Human Genetics - Genomics, Spring 2008
From InformaticsWiki
Please enter your questions about the Human Genetics-Genomics web class/assignment. --Dr. Moss 13:49, 16 April 2008 (EDT)
Dr Moss I am stuck at question no. 3. a)- I have done b) for cancer hits were in large number (more than 1000) and for autism I got numbers in hundred. c) How to count the entries for each term that indicate a gene of known sequence and phenotype? I got huge number for cancer and autism. Do I have to go page by page and count? I am sure there is some method for doing the same. Please give me hint. Thank you--nimish 16:56, 18 April 2008 (EDT)
Hint: redo the search using limits.--Dr. Moss 09:49, 21 April 2008 (EDT)
Dr. Moss,
For # 6F I have done this question twice and both time it is giving me different answer! meaning the change in AminoAcid. Both time I received different answers. Which one I should stick to?
For 6H In your search results do you just count the list of SNPs or there is more to look at for this question?
Thank You.
6(f). The question is simpler than the issue you are having. Is there a change to the protein, yes or no. And if there is, describe the nature of the change. For example, is it a deletion, insertion, inversion, point mutation, etc.
6(h). All I want is the number of SNPs indicated in the 3' UTR of the gene listed in the Hapmap database. You have to find the gene and zoom in exactly as I say (click once to right, then zoom down to 10kb). You also need to recognize where the 3' UTR is. It is indicated by a slightly different color than the coding exons. Look above the UTR and you will see sets of four pie charts. Each set of four is a different SNP. Look at the pie charts to see how the SNPs vary among the four populations. --Dr. Moss 14:51, 21 April 2008 (EDT)
Dr. Moss, your tips for 6(h) are actually for 7(d) which is very helpful, but question 6(h) doesn't use the hapmap database. I have question 7d, but cannot compare it to 6(h) because I'm not sure how to do that. Would you be able to explain 6h?
Oops, my mistake. You should go to the human LIN28B gene page (via Entrez) and find the SNP GeneView in the right hand column. The default display is cSNP, that is, coding SNPs only. Refresh the view so you see all the SNPs in the gene. The list is below. Scroll down to find the SNPs that are in the 3' UTR. Count them, and that is your answer. --Dr. Moss 15:39, 21 April 2008 (EDT)
