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michaelwitting / LipidNetworkPredictR

Model based prediction of C. elegans lipids
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Curate general reactions from RheaDB #5

Open michaelwitting opened 2 years ago

michaelwitting commented 2 years ago

In order to achieve goals from #2 a list of general reactions is required. This can be curated from RheaDB. ToDo:

michaelwitting commented 2 years ago

Reactions need to be also ordered into logical sequences, since substrates and products depend on each other. Maybe a good starting point is always going from fatty acids and then follow lipid biochemistry. At the begin of the functions a test shall be performed if the sequence is logical and if any disconnecte parts exist. This can be performed on the general lipids. Example: LPA --> PA DG --> PC

The two reactions are disconnected since the reaction from PA to DG is missing. Directionality becomes also important. For example one could add DG --> PA, but that also consumes DG and DG is never produced.

michaelwitting commented 2 years ago

Example:

<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

order | name | rhea_id | reaction -- | -- | -- | -- 1 | fatty acid-CoA ligase | RHEA:15421 | FA + ATP + CoA = Acyl-CoA + AMP + PPi 1 | fatty acid-CoA ligase | RHEA:15422 | FA + ATP + CoA => Acyl-CoA + AMP + PPi 1 | fatty acid-CoA ligase | RHEA:15423 | FA + ATP + CoA <= Acyl-CoA + AMP + PPi 1 | fatty acid-CoA ligase | RHEA:15424 | FA + ATP + CoA <=> Acyl-CoA + AMP + PPi 2 | Glycerol-3-phosphate 1-O-acyltransferase | RHEA:15325 | Acyl-CoA + sn-glycerol 3-phosphate = LPA + CoA 2 | Glycerol-3-phosphate 1-O-acyltransferase | RHEA:1536 | Acyl-CoA + sn-glycerol 3-phosphate => LPA + CoA 2 | Glycerol-3-phosphate 1-O-acyltransferase | RHEA:15327 | Acyl-CoA + sn-glycerol 3-phosphate <= LPA + CoA 2 | Glycerol-3-phosphate 1-O-acyltransferase | RHEA:15328 | Acyl-CoA + sn-glycerol 3-phosphate <=> LPA + CoA 3 | 1-acylglycerol-3-phosphate O-acyltransferase | RHEA:19709 | LPA + Acyl-CoA = PA + CoA 3 | 1-acylglycerol-3-phosphate O-acyltransferase | RHEA:19710 | LPA + Acyl-CoA => PA + CoA 3 | 1-acylglycerol-3-phosphate O-acyltransferase | RHEA:19711 | LPA + Acyl-CoA <= PA + CoA 3 | 1-acylglycerol-3-phosphate O-acyltransferase | RHEA:19712 | LPA + Acyl-CoA <=> PA + CoA