1. Locate your gene in humangenome, choose the latest build. On which chromosome and over which positions it is found?
2. Whichgenes lie within close distance of the your gene? Find at least 10 closely locates genes. Find an image of the genome in that region showing the gene locations. List all the genes.
3. Explore each gene. Based on the known functions of these genes, which would be the most plausible candidate(s) for the disease associated with your gen, and can be also a target for the mutation and why?
4. Evaluate the quality of each gene in your test set. How was the intron/exon structure of these genes determined? Given your answer, should we have high confidence that the gene's structure is annotated correctly? (Hint: The mapview entry for the mRNAs of the gene will have details about the source of the sequence.)
5. Using genome browser (UCSC Genome Browser will be better for this task) identify best model organism, which can represent all the genes in your test set and also intergenic regions. Locate every gene from your selected list in the genomes and plot the region, setting the "RefSeq Genes," "Other RefSeq," "N-SCAN," and "Conservation" tracks to "full". (Hint: The resulting pictures for each gene may look like the one on the lecture slide with conservation.)
6. We would expect that introns will evolve more quickly than exons,and therefore we can find likely exon positions by looking for more conserved nucleotides. Based on your plot for problem 5, does conservation within the organisms at the base level provide support for the specific exon locations in the gene model? Why or why not?
7. Again looking at your plot from problem 5, what organism provides the best evidence from conservation for or against the specific human gene structure model?
8. Based on the conservation you can observe here, roughly when in the evolution of modern organisms does the exon structure appear to have emerged for this gene?
9. If we suspect that the genes in your test set might be alternatively spliced, then we can look for evidence in other organisms for alternative splicing of the homologous gene. Use one organism as a more distant homolog for which good experimental data is likely to be available. How many experimentally observed splice forms are there for your genes in this organism? Do they correspond well with the exon model annotated for the human gene? If available, please use the model organism database.
10. We might decide that the best way to resolve the true splice form(s) is to do our own sequencing of the model transcriptome and see mRNAs appear for this gene and what models they support. Suppose we have the option of using an Illumina sequencer or a 454 sequencer. What would be the relative advantages and disadvantages of each for this purpose?
Pat 2:
1. A good place to start is to find a scientific publication(s), which describes your protein/gene and possibly other proteins in relations with its functionality, functionality of proteins together and relations to a disease condition. The paper can be about the disease relations you have identified in previous HWs on a different disease.
(Hint: Paper(s), from gene record or from OMIM collection). Provide A)a reference (or references) and B) brief description of the relation of your gene, possible other genes their functionality and the disease. (you can copy and paste, but, along with that,make your own description in 2-3 sentences.)
2. Find an actual experimental data on expression analysis of your gene correlations with a disease condition (most likely describe in paper(s) in #1); i.e. Find DataSet Record with GDS#.
3. Using clustering tools and gene profiles data find genes with similar expression pattern. A) (3pts) provide a screenshot with your description of it and B) (1pts)list all the co-expressed genes.The target number is to list in about a dozen or two genes with similar pattern; please make sure you list all the genes in the cluster.
4. Find functional relations of you gene with for all the genes in the collected list. As you have collected list of possible genes in #3, now we need to involve additional experimental data, such as X-ray structures or biochemical experiments or other (non-expression based) research on these genes/proteins. You need to evaluate functional relations between your gene and each of the genes on the list and choose at least 5 genes with some functional relation to your gene. (Hint: just being in the same category, like both are transcription factors or both are receptors, does NOT prove the functional relation; while forming a complex in X-ray studies or/and having related enzymatic activitiescan be a solid prove for functional realtions)
(Hint2: any new genes relations you may have already found in #1 can be a lead to follow)
Please do:
A) reduce your list from #3 to genes only, no transcripts (Hint: for example, C17orf99 in #3 is not actual gene, it is just an ORF without any annotations or research data);
B) provide functional description for each remaining actual gene from #3;(it is ok to copy and paste at this step, but in this case provide a link or reference where it came from);
C) write down your short list choice of 5 genes and your reasoning.
5. From your short list of 5 proteins you have chosen in #4, pick one protein for further studies (this will be your NEW protein). The criteria is up to you, but one condition, it should have a good structural data available in PDB, at least one domain of more then > 100 amino acids with its own structure (100%) or close homolog from may be other organism but more then >70% similarity to you protein of choice. We will use this protein in HW7 and 8.
A) pick a protein,
B) write down PDB code of its own structure or its close homolog's; and the criteria why you choose it.
Bonus:
What is the closest enzyme to your protein or to your new protein? (Hint: if your old or new protein is an enzyme by itself, in this case identify the closest enzyme one step before or after on metabolic or signaling pathway).
A) name;
B describe chain of bio-molecular relations/functions to your protein or to your new protein in good details.