BME355 Using the OMIM database information for Type 2 Diabetes Mellitus (T2D): Genomic Sequence Analysis Assessment, SUSS, Singapore, Singapore

Question 1
Using the OMIM database information for Type 2 Diabetes Mellitus (T2D)
(https://omim.org/entry/125853), solve the following tasks.

Question 1a
Extract out the genes associated with T2D and use the list as input in the online tool DAVID (Database for Annotation, Visualization and Integrated Discovery).
(5 marks)

Question 1b
Create a functional annotation clustering of the gene list and paste screenshots of the results from GOTERM_BP/CC/MF_DIRECT and KEGG_PATHWAY. Report the clusters having enrichment score above 1.
(5 marks)

Question 1c
Appraise the results obtained and discuss the relevancy of the findings to the gene list.
(5 marks)

 

Question 2
Using the NCBI database, explore the gene with Gene ID: 79923.
Question 2a State the gene symbol given to this ID and the full official name of the gene.
(2 marks)

Question 2b
Discuss the function of this gene in your own words.
(5 marks)

Question 2c
Determine the mRNA transcripts and protein isoforms of this gene.
(5 marks)

Question 2d
Describe FIVE (5) pathways which the corresponding gene is involved in.
(5 marks)

Question 2e
Identify the conserved domains in the protein isoforms of this gene.
(3 marks)

Question 3
Demonstrate your understanding in molecular genetics and computational biology by critically evaluating the following statements.

Question 3a
Protein alignments are often more informative than DNA alignments.
(5 marks)

Question 3b
When comparing two sequences, it is necessary to repeat the search using different scoring matrices.
(5 marks)

Question 3c
The statistical significance of a BLAST result can be assessed through S values.
(5 marks)

Question 3d
Position specific iterated BLAST (PSI-Blast) is often less sensitive than a regular Blast search in finding distantly related protein sequences.
(5 marks)

Question 3e
Benchmarking is an important approach to compare different software and determine their accuracy.
(5 marks)

Question 4
With the help of an alignment tool you have learnt, examine the human sequence given below, and furnish answers to the following questions:
>SEQ
MCGATSFLHECTRLILVTTQNAEFLQKGLQVHTCFGVYPHASVWHDCASQK
KGCAVYLHVSVEFNKLIPE
NGFIKFHQVRRVMTILFLTMVISYFGCMKAAPMKEANIRGQGGLAYPGVRTH
GTLESVNGPKAGSRGLTS
LADTFEHVIEELLDEDQKVRPNEENNKDADLYTSRVMLSSQVPLEPPLLFLLE
EYKNYLDAANMSMRVRR
HSDPARRGELSVCDSISEWVTAADKKTAVDMSGGTVTVLEKVPVSKGQLKQ
YFYETKCNPMGYTKEGCRG
IDKRHWNSQCRTTQSYVRALTMDSKKRIGWRFIRIDTSCVCTLTIKRGR

Question 4a
Give the name and accession number of the sequence.
(5 marks)

Question 4b
Appraise the function of the corresponding gene.
(5 marks)

Question 4c
Describe FIVE (5) pathways which the genic form is involved in.
(5 marks)

Question 4d
List the Gene Ontology functions and processes.
(5 marks)

 

Question 5
Using the resulting information from the above-mentioned sequence in Question 4, extract out the sequences from Homo sapiens and organisms such Pan troglodytes, Canis lupus familiaris, Bos Taurus and Mus musculus

Question 5a
Paste the sequences in fasta format.
(5 marks)

Question 5b
Create a multiple sequence alignment using any multiple sequence alignment tool. Paste the alignment and the phylogenetic tree.
(10 marks)

Question 5c
Evaluate the alignment and the phylogenetic tree derived in Question 5b.