Evidence map›Paper›PMID 25950236›Full record

ArticleNature protocols2015

NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data.

Jianguo Xia, Erin E Gill, Robert E W Hancock

Abstract read
PubMed Publisher
In one paragraph

Article in Nature protocols, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 543 papers, 7 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
543citing papers in PubMed, 7 pooled it
–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

543 citing papers in PubMed, 7 syntheses or guidelines pooled it.

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  12. Cross-tissue immune profiling of APOE ε4 reveals early dysregulation in Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026
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483 more citing papers are in PubMed but not listed here.

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

3 authors.

Jianguo Xia1] Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada. [2] Institute of Parasitology, and Department of Animal Science, McGill University, Ste. Ann de Bellevue, Québec, Canada. [3] Department of Microbiology and Immunology, McGill University, Montreal, Québec, Canada.
Erin E GillDepartment of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
Robert E W Hancock1] Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada. [2] Wellcome Trust Sanger Institute, Hinxton, United Kingdom.

Funding

Canadian Institutes of Health Research
6 · The paper itself

Abstract

Meta-analysis of gene expression data sets is increasingly performed to help identify robust molecular signatures and to gain insights into underlying biological processes. The complicated nature of such analyses requires both advanced statistics and innovative visualization strategies to support efficient data comparison, interpretation and hypothesis generation. NetworkAnalyst (http://www.networkanalyst.ca) is a comprehensive web-based tool designed to allow bench researchers to perform various common and complex meta-analyses of gene expression data via an intuitive web interface. By coupling well-established statistical procedures with state-of-the-art data visualization techniques, NetworkAnalyst allows researchers to easily navigate large complex gene expression data sets to determine important features, patterns, functions and connections, thus leading to the generation of new biological hypotheses. This protocol provides a step-wise description of how to effectively use NetworkAnalyst to perform network analysis and visualization from gene lists; to perform meta-analysis on gene expression data while taking into account multiple metadata parameters; and, finally, to perform a meta-analysis of multiple gene expression data sets. NetworkAnalyst is designed to be accessible to biologists rather than to specialist bioinformaticians. The complete protocol can be executed in ∼1.5 h. Compared with other similar web-based tools, NetworkAnalyst offers a unique visual analytics experience that enables data analysis within the context of protein-protein interaction networks, heatmaps or chord diagrams. All of these analysis methods provide the user with supporting statistical and functional evidence.

Indexed as

Meta-Analysis as TopicSoftwareComputational BiologyGene Expression ProfilingGene Regulatory NetworksProtein Interaction Mapping

Identifiers

PMID25950236

What OpenQuestion holds

Textmetadata
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.