More Table Browser Queries
From Rous
Exercise 1
- How many known human genes are more than 1,000,000 base pairs in length? ANSWER = 90
Hints: Table Browser query, filter using a free form query and find the number using the summary/statistics function).
- What is the largest gene with respect to genome footprint? Is there evidence that the gene product has a role in human disease?
Hint: Adjust filter to report only the largest.)
- How large is the protein encoded by the gene? Use the proteome browser to see how does this protein’s hydrophobicity compares to other proteins in the genome?
- Use the gene sorter to find genes that have a similar pattern of expression, similar protein sequence and similar protein domain content.
- Obtain 1500 bases of sequence upstream from this gene. Do a blat search to confirm the position of the sequence you obtained.
- How many SNPs are found in this region?
Exercise 2
- How many know and refseq human transcripts have more than 100 exons? ANSWER = 21
- Which transcripts have the largest number of exons in the refseq and known categories and how many exons do they have?
Hint: Instead of obtaining hyperlinks to the genome browser as output, use the “selected fields from primary and related tables” option and select the relevant information.
- How large is the protein encoded by the refseq gene with the greatest number of exons? How long is the gene? How do these data
compare to those of the longest gene examined above?
