Evidence map›Paper›PMID 38724240›Full record

ArticleBioinformatics (Oxford, England)2024

PathwayNexus: a tool for interactive metabolic data analysis.

Philipp Eberhard, Martin Kern, Michael Aichem, Hanna Borlinghaus, Karsten Klein, Johannes Delp, Ilinca Suciu, Benjamin Moser, Daniel Dietrich, Marcel Leist and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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

11 authors.

Philipp EberhardDepartment of Computer and Information Science, University of Konstanz, Konstanz 78464, Germany.
Martin KernDepartment of Computer and Information Science, University of Konstanz, Konstanz 78464, Germany.
Michael AichemDepartment of Computer and Information Science, University of Konstanz, Konstanz 78464, Germany.ORCID 0000-0002-1286-1372
Hanna BorlinghausDepartment of Computer and Information Science, University of Konstanz, Konstanz 78464, Germany.
Karsten KleinDepartment of Computer and Information Science, University of Konstanz, Konstanz 78464, Germany.
Johannes DelpDepartment of In Vitro Toxicology and Biomedicine, University of Konstanz, Konstanz 78464, Germany.
Ilinca SuciuDepartment of In Vitro Toxicology and Biomedicine, University of Konstanz, Konstanz 78464, Germany.
Benjamin MoserDepartment of Computer and Information Science, University of Konstanz, Konstanz 78464, Germany.
Daniel DietrichDepartment of Human and Environmental Toxicology, University of Konstanz, Konstanz 78464, Germany.ORCID 0000-0003-0416-3811
Marcel LeistDepartment of In Vitro Toxicology and Biomedicine, University of Konstanz, Konstanz 78464, Germany.ORCID 0000-0002-3778-8693
Falk SchreiberDepartment of Computer and Information Science, University of Konstanz, Konstanz 78464, Germany.ORCID 0000-0002-9307-3254

Funding

DFG 251654672
6 · The paper itself

Abstract

motivationHigh-throughput omics methods increasingly result in large datasets including metabolomics data, which are often difficult to analyse.

resultsTo help researchers to handle and analyse those datasets by mapping and investigating metabolomics data of multiple sampling conditions (e.g. different time points or treatments) in the context of pathways, PathwayNexus has been developed, which presents the mapping results in a matrix format, allowing users to easily observe the relations between the compounds and the pathways. It also offers functionalities like ranking, sorting, clustering, pathway views, and further analytical tools. Its primary objective is to condense large sets of pathways into smaller, more relevant subsets that align with the specific interests of the user. AVAILABILITY AND IMPLEMENTATION: The methodology presented here is implemented in PathwayNexus, an open-source add-on for Vanted available at www.cls.uni-konstanz.de/software/pathway-nexus. CONTACT: falk.schreiber@unikonstanz.de. SUPPLEMENTARY INFORMATION: Website: www.cls.uni-konstanz.de/software/pathway-nexus.

Indexed as

MetabolomicsSoftwareMetabolic Networks and Pathways

Identifiers

PMID38724240
PMCPMC11153943

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LicenceCC BY
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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.