Table 2.
Functional annotations enriched among transcripts that are downregulated in α-MHC positive cells
| Category | Term | Count | P value |
| GOTERM_BP_5 | DNA metabolism | 76 | 3.17 × e-24 |
| GOTERM_BP_5 | M phase | 41 | 1.79 × e-23 |
| GOTERM_BP_5 | DNA replication | 35 | 2.91 × e-19 |
| GOTERM_BP_5 | Mitotic cell cycle | 35 | 1.92 × e-17 |
| KEGG_PATHWAY | Cell cycle | 32 | 7.70 × e-17 |
| GOTERM_MF_5 | ATP binding | 101 | 3.13 × e-15 |
| GOTERM_CC_5 | Chromosome | 46 | 9.39 × e-13 |
| GOTERM_BP_5 | DNA repair | 27 | 2.88 × e-10 |
| GOTERM_BP_5 | Regulation of cell cycle | 40 | 7.18 × e-10 |
| GOTERM_CC_5 | Chromosome, pericentric region | 15 | 2.39 × e-09 |
| GOTERM_BP_5 | RNA processing | 32 | 5.21 × e-09 |
| GOTERM_BP_5 | mRNA metabolism | 24 | 1.28 × e-08 |
| GOTERM_BP_5 | RNA metabolism | 37 | 1.29 × e-08 |
| GOTERM_CC_5 | Nucleus | 229 | 2.04 × e-07 |
| GOTERM_MF_5 | Exonuclease activity | 12 | 9.96 × e-07 |
| GOTERM_CC_5 | Kinetochore | 9 | 1.68 × e-06 |
| GOTERM_CC_5 | Replication fork | 9 | 1.68 × e-06 |
| GOTERM_CC_5 | Condensed chromosome | 12 | 3.78 × e-06 |
| GOTERM_CC_5 | Replisome | 8 | 8.86 × e-06 |
| GOTERM_MF_5 | Pyrophosphatase activity | 40 | 1.85 × e-05 |
| GOTERM_BP_5 | Regulation of DNA metabolism | 6 | 4.69 × e-05 |
| KEGG_PATHWAY | Pyrimidine metabolism | 14 | 4.94 × e-05 |
| GOTERM_CC_5 | Spindle | 13 | 8.62 × e-05 |
| GOTERM_BP_5 | DNA recombination | 11 | 1.44 × e-04 |
| GOTERM_BP_5 | DNA damage response, signal transduction | 6 | 3.13 × e-04 |
| GOTERM_BP_5 | Coenzyme metabolism | 15 | 8.57 × e-04 |
| GOTERM_BP_5 | Carboxylic acid metabolism | 27 | 1.04 × e-03 |
| GOTERM_BP_5 | Nuclear transport | 11 | 1.07 × e-03 |
| GOTERM_CC_5 | Nucleolus | 16 | 1.22 × e-03 |
| GOTERM_BP_5 | Amine biosynthesis | 9 | 1.23 × e-03 |
| GOTERM_BP_5 | Amino acid metabolism | 16 | 2.25 × e-03 |
| GOTERM_CC_5 | Microtubule cytoskeleton | 24 | 3.62 × e-03 |
| GOTERM_BP_5 | Folic acid and derivative metabolism | 4 | 3.75 × e-03 |
| GOTERM_BP_5 | Nucleocytoplasmic transport | 11 | 4.02 × e-03 |
| GOTERM_BP_5 | Cellular protein metabolism | 135 | 4.25 × e-03 |
| GOTERM_BP_5 | Cytoskeleton organization and biogenesis | 28 | 5.66 × e-03 |
| KEGG_PATHWAY | Purine metabolism | 14 | 6.33 × e-03 |
| KEGG_PATHWAY | Glycine, serine and threonine metabolism | 7 | 1.01 × e-02 |
| KEGG_PATHWAY | DNA polymerase | 6 | 1.10 × e-02 |
| GOTERM_BP_5 | Dna packaging | 15 | 1.16 × e-02 |
| GOTERM_CC_5 | Nuclear chromosome | 8 | 1.17 × e-02 |
| GOTERM_CC_5 | Spindle pole | 8 | 1.17 × e-02 |
| GOTERM_MF_5 | S-adenosylmethionine-dependent methyltransferase activity | 9 | 1.24 × e-02 |
| BIOCARTA | Cell cycle: G2/M checkpoint | 7 | 1.33 × e-02 |
| GOTERM_BP_5 | Chromosome organization and biogenesis | 19 | 1.36 × e-02 |
| BIOCARTA | Cell cycle: G1/S check point | 7 | 1.59 × e-02 |
| GOTERM_CC_5 | Delta DNA polymerase complex | 3 | 1.59 × e-02 |
| BIOCARTA | Role of Ran in mitotic spindle regulation | 5 | 1.60 × e-02 |
| GOTERM_BP_5 | DNA modification | 6 | 1.64 × e-02 |
| GOTERM_BP_5 | Phosphate metabolism | 43 | 1.65 × e-02 |
| GOTERM_BP_5 | Determination of left/right symmetry | 4 | 1.72 × e-02 |
| GOTERM_BP_5 | Sulfur amino acid metabolism | 4 | 1.72 × e-02 |
| GOTERM_BP_5 | Ribosome biogenesis and assembly | 9 | 1.87 × e-02 |
