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Table 1 Functional annotation of developmentally hydroxymethylated regions

From: Ontogeny, distribution and potential roles of 5-hydroxymethylcytosine in human liver function

  Binomial test Hypergeometric test
Biological process Raw P-valuea FDR Q-valueb Fold enrichmentc FDR Q-valued Fold enrichmente
Genes enriched with adult-only 5hmC blocks      
    Nuclear-transcribed mRNA catabolic process 4.30E-182 3.22E-180 2.49 8.82E-03 1.16
    mRNA catabolic process 8.88E-165 5.52E-163 2.25 1.77E-02 1.14
    Carbohydrate transport 3.29E-125 1.51E-123 2.06 5.91E-03 1.15
    Vesicle localization 9.48E-113 4.05E-111 2.20 3.73E-02 1.16
    Fatty acid oxidation 5.52E-102 2.12E-100 2.22 4.59E-03 1.20
    Lipid oxidation 1.44E-100 5.39E-99 2.20 3.97E-03 1.20
    mRNA 3'-end processing 1.73E-98 6.27E-97 2.24 1.11E-02 1.17
    Monocarboxylic acid catabolic process 1.35E-95 4.80E-94 2.21 5.31E-03 1.20
    RNA 3'-end processing 2.92E-94 1.02E-92 2.07 2.13E-02 1.15
    Fatty acid catabolic process 2.99E-90 9.99E-89 2.22 1.00E-02 1.20
Genes enriched with fetal-only 5hmC blocks      
    Regulation of granulocyte differentiation 5.88E-23 2.45E-20 6.20 3.56E-02 2.58
    Regulation of myeloid cell differentiation 9.74E-17 1.67E-14 2.19 1.84E-03 1.64
    Induction of apoptosis by extracellular signals 5.49E-15 7.18E-13 2.18 9.28E-03 1.54
    Positive regulation of steroid metabolic process 1.76E-12 1.61E-10 3.87 9.82E-03 2.37
    Stem cell development 6.00E-12 5.05E-10 2.09 4.16E-04 2.06
    Establishment or maintenance of cell polarity 9.26E-11 6.14E-09 2.02 1.97E-02 1.63
    Regulation of protein binding 6.32E-10 3.38E-08 2.03 2.36E-02 1.64
    Stem cell maintenance 8.22E-10 4.31E-08 2.00 9.44E-04 2.04
    Somatic stem cell maintenance 6.28E-09 2.59E-07 2.15 2.15E-02 2.04
    Negative regulation of lipoprotein particle clearance 1.99E-07 6.11E-06 6.52 3.08E-02 3.73
  1. Shown are the top 10 significantly enriched biological processes sorted according to the binomial P-values. aUncorrected P-value from the binomial test over genomic regions; bfalse discovery rate q-value; cfold enrichment of number of genomic regions in the test set; dfalse discovery rate q-value from the hypergeometric test over genes; efold enrichment of number of genes in the test set.