Bioinformatics Coursework1

Bioin" rel="nofollow">informatics Coursework1 Order Description Exercise 1: In this week's lecture you saw the followin" rel="nofollow">ing example: Cases: 15 CC, 22 CT, 63 TT Controls: 3 CC, 35 CT, 62 TT Generate the correspondin" rel="nofollow">ing genotype and allele contin" rel="nofollow">ingency table. Calculate the chi-square statistic and the correspondin" rel="nofollow">ing p-value for: the 2x3 genotype contin" rel="nofollow">ingency table the 2x2 allele contin" rel="nofollow">ingency table. Compare with results from lecture. NOTE: show steps in" rel="nofollow">involved in" rel="nofollow">in this computation. The correct numerical answer alone (from a calculator) without showin" rel="nofollow">ing in" rel="nofollow">intermediate steps will result in" rel="nofollow">in 0 credit. I strongly encourage you to first compute chi-square by hand, usin" rel="nofollow">ing the example from the “chi square example” file (or see https://onlin" rel="nofollow">inecourses.science.psu.edu/stat500/node/56 for a tutorial on how the chi square statistic is computed). Then verify your results by usin" rel="nofollow">ing a chi square calculator (search onlin" rel="nofollow">ine or use a statistical package, such as R; or excel). Exercise 2: Repeat Exercise 1, usin" rel="nofollow">ing the followin" rel="nofollow">ing data: Cases: 50 CC, 35 CT, 11 TT Controls: 6 CC, 25 CT, 19 TT Exercise 3: Learn about CFH association with AMD. Suggestion: use NCBI’s Entrez, https://www.ncbi.nlm.nih.gov/Entrez/, for your searches. What does CFH stand for? What other aliases are there for CFH? Where is CFH located in" rel="nofollow">in the human genome? Include chromosome, start, end position. What is the length. How many exons does CFH have? Are there any splice variants of CFH? In what pathway(s) is CFH in" rel="nofollow">included? What are some diseases where CFH has been implicated? Are there any structures (entire or partial) for the CFH protein" rel="nofollow">in? If yes, prin" rel="nofollow">int one. Fin" rel="nofollow">ind a SNP in" rel="nofollow">in CFH, and describe (id, position, type) What is a SNP in" rel="nofollow">in CFH that has been associated with some disease? Give reference.