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

query_entity_AtomicRegulon

Query the 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:

    query_entity_AtomicRegulon -a

The AtomicRegulon entity has the following relationship links:

IsAffectedIn Experiment
IsFormedOf Feature
ReflectsStateOf Genome
WasGeneratedFrom ProbeSet

Command-Line Options

-is field,value

Limit the results to entities where the given field has the given value.

-like field,value

Limit the results to entities where the given field is LIKE (in the sql sense) the given value.

-op operator,field,value

Limit the results to entities where the given field is related to the given value based on the given operator.

The operators supported are as follows. We provide text based alternatives to the comparison operators so that extra quoting is not required to keep the command-line shell from confusing them with shell I/O redirection operators.

< or lt
> or gt
<= or le
>= or ge
=
LIKE
-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 containing a column for each requested field.