WS266 release

Please note that the WS266 version of WormBase has been released! The release notes for this release describe the data types and their numbers. A list of all files available on our FTP site can also be viewed.  Changes in this release include the following:

Physical Interaction data curation

We have added over 5000 manually curated physical interactions which include binary protein-protein interactions as well as protein interactions that occur in a protein complex. Protein-protein interaction data can be found as a part of physical interaction data in the Interactions widget on the gene page. The Interactions widget provides different types of interaction data related to the gene of interest, such as physical, genetic, regulatory, and predicted interactions.

 

Protein Identifiers

We have made a change to our internal identifiers for nematode protein sequences. Previously, we prefixed each identifier with *two* prefixes to denote which  species the protein is from, e.g. WP:CE00001. We have removed the first prefix (the “WP:”) from these identifiers.

Since these prefixes are almost entirely invisible on the site and have never been used by external resources hosting worm data (e.g. UniProt), this change should not affect most users.

Paper of Interest: OrthoList 2

The new comparative genomic analysis between C. elegans and humans, OrthoList 2 (OL2), was just published early online in GENETICS.  OL2 comes with a new web-based tool that allows for rapid searches of OL2 by worm or human gene identifiers, protein domains (InterPro and SMART), or human-disease associations (OMIM), and also includes updated RNAi resources. The paper describes OL2 and various findings, including how the content of OL2 compares with the original OrthoList tool. The web-based tool for accessing OL2 is here.

WS265 release

loci with two different protein products

There are a small number of loci which code for two very different protein products. These include dicistronic mRNA operons and loci which have a few small exons in common then have alternate splicing leading to many different exons being used.

The details of some of these can be found in the WormBook chapter “Operon and non-operon gene clusters in the C. elegans genome”.

Previously, these have been curated as isoforms of a single gene. This was causing problems because the description of gene
function would be based on one isoform, leaving the other isoform undescribed or described incorrectly, based on the first isoform.
There are 42 C. elegans and 47 C. briggsae known loci that have now been split to have different Gene IDs.