| BIOCARTA | Role of BRCA1 | 6 | 1.89 × e-02 |
| GOTERM_BP_5 | Response to radiation | 6 | 1.99 × e-02 |
| KEGG_PATHWAY | Methionine metabolism | 4 | 2.03 × e-02 |
| BIOCARTA | CDK regulation of DNA replication | 4 | 2.15 × e-02 |
| BIOCARTA | RB tumor suppressor/checkpoint signaling in response to DNA damage | 4 | 2.15 × e-02 |
| GOTERM_BP_5 | Cellular carbohydrate metabolism | 16 | 2.21 × e-02 |
| GOTERM_BP_5 | rRNA metabolism | 5 | 2.50 × e-02 |
| GOTERM_BP_5 | Nucleic acid transport | 5 | 2.78 × e-02 |
| GOTERM_BP_5 | RNA transport | 5 | 2.78 × e-02 |
| GOTERM_CC_5 | Centrosome | 6 | 2.94 × e-02 |
| BIOCARTA | E2F1 destruction pathway | 4 | 2.96 × e-02 |
| BIOCARTA | Sonic Hedgehog (SHH) receptor Ptc1 regulates cell cycle | 4 | 2.96 × e-02 |
| GOTERM_MF_5 | Amino acid permease activity | 3 | 3.17 × e-02 |
| KEGG_PATHWAY | One carbon pool by folate | 4 | 3.24 × e-02 |
| GOTERM_CC_5 | Nuclear pore | 6 | 3.30 × e-02 |
| GOTERM_BP_5 | Heparan sulfate proteoglycan metabolism | 3 | 3.40 × e-02 |
| GOTERM_BP_5 | Nucleotide metabolism | 13 | 3.93 × e-02 |
| GOTERM_MF_5 | Glycine hydroxymethyltransferase activity | 3 | 3.97 × e-02 |
| GOTERM_MF_5 | Protein kinase activity | 32 | 4.12 × e-02 |
| GOTERM_BP_5 | Nucleobase, nucleoside, nucleotide and nucleic acid transport | 5 | 4.51 × e-02 |
| GOTERM_BP_5 | Positive regulation of programmed cell death | 10 | 4.61 × e-02 |
| GOTERM_MF_5 | DNA-directed DNA polymerase activity | 4 | 4.87 × e-02 |
| BIOCARTA | Activation of Src by protein-tyrosine phosphatase alpha | 3 | 5.41 × e-02 |
| BIOCARTA | Cyclins and cell cycle regulation | 6 | 5.41 × e-02 |
| GOTERM_BP_5 | Steroid metabolism | 9 | 5.54 × e-02 |
| GOTERM_MF_5 | Pre-mRNA splicing factor activity | 5 | 6.43 × e-02 |
| GOTERM_MF_5 | Methylene-tetrahydrofolate dehydrogenase activity | 2 | 7.11 × e-02 |
| GOTERM_BP_5 | Regulation of cell migration | 5 | 7.20 × e-02 |
| BIOCARTA | Cdc25 and chk1 regulatory pathway in response to DNA damage | 3 | 7.55 × e-02 |
| GOTERM_CC_5 | Chromatin | 13 | 8.01 × e-02 |
| GOTERM_BP_5 | Regulation of apoptosis | 16 | 8.13 × e-02 |
| GOTERM_CC_5 | Nuclear membrane | 9 | 8.33 × e-02 |
| GOTERM_BP_5 | Nucleotide biosynthesis | 9 | 8.59 × e-02 |
| GOTERM_CC_5 | Nuclear body | 4 | 8.81 × e-02 |
| GOTERM_BP_5 | Regulation of programmed cell death | 16 | 8.95 × e-02 |
| KEGG_PATHWAY | Urea cycle and metabolism of amino groups | 4 | 9.73 × e-02 |
| BIOCARTA | Regulation of p27 phosphorylation during cell cycle progression | 4 | 9.84 × e-02 |
| GOTERM_CC_5 | Heterochromatin | 4 | 9.89 × e-02 |
Functional annotations that are enriched among transcripts downregulated in myosin heavy chain (MHC) positive cells (intersection of down-regulation in the 15-day-old α-MHC+ cardiomyocytes [twofold, Student's t-test P value < 0.01] compared with the control cells in the 15-day-old embryoid bodies and compared with the undifferentiated α-MHC embryonic stem cells). 'Count' refers to the number of transcripts in the respective category; the 'P value' column shows the value of Fisher's exact t-test, as used by DAVID to measure the enrichment in annotation terms. GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; MAPK, mitogen-activated protein kinase