How to duplicate the process in F1000research article

Outlines

1. Importing KEGG pathway and Exporting KEGG node table
2. Preprocessing the microarray data in ecoliLeucine package
3. How to integrate Pathway and T-test result in Cytoscape

Importing KEGG pathway and Exporting KEGG node table

• Import a pathway(eco00260), please refer https://github.com/idekerlab/KEGGscape/wiki/How-to-import-KGML-with-KEGGscape
  • We recommend you use KEGG API to download kgml quickly

wget http://rest.kegg.jp/get/eco00260/kgml -O eco00260.xml

• Click Export Table to File icon, here we export the node table as keggnode.csv.

Preprocessing the microarray data in ecoliLeucine package

Preprocessing with R(bioconductor)

Following R commands generates t-test results between two groups, mutants and controls, in a global expression profile. Here we filtered the T-test results (with threshold p.value < 0.05).

source("http://bioconductor.org/biocLite.R")
biocLite(c("genefilter", "ecoliLeucine"))
library("ecoliLeucine")
library("genefilter")
data("ecoliLeucine")
eset = rma(ecoliLeucine)
r = rowttests(eset, eset$strain)
filtered = r[r$p.value < 0.05,]
write.csv(filtered, file="ttest.csv")

Preprocessing T-test matrix with Python

Here we append a column for merging KEGG pathway and T-test matrix. To append a column please run following Python script. This Python script generates a table named ttest4pathway.csv.

import csv
import re

ttest_re = re.compile("b[0-9]{4}")
lines = []

with open('ttest.csv') as ttest:
    ttestreader = csv.reader(ttest)
    for ttestrow in ttestreader:
        ttest_match = ttest_re.findall(ttestrow[0])
        if len(ttest_match) > 0:
            bnumber = ttest_match[0]
            bnumber_re = re.compile(bnumber)
            with open('keggnode.csv') as kegg:
                keggreader = csv.reader(kegg)
                for keggrow in keggreader:
                    kegg_match = bnumber_re.findall(keggrow[1])
                    if len(kegg_match) > 0:
                        lines.append(','.join(ttestrow) + ',"' + keggrow[4] + '"\n')

ttest4pathway = open('ttest4pathway.csv', 'w')

ttestheader = open('ttest.csv').readline().strip()
keggheader = open('keggnode.csv').readline().split(',')[4]

ttest4pathway.write(ttestheader + ',' + keggheader + '\n')
ttest4pathway.writelines(set(lines))
ttest4pathway.close()

How to integrate Pathway and T-test result in Cytoscape

Importing T-test result for KEGG pathway

• Click Import Table From File toolbar icon and open ttest4pathway.csv
• Import To an unassigned table like this

Merging tables for microarray data and KEGG pathway

• Click menubar(Tools --> Merge --> Tables...), and set like following image.

Vizmapping T-test P-values to the KEGG Pathway

Click Style from Control Panel, and Click Show All from Properties,and set Vizmap like this.

Finally bundle edges from menubar(Layout --> Bundle Edges --> All Nodes and Edges). And you will get