Learn to use GeneMANIA, a free public resource that offers a simple, intuitive web interface that shows the relationships between genes in a list and analyzes and extends the list to include other related genes. Download the example data file used in the tutorial file by clicking here.
You will learn:
This tutorial is a part of the tutorial group Interaction resources. You might find the other tutorials in the group interesting:
Pathway Interaction Database: A resource of pathway and network data and displays
MINT: Molecular Interaction Database
Cytoscape: An open-source software platform used for visualization and analysis of molecular interaction and network data
BiologicalNetworks: Analyze and visualize molecular interaction networks
BioSystems: Database of Biological Systems
Reactome Legacy: Older version of the current Reactome knowledgebase of biological processes.
Reactome: Knowledgebase of biological processes
GenMAPP: A freely available open source software application for visualizing microarray data in the context of biological pathways.
VisANT: A web-based or downloadable software platform used for visualization and analysis of networks and interaction pathways
InterPro: A comprehensive protein signature resource
IntAct protein interaction database: IntAct is an open source database and analysis resource for protein interaction data
KEGG: KEGG, The Kyoto Encyclopedia of Genes and Genomes
Proteins : Tools that are primarily used in the storage, retrieval, or exploration of amino acid based data. Some tools may also involve nucleotide sequence information.
Pathways and Interactions : Tools that are involved with protein interactions and pathway features. Some tools are primarily repositories and some offer analysis options.
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Recent BioMed Central research articles citing this resource
Serrano-Solano Beatriz et al., How can functional annotations be derived from profiles of phenotypic annotations? Results and data. BMC Bioinformatics (2017) doi:10.1186/s12859-017-1503-5
Altmann Christine et al., Progranulin promotes peripheral nerve regeneration and reinnervation: role of notch signaling. Molecular Neurodegeneration (2016) doi:10.1186/s13024-016-0132-1
Chu Jen-hwa et al., Gene expression network analyses in response to air pollution exposures in the trucking industry. Environmental Health (2016) doi:10.1186/s12940-016-0187-z
Loviglio Nicla Maria et al., Identification of a RAI1 -associated disease network through integration of exome sequencing, transcriptomics, and 3D genomics. Genome Medicine (2016) doi:10.1186/s13073-016-0359-z
Tomar Tushar et al., Genome-wide methylation profiling of ovarian cancer patient-derived xenografts treated with the demethylating agent decitabine identifies novel epigenetically regulated genes and pathways. Genome Medicine (2016) doi:10.1186/s13073-016-0361-5