivity to X-ray irradiation.Oncotarget · 2018Article
- Anticancer Activity of the Goat Antimicrobial Peptide ChMAP-28.Frontiers in pharmacology · 2018Article
- Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers.Frontiers in oncology · 2018Article
- Personalized prescription of tyrosine kinase inhibitors in unresectable metastatic cholangiocarcinoma.Experimental hematology & oncology · 2018Article
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Authors and funding
7 authors.
Funding
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Abstract
We propose a new biomathematical method, OncoFinder, for both quantitative and qualitative analysis of the intracellular signaling pathway activation (SPA). This method is universal and may be used for the analysis of any physiological, stress, malignancy and other perturbed conditions at the molecular level. In contrast to the other existing techniques for aggregation and generalization of the gene expression data for individual samples, we suggest to distinguish the positive/activator and negative/repressor role of every gene product in each pathway. We show that the relative importance of each gene product in a pathway can be assessed using kinetic models for "low-level" protein interactions. Although the importance factors for the pathway members cannot be so far established for most of the signaling pathways due to the lack of the required experimental data, we showed that ignoring these factors can be sometimes acceptable and that the simplified formula for SPA evaluation may be applied for many cases. We hope that due to its universal applicability, the method OncoFinder will be widely used by the researcher community.
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