Table 1.
Gene Families that Are Significantly over (+) or under (-) Represented for Differentially Methylated Genes, their P Values and the KOG Category (Eukaryotic Orthology Groups as Defined by the Joint Genome Institute)
| Name | P value | FDR <0.01 | FDR >0.01 | Proportion (%) with FDR <0.01 | Over/under represented | KOG category |
|---|---|---|---|---|---|---|
| Trypsin | 7.91E−04 | 0 | 75 | 0 | – | Amino acid transport and metabolism |
| Chitinase | 2.85E−02 | 3 | 59 | 4.84 | – | Cell wall/membrane/envelope biogenesis |
| Collagens (type IV and type XIII) | 7.54 E − 06 | 1 | 97 | 1.02 | – | Extracellular structures |
| Bestrophin | 3.96 E − 02 | 0 | 24 | 0 | – | General function prediction only |
| FOG: 7 transmembrane receptor | 4.61 E − 04 | 1 | 70 | 1.41 | – | General function prediction only |
| Low-density lipoprotein receptors | 2.78 E − 02 | 0 | 29 | 0 | – | Intracellular trafficking, secretion, and vesicular transport |
| Nucleolar GTPase/ATPase p130 | 4.97 E − 03 | 1 | 52 | 1.89 | – | Nuclear structure |
| Cytochrome P450 CYP4/CYP19/CYP26 subfamilies | 3.96 E − 02 | 0 | 24 | 0 | - | Secondary metabolites biosynthesis, transport and catabolism |
| C-type lectin | 3.98 E − 02 | 3 | 56 | 5.08 | – | Signal transduction mechanisms |
| Fibroblast/platelet-derived growth factor receptor | 3.96 E − 02 | 0 | 24 | 0 | – | Signal transduction mechanisms |
| RNA polymerase II. large subunit | 3.99 E − 02 | 2 | 48 | 4 | – | Transcription |
| 1-pyrroline-5-carboxylate dehydrogenase | 2.03 E − 02 | 2 | 0 | 100 | + | Amino acid transport and metabolism |
| Cysteine desulfurase NFS1 | 5.85 E − 05 | 5 | 0 | 100 | + | Amino acid transport and metabolism |
| Delta-1-pyrroline-5-carboxylate dehydrogenase | 2.03 E − 02 | 2 | 0 | 100 | + | Amino acid transport and metabolism |
| Cell cycle-regulated histone H1-binding protein | 2.03 E − 02 | 2 | 0 | 100 | + | Cell cycle control, cell division, chromosome partitioning |
| Cyclin B & related kinase-activating proteins | 2.31 E − 02 | 3 | 2 | 60 | + | Cell cycle control, cell division, chromosome partitioning |
| DNA topoisomerase (ATP-hydrolysing) | 2.89 E − 03 | 3 | 0 | 100 | + | Chromatin structure and dynamics |
| DNA topoisomerase type II | 3.10 E − 04 | 5 | 1 | 83.33 | + | Chromatin structure and dynamics |
| Actin regulatory protein | 2.31 E − 02 | 3 | 2 | 60 | + | Cytoskeleton |
| Actin-binding protein Coronin | 2.31 E − 02 | 3 | 2 | 60 | + | Cytoskeleton |
| Von Willebrand factor & related coagulation proteins | 1.23 E − 03 | 0 | 47 | 0 | – | Defense mechanisms |
| Predicted membrane protein | 1.50 E − 02 | 11 | 26 | 29.73 | + | Function unknown |
| Uncharacterized conserved protein with CXXC motifs | 2.03 E − 02 | 2 | 0 | 100 | + | Function unknown |
| F-box protein containing LRR | 7.40 E − 04 | 8 | 8 | 50 | + | General function prediction only |
| FOG: Zn-finger | 5.40 E − 05 | 22 | 43 | 33.85 | + | General function prediction only |
| HMG box-containing protein | 1.94 E − 02 | 5 | 7 | 41.67 | + | General function prediction only |
| Methylase | 2.03 E − 02 | 2 | 0 | 100 | + | General function prediction only |
