Connectivity measure for metabolic map

Question

[guisa.santos]

Dear Biostars,

I would like to infer if the "connectivity" of a particular metabolic sub-graph (nodes are compounds and edges are enzymes) is significantly different from randomly picking edges from the complete metabolic graph of a given species.

WHY: This is to study if the map of candidate horizontally transferred enzymes is more connected than what would be expected if random enzymes were transferred and kept.

WHAT: I would like suggestions of how to do this, or it could be suggestions of tools, packages, metrics or papers describing similar analyses (maybe I am searching with the wrong keywords, because I get no good hits to help me).

Thank you in advance for your help.

Guisa

Answer 1

[natasha.sernova]

Look at these papers:

Properties of metabolic graphs: biological organization or representation artifacts?

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098788/

Concerning tools:

getMetabolicGraph {iSubpathwayMiner}

http://www.inside-r.org/packages/cran/iSubpathwayMiner/docs/getMetabolicGraph

Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2844990/

Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks

MetScape 2.3.2 User Manual

http://metscape.ncibi.org/metscape2/Metscape2_User_Manual.pdf

Pathway discovery in metabolic networks by subgraph extraction

http://bioinformatics.oxfordjournals.org/content/26/9/1211.short

Recent papers:

The MetaboX library: building metabolic networks from KEGG database

https://arxiv.org/pdf/1402.5062.pdf

KEGGgraph: a graph approach to KEGG PATHWAY in R and Bioconductor

https://www.bioconductor.org/packages/devel/bioc/vignettes/KEGGgraph/inst/doc/KEGGgraph.pdf

NIBBS-Search for Fast and Accurate Prediction of Phenotype-Biased Metabolic Systems

http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1002490

Evolution of Hierarchy in Bacterial Metabolic Networks

http://snap.stanford.edu/class/cs224w-2014/projects2014/cs224w-77-final.pdf