visualizeEpistasis

convertGene2PathwayInteractions(E, epSys, uSys)

This function was written to find out the type of epistatic interactions that either exist between two different or within same subsystem

USAGE:

[neg,zer,nd,pos] = convertGene2PathwayInteractions(E,epSys,uSys)

INPUT:

E: A square epistatic interaction matrix (or genes or reactions) epSys: Subsystems belonging to the gene at that index (a second

order cell array) Each cell array may contain one or more subsystems. e.g. for first gene or reaction in E: epCmpt{1,1} = {‘Glycolysis’;’TCA cycle’}

uSys: Unique Subsystems in the epCmpt (use this arguments if

interested in interactions between selected subsystems in the epSys)

OUTPUTS:

neg: matrix of number of aggravating (negative) pathway-pair interactions zer: matrix of number of no-epistatic interactions pathway-pair interactions nd: matrix of number of non-decisive interactions pathway-pair interactions pos: matrix of number of buffering (positive) interactions pathway-pair interactions

Note

See figures in following publication: Joshi CJ and Prasad A, 2014, “Epistatic interactions among metabolic genes depend upon environmental conditions”, Mol. BioSyst., 10, 2578-2589.

findSubsystemOfGenes(model, genes)

This function is used to find out which genes belong to which subsystem

USAGE:

[rxns,subsys,subsysGenes,uSys,Nr,rxnNames]=findSubsystemOfGenes(model,genes)

INPUT:

model: model to which genes belong to genes: genes in question, if not provided will do it for all

the genes, default: model.genes

OUTPUT:

rxns: Reactions governed by these genes subsys: subsystem(s) to which the gene belongs to subsysGenes: which Genes are involved in each subsystem, subsystem

name given by the cell array, usys

uSys: unique subsystems

Note

See figures in following publication: Joshi CJ and Prasad A, 2014, “Epistatic interactions among metabolic genes depend upon environmental conditions”, Mol. BioSyst., 10, 2578-2589.

visualizePathwayInEpistasis(Nall, radius, pathwayNames)

This function creates a circular network such that all the nodes are arranged in a circle. The nodes represent a pathway, the color of the node represents whether the interactions within a pathway are none, positive, negative, or mixed. The size of the node represents the number of interactions. The edges represent which pathways are sharing which type of interaction. The color of the edge represents if the interactions are positive negative or mixed. The with of the edge represent the total number of interactions between any two given pathways.

USAGE:

[both,pos,neg]=visualizePathwayInEpistasis(Nall,radius,pathwayNames)

INPUT:

Nall: a structure representing the epistatic interaction networks:

Nall.pos: a square matrix representing number of positive interactions shared by any two pathways. Nall.neg: a square matrix representing number of negative interactions shared by any two pathways.

radius: radius of the generic circles for clock diagram. pathwayNames: subSystem names corresponding to matrices in Nall

structure

OUTPUT:

both: contains both positive and negative interactions pos: contains only positive interactions neg: contains only negative interactions

Note

See figures in following publication: Joshi CJ and Prasad A, 2014, “Epistatic interactions among metabolic genes depend upon environmental conditions”, Mol. BioSyst., 10, 2578-2589.