Table 1

Functional annotation of developmentally hydroxymethylated regions

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


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.

Ivanov et al. Genome Biology 2013 14:R83   doi:10.1186/gb-2013-14-8-r83

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