SBGN Bricks Dictionary

The previous version of the dictionary is available at http://sbgnbricks.sourceforge.net.

• Metabolic network
  • Metabolic reaction
  • Catalysis
  • Inhibition
• Signalling network
  • Protein phosphorylation
  • Protein dephosphorylation
  • Oligomerisation
  • Complex association
  • Complex dissociation
• Gene regulatory network
  • Transcription
  • Regulation of transcription by a transcription factor
  • Translation
• Transport
  • Passive transport
  • Active transport
• Functional genomics

Metabolic network

Metabolic reaction

Associated GO terms: GO:0008152 metabolic process

Irreversible reaction

	Not applicable	Not applicable

Reversible reaction

	Not applicable	Not applicable

Catalysis

Associated GO terms: GO:0003824 catalytic activity

		Not applicable

Irreversible reaction with multiple substrates and products

		Not applicable

Reversible reaction

	Not applicable	Not applicable

Reversible reaction with multiple substrates and products

	Not applicable	Not applicable

Inhibition

Associated GO terms: GO:0043086 negative regulation of catalytic activity

Irreversible reaction

	Not applicable	Not applicable

Irreversible catalyzed reaction

	Not applicable	Not applicable

Reversible catalyzed reaction

	Not applicable	Not applicable

Irreversible reaction

Signalling network

Associated GO terms: GO:0023052 signaling; GO:0007165 signal transduction; GO:0023051 regulation of signaling

Protein phosphorylation

Associated GO terms: GO:0006468 protein phosphorylation; GO:0001934 positive regulation of protein phosphorylation; GO:0032147 activation of protein kinase activity

For the AF expression, the assumption is that phosporylation of X leads to its activation. Phosphorylation could also lead to its deactivation, and then the stimulation arc in AF would need to be replaced by an inhibition arc.

In a similar way other types of post-translational modifications can be expressed:

Acetylation	Ac	SBO:0000215	Palmytoylation	Pa	SBO:0000218
Glycosylation	G	SBO:0000217	Prenylation	Pr	SBO:0000221
Hydroxylation	OH	SBO:0000233	Protonation	H	SBO:0000212
Methylation	Me	SBO:0000214	Sulfation	S	SBO:0000220
Myristoylation	My	SBO:0000219	Ubiquitination	Ub	SBO:0000224

Protein dephosphorylation

For the AF expression, the assumption is that dephosporylation of X leads to its deactivation. Dephosphorylation could also lead to its activation, and then the inhibition arc in AF would need to be replaced by a stimulation arc.

Oligomerisation

Associated GO terms: GO:0051259 protein complex oligomerization

For the AF expression, the assumption is that the dimer X/X has some activity.

Complex association

Associated GO terms: GO:0065003 protein-containing complex assembly

For the AF expression, the assumption is that the complex X/Y has some activity.

Complex dissociation

Associated GO terms: GO:0032984 protein-containing complex disassembly

		Not applicable

Gene regulatory network

Transcription

Associated GO terms: GO:0006351 transcription, DNA-templated; GO:0009299 mRNA transcription

Regulation of transcription by a transcription factor

Associated GO terms: GO:0006351 transcription, DNA-templated; GO:0065004 protein-DNA complex assembly; GO:0009299 mRNA transcription; GO:0006355 regulation of transcription, DNA-templated

Translation

Associated GO terms: GO:0006412 translation

For the AF expression, the assumption is that protein X has some activity.

Transport

Associated GO terms: GO:0006810 transport

Passive transport

Active transport

For the AF expression, the assumption is that X has some activity in the nucleus.

Functional genomics

Associated GO terms: GO:0008150 biological_process

Not applicable		Not applicable