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
Landeghem Van Sofie et al., Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks Networks analysis. BMC Bioinformatics (2016) doi:10.1186/s12859-015-0863-y
Azevedo Hátylas et al., Intragraft transcriptional profiling of renal transplant patients with tubular dysfunction reveals mechanisms underlying graft injury and recovery. Human Genomics (2016) doi:10.1186/s40246-015-0059-6
Yatsu Ryohei et al., RNA-seq analysis of the gonadal transcriptome during Alligator mississippiensis temperature-dependent sex determination and differentiation Non-human and non-rodent vertebrate genomics. BMC Genomics (2016) doi:10.1186/s12864-016-2396-9
Shifman R. Aaron et al., Cascade: an RNA-seq visualization tool for cancer genomics Transcriptomic methods. BMC Genomics (2016) doi:10.1186/s12864-016-2389-8