Table 4 Gene ontology enrichment analyses: top 10 terms for phenotype-associated DNAm sites showing change from birth to childhood

Biological processes (BP)

 BP

Vesicle cytoskeletal trafficking

1.0E − 03

Neurogenesis

2.2E − 04

Proximal/distal pattern formation

3.6E − 04

Positive regulation of RNA biosynthetic process

4.5E − 05

Cell morphogenesis

3.6E − 05

 BP

G protein-coupled glutamate receptor signaling pathway

2.7E − 03

Generation of neurons

1.0E − 03

Cell morphogenesis involved in neuron differentiation

5.8E − 04

Morphogenesis of an epithelium

4.8E − 05

Cell junction organization

1.4E − 04

BP

Cerebral cortex development

3.3E − 03

Neuron projection development

1.6E − 03

Anatomical structure arrangement

1.7E − 03

Nervous system development

4.8E − 05

Plasma membrane-bounded cell projection morphogenesis

2.1E − 04

 BP

Toll-like receptor 2 signaling pathway

4.3E − 03

Platelet-derived growth factor receptor signaling pathway

1.6E − 03

Cranial nerve morphogenesis

1.7E − 03

Positive regulation of DNA-templated transcription

4.9E − 05

Cell projection morphogenesis

2.6E − 04

 BP

Mucus secretion

4.7E − 03

Neuron differentiation

1.7E − 03

Central nervous system development

1.8E − 03

Regulation of cell projection organization

9.0E − 05

Cellular localization

3.6E − 04

 BP

Peptidyl-threonine dephosphorylation

6.5E − 03

Neuron development

1.9E − 03

Brain development

2.1E − 03

Dendritic spine morphogenesis

1.1E − 04

Neuron projection morphogenesis

3.7E − 04

 BP

Response to nutrient

6.7E − 03

Regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway

1.9E − 03

Regulation of DNA-templated DNA replication

2.5E − 03

Regulation of plasma membrane-bounded cell projection organization

1.1E − 04

Cell junction assembly

6.6E − 04

 BP

Corticosteroid hormone secretion

7.0E − 03

Regulation of Notch signaling pathway

2.2E − 03

Chorionic trophoblast cell differentiation

3.0E − 03

Cell morphogenesis involved in neuron differentiation

1.1E − 04

mRNA export from nucleus

7.0E − 04

 BP

Regulation of lysosome size

7.1E − 03

Negative regulation of T cell-mediated immunity

2.2E − 03

Head development

3.3E − 03

Cell morphogenesis

1.4E − 04

Adherens junction organization

8.0E − 04

 BP

Modification of postsynaptic actin cytoskeleton

7.8E − 03

Negative regulation of DNA-templated transcription initiation

2.3E − 03

Skeletal system morphogenesis

3.4E − 03

Neuron differentiation

1.4E − 04

Cell part morphogenesis

8.1E − 04

Cellular components (CC)

