.. _Exercise2: exploring_a_gene



.. _tabs:

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 :ref:`reportpages`




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


.. image:: ../../_images/exercise2.png


**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).

.. image:: ../../_images/exercise2.3a.png


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

.. image:: ../../_images/exercise2.3b.png


**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/


.. image:: ../../_images/exercise2.4a.png



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


.. image:: ../../_images/exervise2.4b.png


**C. Curated comments from Uniprot:**



.. image:: ../../_images/exercise2.4c.png

**5. Does the PPARG protein have any know isoforms?**


a. Navigate to the proteins table using the quick links

.. image:: ../../_images/exercise2.5a.png


b. 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


c. Navigate to the Isoforms table on the protein report page. Note that this table links to a report page for each of the isoforms.

.. image:: ../../_images/exercise2.5b.png


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


.. image:: ../../_images/exercise2.6.png


**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. 



.. image:: ../../_images/exercise2.7.png



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


.. image:: ../../_images/exercise2.8.png