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Table 1 The types of influences I on an entity X and their edge costs

From: The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database

TYPE OF INFLUENCER

EDGE COST FORMULA

X is a reaction substrate (including proteins in ligand-binding reactions) a:

 

Reactant I of reaction producing X

1+(|RX=sub|+|RI=sub|)/20

Reactant I of reaction consuming X

1+(|RX=sub|+|RI=sub|)/10

Product I of reaction consuming X

2+(|RX=sub|+|RI=sub|)/10

Enzyme I of reaction producing X

1+|RI=enz|/20

Enzyme I of reaction consuming X

2+|RI=enz|/20

Transporter I of X

1+|RI=transporter|/20

X is a gene, gene product, or protein complex:

 

Activator or inhibitor I of enzyme X

1+|EnzsI=modulator|/20

Cofactor I of enzyme X

1+|EnzsI=cofactor|/20

Transcriptional regulator I of X

1+(|RegsX|+|GI=reg|)/20

Translational regulator I of X

1+(|RegsX|+|GI=reg|)/20

Sigma factor I for transcription of X

1+|GI=reg|/20

Component I of protein complex X

0.1

Transcription unit I of gene Xb

0

  1. |RX=sub| should be read as the number of other reactions in which X is a substrate (reactant or product), and so forth. Other abbreviations: G=genes, Enz=enzyme, Reg=regulator.
  2. aWe use the term substrate to refer to both reactants and products of a reaction. We exclude certain compounds that appear in very large numbers of reactions, such as water, ATP, etc. Also, if X is a small molecule, we exclude reactions in which proteins bind X, on the grounds that such interactions typically affect the quantity or activity of the protein but not, to any appreciable extent, the small molecule.
  3. bWhile transcription units are not among the classes of entities we handle, are not added to the queue, and are therefore dead-ends in the graph, these are useful interactions to add in undirected mode because they explain why two genes might be correlated.
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BMC Bioinformatics

ISSN: 1471-2105

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