PutidaNET: Interactome database service and network analysis of Pseudomonas putida KT2440

BMC Genomics

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.

ISSN: 1471-2164