| Predicted methyltransferase | 1.85 E − 05 | 8 | 3 | 72.73 | + | General function prediction only |
| Sulfotransferases | 2.03 E − 02 | 2 | 0 | 100 | + | General function prediction only |
| H(+)-transporting two-sector ATPase | 2.03 E − 02 | 2 | 0 | 100 | + | Inorganic ion transport and metabolism |
| P-type ATPase | 1.00 E − 02 | 4 | 3 | 57.14 | + | Inorganic ion transport and metabolism |
| Emp24/gp25L/p24 membrane trafficking proteins | 2.03 E − 02 | 2 | 0 | 100 | + | Intracellular trafficking, secretion, and vesicular transport |
| Karyopherin (importin) alpha | 1.15 E − 07 | 11 | 3 | 78.57 | + | Intracellular trafficking, secretion, and vesicular transport |
| Sphingosine N-acyltransferase | 2.03 E − 02 | 2 | 0 | 100 | + | Lipid transport and metabolism |
| Beta-tubulin folding cofactor D | 1.82 E − 03 | 4 | 1 | 80 | + | Posttranslational modification, protein turnover, chaperones |
| Glutathione transferase | 2.89 E − 03 | 3 | 0 | 100 | + | Posttranslational modification, protein turnover, chaperones |
| Molecular chaperone (HSP90 family) | 9.56 E − 04 | 5 | 2 | 71.43 | + | Posttranslational modification, protein turnover, chaperones |
| Thioredoxin-like protein | 4.12 E − 04 | 4 | 0 | 100 | + | Posttranslational modification, protein turnover, chaperones |
| Ubiquitin-protein ligase | 4.74 E − 04 | 6 | 3 | 66.67 | + | Posttranslational modification, protein turnover, chaperones |
| Nuclear 5-3 exoribonuclease-interacting protein | 2.03 E − 02 | 2 | 0 | 100 | + | Replication, recombination and repair |
| FtsJ-like RNA methyltransferase | 2.03 E − 02 | 2 | 0 | 100 | + | RNA processing and modification |
| Heterogeneous nuclear ribonucleoprotein R | 1.69 E − 07 | 10 | 2 | 83.33 | + | RNA processing and modification |
| Leucine rich repeat proteins | 1.15 E − 06 | 15 | 13 | 53.57 | + | RNA processing and modification |
| Putative N2.N2-dimethylguanosine tRNA methyltransferase | 2.03 E − 02 | 2 | 0 | 100 | + | RNA processing and modification |
| TPR repeat-containing protein | 1.03 E − 02 | 3 | 1 | 75 | + | RNA processing and modification |
| Dehydrogenases (related to short-chain alcohol dehydrogenases) | 4.47 E − 03 | 5 | 4 | 55.56 | + | Secondary metabolites biosynthesis, transport and catabolism |
| Ca2+/calmodulin-dependent protein phosphatase | 2.03 E − 02 | 2 | 0 | 100 | + | Signal transduction mechanisms |
| Failed axon connections (fax) proteins | 2.89 E − 03 | 3 | 0 | 100 | + | Signal transduction mechanisms |
| Predicted GTPase-activating protein | 2.85 E − 02 | 4 | 5 | 44.44 | + | Signal transduction mechanisms |
| Tyrosine kinases | 2.31 E − 02 | 3 | 2 | 60 | + | Signal transduction mechanisms |
| RNA polymerase II transcription initiation factor TFIIH | 2.03 E − 02 | 2 | 0 | 100 | + | Transcription |
| Site-specific DNA-methyltransferase | 2.03 E − 02 | 2 | 0 | 100 | + | Transcription |
| Ubiquitin/60s ribosomal protein L40 | 2.03 E − 02 | 2 | 0 | 100 | + | Translation, ribosomal structure and biogenesis |
Genes are defined as differentially expressed at a false discovery rate (fdr) smaller than 0.01.