ArticlePloS one2013
Statistical assessment of crosstalk enrichment between gene groups in biological networks.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Exploring adaptation routes to cold temperatures in the Saccharomyces genus.PLoS genetics · 2025Article
- Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review.Briefings in bioinformatics · 2024Review
- Detecting and dissecting signaling crosstalk via the multilayer network integration of signaling and regulatory interactions.Nucleic acids research · 2024Article
- Differences and Similarities between the Lung Transcriptomic Profiles of COVID-19, COPD, and IPF Patients: A Meta-Analysis Study of Pathophysiological Signaling Pathways.Life (Basel, Switzerland) · 2022Article
- Benefits and Challenges of Pre-clustered Network-Based Pathway Analysis.Frontiers in genetics · 2022Article
- Characterization and Validation of ceRNA-Mediated Pathway-Pathway Crosstalk Networks Across Eight Major Cardiovascular Diseases.Frontiers in cell and developmental biology · 2022Article
- Network Crosstalk as a Basis for Drug Repurposing.Frontiers in genetics · 2022Article
- Analysing the meta-interaction between pathways by gene set topological impact analysis.BMC genomics · 2020Article
- Pathway-specific model estimation for improved pathway annotation by network crosstalk.Scientific reports · 2020Article
- NGSEA: Network-Based Gene Set Enrichment Analysis for Interpreting Gene Expression Phenotypes with Functional Gene Sets.Molecules and cells · 2019Article
- Identifying cancer prognostic modules by module network analysis.BMC bioinformatics · 2019Article
- Article
- The Pathway Coexpression Network: Revealing pathway relationships.PLoS computational biology · 2018Article
- FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets.BMC genomics · 2018Article
- Article
- NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis.BMC bioinformatics · 2017Article
- A novel method for crosstalk analysis of biological networks: improving accuracy of pathway annotation.Nucleic acids research · 2017Article
- Article
- NEAT: an efficient network enrichment analysis test.BMC bioinformatics · 2016Article
- PathwAX: a web server for network crosstalk based pathway annotation.Nucleic acids research · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationAnalyzing groups of functionally coupled genes or proteins in the context of global interaction networks has become an important aspect of bioinformatic investigations. Assessing the statistical significance of crosstalk enrichment between or within groups of genes can be a valuable tool for functional annotation of experimental gene sets.
resultsHere we present CrossTalkZ, a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks. We demonstrate that the standard z-score is generally an appropriate and unbiased statistic. We further evaluate the ability of four different methods to reliably recover crosstalk within known biological pathways. We conclude that the methods preserving the second-order topological network properties perform best. Finally, we show how CrossTalkZ can be used to annotate experimental gene sets using known pathway annotations and that its performance at this task is superior to gene enrichment analysis (GEA). AVAILABILITY AND IMPLEMENTATION: CrossTalkZ (available at http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/) is implemented in C++, easy to use, fast, accepts various input file formats, and produces a number of statistics. These include z-score, p-value, false discovery rate, and a test of normality for the null distributions.
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