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Bio-KBase-0.06
River stage zero No dependents
/ er_scripts/get_entity_AtomicRegulon

get_entity_AtomicRegulon

An atomic regulon is an indivisible group of coregulated features on a single genome. Atomic regulons are constructed so that a given feature can only belong to one. Because of this, the expression levels for atomic regulons represent in some sense the state of a cell. An atomicRegulon is a set of protein-encoding genes that are believed to have identical expression profiles (i.e., they will all be expressed or none will be expressed in the vast majority of conditions). These are sometimes referred to as "atomic regulons". Note that there are more common notions of "coregulated set of genes" based on the notion that a single regulatory mechanism impacts an entire set of genes. Since multiple other mechanisms may impact overlapping sets, the genes impacted by a regulatory mechanism need not all share the same expression profile. We use a distinct notion (CoregulatedSet) to reference sets of genes impacted by a single regulatory mechanism (i.e., by a single transcription regulator).

Example:

get_entity_AtomicRegulon -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.

The AtomicRegulon entity has the following relationship links:

IsAffectedIn Experiment
IsFormedOf Feature
ReflectsStateOf Genome
WasGeneratedFrom ProbeSet

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:

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.