Exercise2: Exploring a gene

You are interested in the Human PPARG gene and want to know the following things about it:

Use HumanMine for this exercise

1. On which chromosome is the PPARG gene located?

2. Can I access the sequence for the PPARG gene?

3. With which diseases is PPARG associated?

4. In which tissues is PPARG most highly expressed?

5. Does the PPARG protein have any know isoforms?

6. Is there a PPARG orthologue in D. melanogaster?

7. Does this orthologue interact with any other Genes/proteins? Identify the interaction type (genetic/physical)?

8. For the interaction with CG3040, what was the original experiment and publication that determined this interaction?

Need a hint? Take a look at Report Pages

Exercise2: Answers

1. On which chromosome is the PPARG gene located? 2. Can I access the sequence for the PPARG gene?

The first section on the gene report page provides information about the chromosome location of the gene along with identifiers and synonyms and a link to the FASTA DNA sequence

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3. With which diseases is PPARG associated?

In HumanMine a summary of data is provided at the top of the report page (note this feature is not available in all InterMine’s).

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Further disease information is sometimes available from the “Curated comments from Uniprot”:

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4. In which tissues is PPARG most highly expressed?

Data on tissue expression can be found from three sources:

A. Human gene expression atlas of 5372 samples representing 369 different cell and tissue types, disease states and cell lines: from http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-62/

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B. Human Protein Atlas: http://www.proteinatlas.org/

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C. Curated comments from Uniprot:

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5. Does the PPARG protein have any know isoforms?

  1. Navigate to the proteins table using the quick links
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  1. Select the PPARG_HUMAN protein (the canonical uniprot annotated protein) to be taken to the protein report page. Note: we can also see from this table that PPARG has two isoforms: PPARG_HUMAN2 and PPARG_HUMAN3
  2. Navigate to the Isoforms table on the protein report page. Note that this table links to a report page for each of the isoforms.
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6. Is there a PPARG orthologue in D. melanogaster?

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7. Does this orthologue interact with any other proteins? Identify the interaction type (genetic/physical)?

Use the “Interactions” quick link to navigate to protein and genetic Interaction data. Eip75B has a genetic interaction with genes Nos, Ph-p, Smn, S6K, Kr, Rheb and Hr51 and physical interactions with CG3040, COX5B and Hr51.

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8. For the interaction with CG3040, what was the original experiment and publication that determined this interaction?

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