BioStar is a site for asking, answering and discussing bioinformatics question
s. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.
Today’s question and answer is:
What is the best resource for Protein/Genetic interactions?
One of several answers:
Protein interactions: If you are interested primary in protein interactions, look first at the IMEx consortium; all of the databases that you mention are a part of it. Their interactions are available through PSICQUIC web services, described here: http://code.google.com/p/psicquic/
Some websites combine data from multiple molecular interaction databases, e.g., Pathway Commonsand IRefWeb. I know you can download a combined dataset of interactions from Pathway Commons but I haven’t tried doing this with IRefWeb.
Genetic interactions: I think that BioGRID is the only major database that currently curates genetic interactions.
This tip of the week comes to you by way of the recent NAR Database issue article and a twitter from Francis Ouillette. The Gene-Oriented Orthology Database (or GOOD) is a relatively new database of orthologous regions found in four genomes (human, mouse, chimpanzee and cow) using gene regions (hence the name) instead of proteins to determine orthology. As the authors state in the paper:
Several ortholog databases are now available online. Most of them, however, consider orthology from the aspect of protein sequences individually, including HomoloGene, EnsemblCompara, Inparanoid , Roundup , OrthoMCL and OrthoDB . There exist ambiguous and incomplete ortholog assignments because of the interference mediated by alternative splicing (AS). Isoforms of one gene might beassigned to different orthologous clusters.
They also use GO terms in depth to help determine functions and annotations. The tip of the week this week is a quick introduction to this new database.
Just a few links for your reading pleasure from the last week.
While the mainstream news is reporting on the demise (redefinition) of the ‘gene‘, some high schools kids are doing amazing things with ‘genes.’
Oh, and if, like us, you can’t wait till the annual NAR database is published officially, you can always check out the advanced online publication of the articles to find new and updated databases (like the SpBase, sea urchin, database that went public earlier this year and SuperToxic, a database of over 60,000 toxic compounds) and genome resources!
So, in the spirit of friday fun where we’ve done puzzles, genome music and other fun stuff (so, ok, not always on Friday), I thought I’d show you an interesting site: Genome Quilts. The creator of these quilts created a one square pattern for each nucleotide and then quilts these squares in order of a particular gene (the one to the left is this one I believe). So, as an example she posts what I’ve included on the right. Some beautiful quilts. Genomics can be beautiful. So, now I’m thinking, I like to knit… I wonder what patterns I could do for nucleotides or amino acids… hmm, could be a mess, or beautiful. I’ll have to think about that one.