ArticleFrontiers in genetics2021
Algorithmic Annotation of Functional Roles for Components of 3,044 Human Molecular Pathways.
Article in Frontiers in genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Machine Learning for Multi-Omics Characterization of Blood Cancers: A Systematic Review.Cells · 2025Pooled it
- Integrated Cell-Based Transcriptomic and Pathway Profiling Enables Scalable Functional Screening of Bioactive Microalgal Extracts.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Bioinformatic and clinical experimental assay uncovers resistance and susceptibility mechanisms of human glioblastomas to temozolomide and identifies new combined and individual survival biomarkers outperformingTherapeutic advances in medical oncology · 2024Article
- Lapatinib-induced enhancement of mitochondrial respiration in HER2-positive SK-BR-3 cells: mechanism revealed by analysis of proteomic but not transcriptomic data.Frontiers in molecular biosciences · 2024Article
- A single-cell multi-omic atlas spanning the adult rhesus macaque brain.Science advances · 2023Article
- Algorithmically Reconstructed Molecular Pathways as the New Generation of Prognostic Molecular Biomarkers in Human Solid Cancers.Proteomes · 2023Article
- Article
- Transcriptome-Based Traits of Radioresistant Sublines of Non-Small Cell Lung Cancer Cells.International journal of molecular sciences · 2023Article
- Large-scale assessment of pros and cons of autopsy-derived or tumor-matched tissues as the norms for gene expression analysis in cancers.Computational and structural biotechnology journal · 2023Article
- Reclassification of TCGA Diffuse Glioma Profiles Linked to Transcriptomic, Epigenetic, Genomic and Clinical Data, According to the 2021 WHO CNS Tumor Classification.International journal of molecular sciences · 2022Article
- Personalized targeted therapy prescription in colorectal cancer using algorithmic analysis of RNA sequencing data.BMC cancer · 2022Article
- Human Blood Serum Inhibits Ductal Carcinoma Cells BT474 Growth and Modulates Effect of HER2 Inhibition.Biomedicines · 2022Article
- Transcriptomic Analysis of DNA Repair Pathways in Human Non-Small Cell Lung Cancer Cells Surviving Multifraction X-Ray Irradiation.Bulletin of experimental biology and medicine · 2022Article
- Subtype of Neuroblastoma Cells with High KIT Expression Are Dependent on KIT and Its Knockdown Induces Compensatory Activation of Pro-Survival Signaling.International journal of molecular sciences · 2022Article
- Next-Generation Grade and Survival Expression Biomarkers of Human Gliomas Based on Algorithmically Reconstructed Molecular Pathways.International journal of molecular sciences · 2022Article
- 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
- Article
- OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization.Computational and structural biotechnology journal · 2022Article
- YAP1 Is a Potential Predictive Molecular Biomarker for Response to SMO Inhibitor in Medulloblastoma Cells.Cancers · 2021Article
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7 authors.
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Abstract
Current methods of high-throughput molecular and genomic analyses enabled to reconstruct thousands of human molecular pathways. Knowledge of molecular pathways structure and architecture taken along with the gene expression data can help interrogating the pathway activation levels (PALs) using different bioinformatic algorithms. In turn, the pathway activation profiles can characterize molecular processes, which are differentially regulated and give numeric characteristics of the extent of their activation or inhibition. However, different pathway nodes may have different functions toward overall pathway regulation, and calculation of PAL requires knowledge of molecular function of every node in the pathway in terms of its activator or inhibitory role. Thus, high-throughput annotation of functional roles of pathway nodes is required for the comprehensive analysis of the pathway activation profiles. We proposed an algorithm that identifies functional roles of the pathway components and applied it to annotate 3,044 human molecular pathways extracted from the Biocarta, Reactome, KEGG, Qiagen Pathway Central, NCI, and HumanCYC databases and including 9,022 gene products. The resulting knowledgebase can be applied for the direct calculation of the PALs and establishing large scale profiles of the signaling, metabolic, and DNA repair pathway regulation using high throughput gene expression data. We also provide a bioinformatic tool for PAL data calculations using the current pathway knowledgebase.
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