Exercises

Exercises 1

1. Regulatory Features: cell type specific data.

a) Using the human DB, fetch the all the cell type specific regulatory features with stable ID 'ENSR00000623613'.

b)Print out the stable ID, bound_start/end and start/end values, name of the cell- and feature type for each.

Hint: To get all the cell type specific RegulatoryFeatures use the fetch_all_by_stable_ID method.


2. Regulatory Features: What RegulatoryFeatures are near the oncogene BRCA2?

a) Create a script which fetches all the RegulatoryFeatures within 1kb of the gene.

b) Print out their stable IDs, bound_start/end and start/end values, name of the cell and feature types.

Hint: Use fetch_all_by_external_name with 'BRCA2' to get the gene object.
Look at the arguments for fetch_by_gene_stable_id, or use the Gene->feature_Slicemethod and Slice->expand methods.

3. Regulatory Features: associated experimental evidence.

a) Now fetch just the ENSR00000623613 MultiCell feature.

b) Print out the display_label, start/end values of all the evidence features.

c) Compare with the start/end values of the regulatory feature itself.

Hint: By default the fetch_by_stable_id method returns just the MultiCell features.


Answer

Nathan explains the answers to these questions in this 11 min video. You can download his sample scripts and outputs:

1. sample script and output

2. sample script and output

3. sample script and output