all_entities_AtomicRegulon
Return all instances of the AtomicRegulon entity.
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:
all_entities_AtomicRegulon -a would retrieve all entities of type AtomicRegulon and include all fields in the entities in the output.
Related entities
The AtomicRegulon entity has the following relationship links:
Command-Line Options
- -a
-
Return all fields.
- -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.