Orthologus Genes

Question

[Manish]

hello frnds, i have a set of genes in humans. how can i get same orthologus genes in chicken? please help me.

[Michael]

question without sufficient spelling nor own effort = downvote

[Bert Overduin]

@Larry, I do agree with you, but reactions as those of Michael I do not find cool, especially when it concerns a first time user. The decent way to deal with a question like this would be to point out the lack of effort / detail / correct spelling but nevertheless provide the user also with an answer. But maybe I am, as someone who works in user support and outreach, just too helpful and too friendly .... ;)

[Larry_Parnell]

Spelling I can handle (barely), but the lack of effort and/or detail of what was already attempted is just not cool.

[Bert Overduin]

@ Michael: Very helpful!

[Bert Overduin]

Very helpful, Michael!

[Andrew W]

This might help: http://biostar.stackexchange.com/questions/15027/hello-how-we-can-convert-human-entrez-gene-ids-into-mouse-gene-ids/15031#15031

[Michael]

Normally I wouldn't like to do this ever with a first-time user, and I agree that my reaction is not cool (given it might have repelled the new user), however I would still think it is justified. I must simply assume that this is a one-off question and the user will never come back anyway. If I am wrong and he/she has something to contribute, the op will maybe be challenged to edit the question. If not, then it is very unlikely that the op has anything significant to gain or contribute, such that it is no loss for either party.

[Larry_Parnell]

The user may not be new but newly re-registered. There are 3 users with this name and 2 that look identical. When I added responses, I recalled the username from earlier.

[Michael]

Then it is even more justified to tell them the reason why the question gets downvoted. And, as I said, he didn't come back.

Answer 1

[Bert Overduin]

You can use Ensembl BioMart for this:

Step 1:

• Go to the Ensembl homepage.
• Click on the ‘BioMart’ link on the toolbar.
• Choose the ‘Ensembl Genes 65’ database.
• Choose the ‘Homo sapiens genes (GRCh37.p5)’ dataset.

Step 2:

• Click on ‘Filters’ in the left panel.
• Expand the ‘GENE’ section by clicking on the + box.
• Select ‘ID list limit – [your type of IDs for your human genes]’.
• Enter the list of IDs for your human genes in the text box (either comma separated or as a list).

Step 3:

• Click on ‘Attributes’ in the left panel.
• Select the ‘Homologs’ attributes page.
  
• Expand the ‘GENE’ section by clicking on the + box.
  
• Deselect ‘Ensembl Transcript ID’.
  
• Expand the ‘ORTHOLOGS’ section by clicking on the + box.
  
• Select ‘Chicken Ensembl Gene ID’ and ‘Homology Type’.

Step 4:

• Click the [Results] button on the toolbar.
  
• Select ‘View All rows as HTML’ or export all results to a file. Tick the box ‘Unique results only’.

Hope this helps.

[Larry_Parnell]

Not only are the details of this response helpful, but they also provide an example of the detail that should be in a question: good spelling, what worked and what did not, where did you/did you not look (for data, code, etc). 43 views thus far!? This question and this response deserve 10- to 20-times because this is an example to teach BioStar users how not to ask and how best to reply.

[Sean Davis]

The set of questions with negative votes for the question and high voted answers would be an interesting set to see, wouldn't it? Several of those questions probably fit the bill.