get_entity_CoregulatedSet

We need to represent sets of genes that are coregulated via some regulatory mechanism. In particular, we wish to represent genes that are coregulated using transcription binding sites and corresponding transcription regulatory proteins. We represent a coregulated set (which may, or may not, be considered an atomic regulon) using CoregulatedSet.

Example:

get_entity_CoregulatedSet -a < ids > table.with.fields.added

would read in a file of ids and add a column for each filed in the entity.

The standard input should be a tab-separated table (i.e., each line is a tab-separated set of fields). Normally, the last field in each line would contain the id. If some other column contains the id, use

-c N

where N is the column (from 1) that contains the id.

This is a pipe command. The input is taken from the standard input, and the output is to the standard output.

Related entities

The CoregulatedSet entity has the following relationship links:

IsBoundBy Feature

IsControlledUsing Feature

IsRegulatedSetOf Feature

WasFormulatedBy Source

Command-Line Options

-c Column

Use the specified column to define the id of the entity to retrieve.

-h

Display a list of the fields available for use.

-fields field-list

Choose a set of fields to return. Field-list is a comma-separated list of strings. The following fields are available:

source_id

Output Format

The standard output is a tab-delimited file. It consists of the input file with an extra column added for each requested field. Input lines that cannot be extended are written to stderr.