Table 1

Pathway analysis of five modules obtained from MCODE

aModule

bPathway

cMatched proteins

Total

proteins

dp-value

eGene list


Module 1

Ribosome

4

12

3.6E-04

rpsM, rpsD, rpsE, rplC


Module2

Ribosome

8

30

5.10E-08

rplV, rplA, rpsT, rplD, rpsC, rplM, rpsB, rpsA

1,2-Dichloroethane degradation

3

5.90E-04

PP_2589, PP_3463, PP_2680

Urea cycle and metabolism of amino groups

4

7.80E-04

PP_2589, PP_5278, PP_3463, PP_2680

3-Chloroacrylic acid degradation

3

1.00E-03

PP_2589, PP_3463, PP_2680

Ascorbate and aldarate metabolism

3

1.30E-03

PP_2589, PP_3463, PP_2680

Glycerolipid metabolism

3

2.90E-03

PP_2589, PP_3463, PP_2680

Butanoate metabolism

4

3.00E-03

PP_2589, PP_3463, PP_2680, ilvB

Bile acid biosynthesis

3

3.70E-03

PP_2589, PP_3463, PP_2680

Histidine metabolism

3

6.70E-03

PP_2589, PP_3463, PP_2680

Limonene and pinene degradation

3

7.30E-03

PP_2589, PP_3463, PP_2680

beta-Alanine metabolism

3

8.60E-03

PP_2589, PP_3463, PP_2680


Module3

ABC transporters - General

4

9

3.8E-03

PP_0225, aapP, PP_1068, PP_5022


Module4

Ribosome

8

45

9.9E-07

rplI, rplB, rplQ, rplL, rpmB, rplP, rplE, rplX

Glycolysis/Gluconeogenesis

4

4.1E-03

aceE, eno, aceF, lpdG


Module 5

Ribosome

6

30

2.8E-05

rpsG, rpsN, rplR, rplS, rplW, rpsH


aWe made five modules using MCODE.

bWe analyzed pathway analysis using KEGG pathway information.

cCount column displays the number of protein containing each pathway in module.

dThe p-value is confidence score by Fisher's exact test algorithm.

eGene list column shows gene symbols containing each pathway.

Park et al. BMC Genomics 2009 10(Suppl 3):S18   doi:10.1186/1471-2164-10-S3-S18

Open Data