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:

  • how to do basic searches and understand result displays
  • the importance of selecting the data types and datasets included in analyses
  • how changing network weighting can improve your output predictions
  • to format your own data and upload it for inclusion in GeneMANIA analyses
  • the many advantages of using GeneMANIA
TUTORIAL RELATED CONTENT

TUTORIALS

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

CATEGORIES

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.

BLOG POSTS

Friday SNPpets: This week's SNPpets include something unusual: bioinformatics software becoming a mainstream discussion. A recent NYT piece about Zika genomics included a Bandage software-based illustrations, and a su...

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Video Tip of the Week: Integrative Multi-species Prediction (IMP) Network Analysis Resource: A while back Mary saw the following tweet go by & collected it as a possible topic for one of our weekly tips: RT @moorejh: #bioinformatics #genomics RT @GreeneScientist Interactive and video tutorials...

What's the Answer? (Online mouse resources): BioStarĀ is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to...

What's the Answer? Open Thread (gene networks): BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to...

BIOMED CENTRAL

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