It was just a little tweet, with hardly any information about the function or purpose of the resource mentioned. But the cute name drove a lot of people to take a look at GeneFriends from our blog recently, so I figured it was worth highlighting this tool as our Video Tip of the Week.
So here’s the original tweet, hat tip to Jack Scanlan:
“GeneFriends”?! So cute. http://t.co/d4JU6onGY5
— Jack Scanlan (@JackLScanlan) November 1, 2014
I admit, I looked too. I had imagined something like a personal genomics matching site, but that’s not what it is. GeneFriends is a tool that uses gene co-expression data to try to identify which genes are “friends” with other genes in networks. These can be known genes, or they can be uncharacterized genes. The current implementation is for human data.
Not a new tool, the original implementation of GeneFriends with microarray-based data sets came out some time ago. There are 3000 data sets in that part of the previous tool. But their new paper describes a different version, now done with RNA-seq data. The paper says there are over 4000 RNA-seq samples from 240 studies, via the SRA database. In the new paper they describe the criteria for selection and their strategy for calling co-expression. They state that their goal is to help unearth leads on annotation for uncharacterized genes, and this also includes non-coding RNA sequences.
GeneFriends employs a RNAseq based gene co-expression network for candidate gene prioritization, based on a seed list of genes, and for functional annotation of unknown genes in humans.
There is a short video with their foundation and philosophy about the GeneFriends tool:
Another video goes a bit further and illustrates an example of the functionality. On the site you can try this yourself with the handy “show example” buttons they have. In addition to what you’ll find at their site, they also demonstrate that you can bring your results over to the BioLayout tool to work with them further. They also note that you can upload the results into Cytoscape.
It’s pretty straightforward to use the basic features of GeneFriends, but there is additional detail on the underpinnings from their “about” page. The papers below also cover the foundations and their new directions. You should also be aware of the limitation of the RNA-seq data that they discuss in the new paper. But check it out to see if you can discover some new relationships among transcripts of interest with GeneFriends.
GeneFriends main page: http://genefriends.org/
GeneFriends previous microarray version: http://genefriends.org/microArray/
van Dam S., Rui Cordeiro, Thomas Craig, Jesse van Dam, Shona H Wood & João de Magalhães (2012). GeneFriends: An online co-expression analysis tool to identify novel gene targets for aging and complex diseases, BMC Genomics, 13 (1) 535. DOI: http://dx.doi.org/10.1186/1471-2164-13-535
van Dam S., T. Craig & J. P. de Magalhaes (2014). GeneFriends: a human RNA-seq-based gene and transcript co-expression database, Nucleic Acids Research, DOI: http://dx.doi.org/10.1093/nar/gku1042