ArticleBMC systems biology2014
KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape.
Article in BMC systems biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
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- Multi-omics integration in biomedical research - A metabolomics-centric review.Analytica chimica acta · 2021Review
- KeyPathwayMineR:Frontiers in genetics · 2021Review
- Mapping Transcriptome Data to Protein-Protein Interaction Networks of Inflammatory Bowel Diseases Reveals Disease-Specific Subnetworks.Frontiers in genetics · 2021Article
- A Genome-Wide Integrative Association Study of DNA Methylation and Gene Expression Data and Later Life Cognitive Functioning in Monozygotic Twins.Frontiers in neuroscience · 2020Article
- Molecular signature of different lesion types in the brain white matter of patients with progressive multiple sclerosis.Acta neuropathologica communications · 2019Article
- New insights into radioresistance in breast cancer identify a dual function of miR-122 as a tumor suppressor and oncomiR.Molecular oncology · 2019Article
- Unique RNA signature of different lesion types in the brain white matter in progressive multiple sclerosis.Acta neuropathologica communications · 2019Article
- Identification of pathways associated with chemosensitivity through network embedding.PLoS computational biology · 2019Article
- Time-Resolved Systems Medicine Reveals Viral Infection-Modulating Host Targets.Systems medicine (New Rochelle, N.Y.) · 2019Article
- Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin.BMC systems biology · 2018Article
- Identification of highly connected and differentially expressed gene subnetworks in metastasizing endometrial cancer.PloS one · 2018Article
- Network module identification-A widespread theoretical bias and best practices.Methods (San Diego, Calif.) · 2018Article
- A Computational Method of Defining Potential Biomarkers based on Differential Sub-Networks.Scientific reports · 2017Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOver the last decade network enrichment analysis has become popular in computational systems biology to elucidate aberrant network modules. Traditionally, these approaches focus on combining gene expression data with protein-protein interaction (PPI) networks. Nowadays, the so-called omics technologies allow for inclusion of many more data sets, e.g. protein phosphorylation or epigenetic modifications. This creates a need for analysis methods that can combine these various sources of data to obtain a systems-level view on aberrant biological networks.
resultsWe present a new release of KeyPathwayMiner (version 4.0) that is not limited to analyses of single omics data sets, e.g. gene expression, but is able to directly combine several different omics data types. Version 4.0 can further integrate existing knowledge by adding a search bias towards sub-networks that contain (avoid) genes provided in a positive (negative) list. Finally the new release now also provides a set of novel visualization features and has been implemented as an app for the standard bioinformatics network analysis tool: Cytoscape.
conclusionWith KeyPathwayMiner 4.0, we publish a Cytoscape app for multi-omics based sub-network extraction. It is available in Cytoscape's app store http://apps.cytoscape.org/apps/keypathwayminer or via http://keypathwayminer.mpi-inf.mpg.de.
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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.