Growing functional modules from a seed protein via integration of protein interaction and gene expression data

BMC Bioinformatics

Table 2 MIPS functional distribution of gene representative clusters

Cluster/Genes	Functional distribution (MIPS)	Percentage (fraction of genes)	p-value
1/n = 376	14 protein fate	27.2% (102)	2.64 e-05
	14.07 protein modification	17% (64)	1.03 e-05
	11.02.03 mRNA synthesis	15.2% (57)	1.35 e-04
4/n = 259	11 transcription	29.7% (77)	6.45 e-07
	10.03 cell cycle	19.3% (50)	1.58 e-05
	10.03.01 mitotic cell cycle and cell cycle control	12.7% (33)	9.93 e-04
7/n = 189	42 biogenesis of cellular components	21.6% (41)	2.47 e-03
	14.07 protein modification	16.4% (31)	3.91 e-03
	11.01.03 mRNA processing	9% (17)	5.22 e-05
16/n = 82	16 protein with binding function or cofactor requirement	32.9% (27)	3.31 e-04
	43.01 fungal/microorganismic cell type differentiation	18.2% (15)	8.20 e-04
	43.01.03 fungal and other eukaryotic cell type differentiation	18.2% (15)	8.20 e-04
3/n = 183	01 metabolism	30% (55)	5.48 e-02
	10.03 cell cycle	14% (26)	7.48 e-02
	11.04.03 mRNA processing	8% (13)	3.57 e-03
6/n = 181	01 metabolism	39.7% (72)	3.91 e-06
	10.01 DNA processing	15.4% (28)	1.05 e-03
	11.02.03 mRNA synthesis	17.6% (32)	2.99 e-04

Examples of gene clusters after clustering the gene expression data. The first column represents the number of cluster and the number of genes in it. The second column represents the functional distribution of every cluster according to MIPS from the main category up to the third-level subcategory. The third column shows the percentage of genes belonging to this category and in the brackets the corresponding actual number. The last column displays the p-value found by MIPS in every functional category.

ISSN: 1471-2105