Tag Archives: orthology

Video Tip of the Week: eggNOG for the holidays (or to explore orthologous genes)


ResearchBlogging.org Who can resist a nice cup of eggnog for the holidays (especially with added brandy). I know I can’t. I make my grandpa’s recipe every December and, considering it uses tons of sugar, eggs, heavy cream and alcohol and that 1/2 & 1/2 is the lightest ingredient, only December.

Oh, that’s not what this tip is about, it’s about database of orthologous groups of genes, eggNOG. We’ve mentioned eggNOG before several times, but only in passing or in relation (orthologous? :D) to another database or tool. Today, in perfect timing for the season, thought I’d do a quick tip to introduce eggNOG.

eggNOG is brought to you by the same research group that developed a lot of other excellent tools such as SMART (protein domains), STRING (protein-protein interactions, STITCH (protein-chemical interactions) , iTOL and so much more. Of course they do some fascinating research too.

eggNOG is a relatively straightforward database to use, but it has a wealth of information you might want to check out. As the recent paper in NAR states:

Orthologous relationships form the basis of most comparative genomic and metagenomic studies and are essential for proper phylogenetic and functional analyses…. Orthology, defined as homology via speciation, is a crucial concept in evolutionary biology and is essential for disciplines such as comparative genomics, metagenomics and phylogenomics. The concepts of orthology and paralogy, with the latter being defined as homology via duplication, have been used as a foundation to introduce the concept of clusters of orthologous groups: proteins that have evolved from a single ancestral sequence existing in the last common ancestor (LCA) of the species that are being compared, through a series of speciation and duplication events. Orthologous groups (OGs) have proven useful for functional analyses and the annotation of newly sequenced genomes  as orthologs tend to have equivalent functions.

eggNOG contains:

721 801 orthologous groups, encompassing a total of 4 396 591 genes…. from 1133 species.

For more about orthologous groups, methods used and pros and cons of methodology, you might want to check out the paper referenced below. They’ve included several informative and helpful reviews and references.

Right now, take a quick tour of what eggNOG can offer.

Quick Links:
eggNOG
STRING tutorial
SMART tutorial
Tip of the Week: iTOL

Powell, S., Szklarczyk, D., Trachana, K., Roth, A., Kuhn, M., Muller, J., Arnold, R., Rattei, T., Letunic, I., Doerks, T., Jensen, L., von Mering, C., & Bork, P. (2011). eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges Nucleic Acids Research DOI: 10.1093/nar/gkr1060

What’s the Answer? Open Thread (Orthology)

BioStar is a site for asking, answering and discussing bioinformatics questions. 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.

Question of the week (it was much longer than below, but this is the crux of the matter):

I want to know which is the best tool if I want to find ortholog genes of all human genes in primates, mouse.

There were some great answers, all with great resources. The top rated one (one of the best rated answers I’ve seen), writes almost a review article in answer. It’s excellent. I’m having a difficult time distilling it down for this, he goes through lots of criteria and tools, but his last sentence is:

Human, other primates and mouse are well represented in MetaPhOrs (combining Ensembl and other DB predictions). Following the above reasoning, I would give it a try.

 

Tip of the Week: PhylomeDB

Gene phylogenies (as opposed to species phylogenies) can be very useful in determined gene function, history, orthology and paralogy predictions. PhylomeDB (link added!) is a database of gene phylogenies (or as they call them, Phylomes.. no end to the ‘omes is there? :). Currently there are over a dozen such phylomes from species like humans and yeast. The database allows you to obtain phylogenies of genes based on gene ID or BLAST, you can also get orthology predictions and alignments and more. Today’s tip is introducing you to the database.

Tip of the Week: GOOD

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.