ArticleComputational and structural biotechnology journal2022
OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization.
Article in Computational and structural biotechnology journal, 2022. 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
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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, 52 citations in OpenAlex.
- Integrated Cell-Based Transcriptomic and Pathway Profiling Enables Scalable Functional Screening of Bioactive Microalgal Extracts.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Molecular Context of ADAR-Mediated Editing of Coding RNA in Colorectal and Lung Cancers.International journal of molecular sciences · 2026Article
- Transcriptome-Wide Analysis of Pituitary and Ectopic Adrenocorticotropic Hormone-Secreting Tumors.Cancers · 2025Article
- Forced Overexpression and Knockout Analysis of SLC30A and SLC39A Family Genes Suggests Their Involvement in Establishing Resistance to Cisplatin in Human Cancer Cells.International journal of molecular sciences · 2024Article
- Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review.Briefings in bioinformatics · 2024Review
- Biomarkers of success of anti-PD-(L)1 immunotherapy for non-small cell lung cancer derived from RNA- and whole-exome sequencing: results of a prospective observational study on a cohort of 85 patients.Frontiers in immunology · 2024Observational
- Pan-cancer experimental characteristic of human transcriptional patterns connected with telomerase reverse transcriptase (Frontiers in genetics · 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
- 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
- Number of human protein interactions correlates with structural, but not regulatory conservation of the respective genes.Frontiers in genetics · 2024Article
- A single-cell multi-omic atlas spanning the adult rhesus macaque brain.Science advances · 2023Article
- Article
- Algorithmically Reconstructed Molecular Pathways as the New Generation of Prognostic Molecular Biomarkers in Human Solid Cancers.Proteomes · 2023Article
- Article
- Article
- In Silico Drug Repurposing in Multiple Sclerosis Using scRNA-Seq Data.International journal of molecular sciences · 2023Article
- Meta-analysis of expression and the targeting of cell adhesion associated genes in nine cancer types - A one research lab re-evaluation.Computational and structural biotechnology journal · 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
- 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
- Comprehensive Pan-Cancer Analyses of Immunogenic Cell Death as a Biomarker in Predicting Prognosis and Therapeutic Response.Cancers · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
OncoboxPD (Oncobox pathway databank) available at https://open.oncobox.com is the collection of 51 672 uniformly processed human molecular pathways. Superposition of all pathways formed interactome graph of protein-protein interactions and metabolic reactions containing 361 654 interactions and 64 095 molecular participants. Pathways are uniformly classified by biological processes, and each pathway node is algorithmically functionally annotated by specific activator/repressor role. This enables online calculation of statistically supported pathway activation levels (PALs) with the built-in bioinformatic tool using custom RNA/protein expression profiles. Each pathway can be visualized as static or dynamic graph, where vertices are molecules participating in a pathway and edges are interactions or reactions between them. Differentially expressed nodes in a pathway can be visualized in two-color mode with user-defined color scale. For every comparison, OncoboxPD also generates a graph summarizing top up- and downregulated pathways.
Indexed as
Identifiers
What OpenQuestion holds
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.