GeneProductAssociation¶
The genes a reaction needs, as the tree of operators over them.
A gene product association is what a genome scale reconstruction knows about the genetics of a reaction: which genes have to be expressed for the reaction to carry a flux. It belongs to one reaction and holds exactly one node, which is an and, an or or a single gene product reference.
The tree is the meaning of the construct, not a decoration of it. A knockout analysis removes a gene, evaluates the tree of every reaction and switches off the reactions whose tree becomes false, so an and and an or of the same genes describe two different organisms.
The report shows the association in the inspector of its reaction and gives every node of the tree a page of its own, so that a reader can follow a gene into the reactions which depend on it.
Attributes¶
| attribute | type | required | meaning | specification |
|---|---|---|---|---|
| association | Association |
required | the single node the association holds | fbc v3 3.9 |
Every element of a model also carries the common attributes of SBase.
association
The node is an and, an or or a gene product reference; the last of them is the whole association of a reaction which depends on one gene alone.
The report renders the node and everything below it as the expression it stands for.
2020805(error): A <GeneProductAssociation> object must have one and only one of the concrete <Association> objects: <GeneProductRef>, <And> or <Or>.
Validation rules¶
2010301(error): (Extends validation rule #10301 in the SBML Level 3 Version 1 Core specification.) Within a <model> object the values of the attributes id and fbc:id on every instance of the following classes of objects must be unique across the set of all id and fbc:id attribute values of all such objects in a model: the model itself, plus all contained <functionDefinition>, <compartment>, <species>, <reaction>, <speciesReference>, <modifierSpeciesReference>, <event>, and <parameter> objects, plus the <fluxBound>, <objective>, <fluxObjective>, <geneProduct> and <geneProductAssociation> objects defined by the Flux Balance Constraints package.2020801(error): A <GeneProductAssociation> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'. No other attributes from the SBML Level 3 Core namespace are permitted on a <GeneProductAssociation.2020802(error): A <GeneProductAssociation> object may have the optional SBML Level 3 Core subobjects for notes and annotations. No other elements from the SBML Level 3 Core namespace are permitted on a <GeneProductAssociation.2020803(error): A <GeneProductAssociation> object may have the optional attributes 'fbc:id' and 'fbc:name'. No other attributes from the SBML Level 3 Flux Balance Constraints namespace are permitted on a <GeneProductAssociation> object.2020805(error): A <GeneProductAssociation> object must have one and only one of the concrete <Association> objects: <GeneProductRef>, <And> or <Or>.
Related elements¶
- Reaction: a process which changes the quantities of species
- And: the associations below it are all needed at once
- Or: one of the associations below it suffices
- GeneProductRef: the leaf of an association: one gene product the reaction depends on
- GeneProduct: a gene or one of its products which the reactions of the model depend on
Specification¶
SBML Level 3 Package: Flux Balance Constraints, Version 3 Release 1, Section 3.9 (Olivier and Bergmann, COMBINE specification).