 CC

Synapse

1.0E − 03

Cell junction

6.7E − 03

Dendritic tree

9.9E − 06

Cell-substrate junction

1.4E − 05

Nucleoplasm

2.3E − 04

 CC

Neuron spine

1.5E − 03

Neurofilament

7.5E − 03

Dendrite

1.6E − 05

Focal adhesion

2.3E − 05

Exon-exon junction complex

1.3E − 03

 CC

Dendritic spine

1.6E − 03

Protein phosphatase type 2A complex

9.0E − 03

Dendritic spine

2.8E − 05

Glutamatergic synapse

3.5E − 05

Nuclear body

2.3E − 03

 CC

Postsynapse

2.3E − 03

Cell leading edge

1.0E − 02

Neuron spine

5.2E − 05

Anchoring junction

5.0E − 04

Adherens junction

2.8E − 03

 CC

Plasma membrane protein complex

3.4E − 03

Synaptic membrane

1.0E − 02

Somatodendritic compartment

6.7E − 04

Cell leading edge

7.7E − 04

Sarcoplasm

2.9E − 03

 CC

Voltage-gated potassium channel complex

4.2E − 03

Glutamatergic synapse

1.1E − 02

Neuron-to-neuron synapse

1.7E − 03

Actin-based cell projection

1.2E − 03

Cell leading edge

3.0E − 03

 CC

Cell junction

4.4E − 03

Leading edge membrane

1.2E − 02

Asymmetric synapse

2.4E − 03

Postsynapse

1.3E − 03

Junctional sarcoplasmic reticulum membrane

4.3E − 03

 CC

Potassium channel complex

5.0E − 03

Cell tip

1.3E − 02

Postsynaptic density

2.4E − 03

Cell cortex

2.7E − 03

Chromosomal region

5.4E − 03

 CC

BORC complex

7.1E − 03

Postsynaptic cytoskeleton

1.4E − 02

Neuron projection

2.5E − 03

Adherens junction

3.1E − 03

Cell junction

6.5E − 03

 CC

Axolemma

7.7E − 03

Eukaryotic translation initiation factor 3 complex, eIF3m

1.5E − 02

Main axon

6.3E − 03

Lamellipodium

3.2E − 03

Postsynapse

6.9E − 03

Molecular functions (MF)

 MF

Phospholipase binding

1.7E − 03

Lysine-acetylated histone binding

4.7E − 04

Ubiquitin-conjugating enzyme binding

2.4E − 03

Transcription factor binding

2.4E − 04

Protein serine kinase activity

9.2E − 04

 MF

Efflux transmembrane transporter activity

3.7E − 03

Acetylation-dependent protein binding

4.7E − 04

Cytoskeletal anchor activity

7.2E − 03

Enzyme binding

3.0E − 04

Cell adhesion molecule binding

1.9E − 03

 MF

GTPase regulator activity

7.6E − 03

Transcription coregulator binding

1.1E − 03

1-Phosphatidylinositol-4-phosphate 3-kinase activity

8.5E − 03

DNA-binding transcription factor binding

4.2E − 04

Beta-catenin binding

4.6E − 03

 MF

Nucleoside-triphosphatase regulator activity

7.6E − 03

Proline-rich region binding

1.2E − 03

1-Phosphatidylinositol-3-kinase activity

8.5E − 03

Transcription coregulator activity

7.6E − 04

Phosphatidylinositol-3,4,5-trisphosphate binding

5.8E − 03

 MF

Demethylase activity

8.4E − 03

Prostaglandin E receptor activity

5.8E − 03

Poly-pyrimidine tract binding

1.0E − 02

RNA polymerase II-specific DNA-binding transcription factor binding

8.5E − 04

Transferase activity, transferring phosphorus-containing groups

5.8E − 03

 MF

bHLH transcription factor binding

9.2E − 03

Prostaglandin receptor activity

6.1E − 03

Ephrin receptor binding

1.1E − 02

Protein tyrosine kinase activity

9.8E − 04

Phosphatidylinositol-3,5-bisphosphate binding

7.0E − 03

 MF

Histone demethylase activity

1.1E − 02

Transmembrane receptor protein tyrosine kinase activity

8.3E − 03

Branched-chain amino acid transmembrane transporter activity

1.2E − 02

Kinase activity

1.0E − 03

Cysteine-type endopeptidase regulator activity involved in apoptotic process

7.7E − 03

 MF

Protein demethylase activity

1.1E − 02

Bicarbonate transmembrane transporter activity

9.2E − 03

Poly(U) RNA binding

1.2E − 02

ATP binding

1.9E − 03

Histone H3K9 methyltransferase activity

9.2E − 03

 MF

RS domain binding

1.1E − 02

Transcription coactivator binding

9.8E − 03

Scaffold protein binding

1.3E − 02

Transcription coregulator binding

1.9E − 03

Ubiquitin-like protein transferase activity

9.2E − 03

 MF

Transcription coregulator activity

1.3E − 02

Modification-dependent protein binding

1.3E − 02

Ubiquitin-like protein conjugating enzyme binding

1.4E − 02

Adenyl nucleotide binding

2.7E − 03

Cadherin binding

9.5E − 03