Evidence map›Paper›PMID 41530107›Full record

ArticleBioinformatics (Oxford, England)2026

ChemGenXplore: an interactive tool for exploring and analysing chemical genomic data.

Huda Ahmad, Hannah M Doherty, Sam T Benedict, James R J Haycocks, Ge Zhou, Patrick J Moynihan, Danesh Moradigaravand, Manuel Banzhaf

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Huda AhmadInstitute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom.
Hannah M DohertyInstitute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom.
Sam T BenedictNewcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom.
James R J HaycocksNewcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom.
Ge ZhouLaboratory of Infectious Disease Epidemiology, KAUST Center of Excellence for Smart Health and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
Patrick J MoynihanInstitute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom.
Danesh MoradigaravandLaboratory of Infectious Disease Epidemiology, KAUST Center of Excellence for Smart Health and Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
Manuel BanzhafInstitute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom.ORCID 0000-0002-4682-1037

Funding

Darwin Trust of EdinburghKAUST BAS/1/1108-01-01KAUST Center of Excellence for Smart HealthUKRI Future Leaders Fellowship FCC/1/5932-01-03UKRI Future Leaders Fellowship MR/V027204/1
6 · The paper itself

Abstract

motivationChemical genomics is a powerful high-throughput approach to systematically link phenotypes to genotypes. However, the vast datasets generated remain challenging to explore due to the lack of integrated, interactive tools for visualization and analysis. Existing workflows often require multiple independent software tools, limiting data accessibility and collaboration. Therefore, we created a user-friendly platform that enables efficient exploration and sharing of chemical genomics data.

resultsWe developed ChemGenXplore, a web-based Shiny application designed to streamline the visualization and analysis of chemical genomic screens. It offers two primary functionalities: one for exploring pre-implemented datasets and another for analysing user-uploaded datasets. ChemGenXplore enables users to visualize phenotypic profiles, assess gene-gene and condition-condition correlations, perform GO and KEGG enrichment analysis, and generate customizable, interactive heatmaps. To further support collaborative research, ChemGenXplore also facilitates the comparative analysis of chemical genomic and other omics datasets. By consolidating these features into a single interactive and accessible tool, ChemGenXplore facilitates data sharing, enhances reproducibility, and promotes collaboration within the research community. AVAILABILITY AND IMPLEMENTATION: ChemGenXplore is freely accessible as a web application at https://chemgenxplore.kaust.edu.sa/. Source code and documentation, including instructions for local installation, are provided on GitHub (https://github.com/Hudaahmadd/ChemGenXplore). A Docker image is also available on DockerHub (https://hub.docker.com/r/hudaahmad/chemgenxplore) to ensure reproducibility and simplify installation.

Indexed as

GenomicsSoftwareInternetUser-Computer Interface

Identifiers

PMID41530107
PMCPMC12872398

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.