4 Homework Assignment: Annotation Sources
GeneMania is a platform for analysing gene lists and other genes that are functionally related to them. It allows users to input a list of genes and predict of their functional relationships based on an integration of data sources, including protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity (Warde-Farley et al., 2010).
GeneMANIA was first published on 27 June 2008 in Genome Biology (Mostafavi et al., 2008). Since then, GeneMANIA has had several updates, including the addition of new organisms and data sources, and user interface updates (Franz et al., 2018).
The network data is collected from a variety of publicly available databases, such as Gene Expression Omnibus (GEO), Pathway Commons and BioGrid. The full list of data sources can be found here. Users are also able to upload their own data to include in analyses.
GeneMANIA interaction networks are available for download in plain text format. The data from the current release was updated on 27 April 2021 (data archive available here).
The data includes a table of recognised identifiers (filename: identifier_mappings.txt). These include preferred gene names (from HUGO), Ensembl Gene and Protein IDs, Entrez Gene IDs, RefSeq Protein IDs and Uniprot IDs. The preferred gene name will be included in the interaction network produced on GeneMANIA, but any of these recognised identifiers will be accepted when inputting a list of genes.
The user inputs a gene or list of genes to produce a network of functional relationships with other genes. For example, below is the network produced for genes BRCA1 and BRCA2.
The user can interact with the network get information on genes and interactions. A comprehensive report of the output, including information on the networks, attributes, genes, functions and interactions, is available for download.
Warde-Farley, D., Donaldson, S. L., Comes, O., Zuberi, K., Badrawi, R., Chao, P., Franz, M., Grouios, C., Kazi, F., Lopes, C. T., Maitland, A., Mostafavi, S., Montojo, J., Shao, Q., Wright, G., Bader, G. D., & Morris, Q. (2010). The genemania prediction server: Biological network integration for gene prioritization and predicting gene function. Nucleic Acids Research, 38(suppl_2). https://doi.org/10.1093/nar/gkq537
Mostafavi, S., Ray, D., Warde-Farley, D., Grouios, C., & Morris, Q. (2008). GeneMANIA: A real-time multiple association network integration algorithm for predicting gene function. Genome Biology, 9(Suppl 1). https://doi.org/10.1186/gb-2008-9-s1-s4
Franz, M., Rodriguez, H., Lopes, C., Zuberi, K., Montojo, J., Bader, G. D., & Morris, Q. (2018). GeneMANIA update 2018. Nucleic Acids Research, 46(W1). https://doi.org/10.1093/nar/gky311