Table 1: (a) Differentially expressed GO classes resulting from comparative GO-based analysis of paired DNMC and MC sample sets of 18 patients. (b) Genes from the top 4 identified differentially expressed GO classes.
(a)

GO category1GO term2GO descriptionNumber of genesLS permutation KS permutation
value3 value4

1313CCOrganellar ribosome30 0.0120303
25761CCMitochondrial ribosome30 0.0120303
315078MFHydrogen ion transporter activity94
416272CCPrefoldin complex130.00030820.001475
58603MFcAMP-dependent protein kinase regulator activity90.00060460.0080679
64164MFDiphthine synthase activity50.0006262
78629BPInduction of apoptosis by intracellular signals170.00062920.0060299
879BPRegulation of cyclin-dependent protein kinase activity300.00096820.0006918
98022MFProtein C-terminus binding280.00101780.0332401
1030274MFLIM domain binding50.00272410.0278159
1117182BPPeptidyl-diphthamide metabolism80.00310290.001998
1217183BPPeptidyl-diphthamide biosynthesis from peptidyl-histidine80.00310290.001998
1318202BPPeptidyl-histidine modification80.00310290.001998
148428MFRibonuclease inhibitor activity50.00318160.0130247
1545815BPPositive regulation of gene expression, epigenetic70.00321920.0187543
1643028MFCaspase regulator activity50.00354320.3403788
1731202MFRNA splicing factor activity, transesterification mechanism230.00424510.0013586
188757MFS-adenosylmethionine-dependent methyltransferase activity760.00447280.0618698
197021BPTubulin folding50.00462180.0028239
208013MFBeta-catenin binding70.00488260.0031594
21118CCHistone deacetylase complex380.00802480.0020909
229897CCExternal side of plasma membrane90.00856320.0021181
2345736BPNegative regulation of cyclin-dependent protein kinase activity50.01820210.0028634
243747MFTranslation release factor activity80.0459470.0046691
258079MFTranslation termination factor activity80.0459470.0046691
2642393MFHistone binding180.1723880.0043185

1The 26 GO categories found to be significant at the nominal 0.005 level of the LS permutation test or KS permutation test (sorted by values of the LS permutation test). For each GO category, the table lists the unique identifier, the number of genes in the project gene list that belong to the GO category, and the LS and KS values.
The presented GO categories are ordered by the value of the LS test (smallest first).
2Goterm: CC: cellular component, BP: biological process, and MF: molecular function.
3Fisher (LS) statistic is defined as the mean negative natural logarithm of the values of the appropriate single gene univariate test.
4Kolmogorov-Smirnov (KS) statistic is used for testing if the values are of a uniform distribution.
(b)

GO term1
Parametric
GO descriptionProbesetDescription2Gene symbolParametric 
values

1CCOrganellar ribosome219220_x_atMitochondrial ribosomal protein S22MRPS220.0001097
2CCOrganellar ribosome223480_s_atMitochondrial ribosomal protein L47MRPL470.000131
3CCOrganellar ribosome218558_s_atMitochondrial ribosomal protein L39MRPL390.006304
4CCOrganellar ribosome224869_s_atMitochondrial ribosomal protein S25MRPS250.0151834
5CCOrganellar ribosome222775_s_atMitochondrial ribosomal protein L35MRPL350.0171902
6CCMitochondrial ribosome219220_x_atMitochondrial ribosomal protein S16MRPS160.0005530
7CCMitochondrial ribosome223480_s_atMitochondrial ribosomal protein L44MRPL440.000131
8CCMitochondrial ribosome219819_s_atMitochondrial ribosomal protein S28MRPS280.0029398
9CCMitochondrial ribosome217919_s_atMitochondrial ribosomal protein L42MRPL420.0303516
10CCMitochondrial ribosome222993_atMitochondrial ribosomal protein S37MRPL370.003539
11MFHydrogen ion transporter activity213846_atCytochrome c oxidase subunit VIIcCOX7C0.0020774
19MFHydrogen ion transporter activity218484_atNADH dehydrogenase (ubiquinone) 1 NDUFA4L20.00585351
12MFHydrogen ion transporter activity238765_atATPase, H+ transporting, lysosomal 13 kDa, V1 subunit G1ATP6V1G10.0059421
13MFHydrogen ion transporter activity209065_atUbiquinol-cytochrome c reductase-binding proteinUQCRB0.0171665
14MFHydrogen ion transporter activity231487_atCytochrome c oxidase subunit 8CCOX8C0.021483
15MFHydrogen ion transporter activity1552286_atATPase, H+ transporting, lysosomal 31 kDa, V1 subunit E2ATP6V1E20.0279023
16MFHydrogen ion transporter activity202698_x_atCytochrome c oxidase subunit IV isoform 1COX4I10.0380242
17MFHydrogen ion transporter activity228142_atUbiquinol-cytochrome c reductase complex (7.2 kD)UCRC0.0389511
18MFHydrogen ion transporter activity220834_atMembrane-spanning 4-domains, subfamily A, member 12MS4A120.0460068
20CCPrefoldin complex207132_x_atPrefoldin subunit 5PFDN50.0086113
21CCPrefoldin complex218336_atPrefoldin subunit 2PFDN20.0225808
22CCPrefoldin complex222019_atPrefoldin subunit 6PFDN60.0326926
23CCPrefoldin complex201472_atVon Hippel-Lindau binding protein 1VBP10.0345687
25CCPrefoldin complex205963_s_atDnaJ homolog, subfamily A, member 3DNAJA30.04568034
26MFOxidoreductase activity207843_x_atCytochrome b5 type ACYB5A0.01245134
27MFOxidoreductase activity1560609_atCrystallin zeta (quinone reductase)-like 1CRYZL10.0496658

1The different GOterms: CC: cellular component; MF: molecular function; BP: biological process.
2Genes found to be differentially expressed with a parametric value of less than 0.05 in the top 5 of GO categories.
They are ordered by the parametric value associated with the GO category for each class.