how to find big gene families

Model Organism: Worms Methods & Reagents
1

Hi, Dear,

Can any one give some hints how to identify big gene families in worm genome, such as collagen family which contains more than 100 members?

thanks very much.

shouhong

2

Hi,
I think there are 2 ways to do this. The 1st way is just type in “Collagen” and select search gene. It would give you a big list of all the genes in worm genome encoding “Collagen” or related. You might have to manually purify the set by looking at the gene results. E.g I did the search with the word “Collagen” and these are the results http://www.wormbase.org/db/searches/basic?class=Any&query=collagen&Search=Search. This is more of a rough approach. For a more specific approach, I would recommend using “Worm mart”. with following filters:

Dataset
Gene
Gene

Filters:
[Gene] Species : Caenorhabditis elegans
[Gene] Status : Live

Attributes
Gene WB ID
Gene Public Name

For your help, I pulled out this List too http://www.wormbase.org/biomart/martview/547a0b7a995587ab6c2b09d0618ab4c7.

Hope this helps.

Luv ;D

3

Just an update…you could also use UCSC gene browser tool called “Gene Sorter”. This program displays a sorted table of genes that are related to one another. The relationship can be one of several types, including protein-level homology, similarity of gene expression profiles, or genomic proximity. This would sort a similar group of genes for you. In your case its obviously “collagen”. Here is the Link http://genome.ucsc.edu/index.html ;D

HOPE This helps

Luv

4

Thanks so much.

Shouhong