Evidence map›Paper›PMID 38009735›Full record

ArticleJournal of visualized experiments : JoVE2023

CorrelationCalculator and Filigree: Tools for Data-Driven Network Analysis of Metabolomics Data.

Gayatri Iyer, Marci Brandenburg, Christopher Patsalis, George Michailidis, Alla Karnovsky

Abstract readVideo-Audio Media
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of visualized experiments : JoVE, 2023. 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

5 authors.

Gayatri IyerDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor.
Marci BrandenburgDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor; Taubman Health Sciences Library, University of Michigan, Ann Arbor.
Christopher PatsalisDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor.
George MichailidisDepartment of Statistics, University of Florida; gmichail@ufl.edu.
Alla KarnovskyDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor; akarnovs@med.umich.edu.

Funding

Methods and Tools for Integrative Functional Enrichment Analysis of Metabolomics DataU01CA235487 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI KARNOVSKY, ALLA, MICHAILIDIS, GEORGE · 2018 to 2021
$1.7M
NCI NIH HHS U01 CA235487
6 · The paper itself

Abstract

A significant challenge in the analysis of omics data is extracting actionable biological knowledge. Metabolomics is no exception. The general problem of relating changes in levels of individual metabolites to specific biological processes is compounded by the large number of unknown metabolites present in untargeted liquid chromatography-mass spectrometry (LC-MS) studies. Further, secondary metabolism and lipid metabolism are poorly represented in existing pathway databases. To overcome these limitations, our group has developed several tools for data-driven network construction and analysis. These include CorrelationCalculator and Filigree. Both tools allow users to build partial correlation-based networks from experimental metabolomics data when the number of metabolites exceeds the number of samples. CorrelationCalculator supports the construction of a single network, while Filigree allows building a differential network utilizing data from two groups of samples, followed by network clustering and enrichment analysis. We will describe the utility and application of both tools for the analysis of real-life metabolomics data.

Indexed as

MetabolomeMetabolomicsChromatography, LiquidDatabases, FactualMass Spectrometry

Identifiers

PMID38009735
PMCPMC11785453

What OpenQuestion holds

Textmetadata
LicenceTDM
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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.