TABLE 2.
Enriched GO terms for the categories “biological process” and “molecular function” for clusters A and Ba
| Cluster | Enriched GO term (category) | Corrected P valueb |
|---|---|---|
| A (genes upregulated toward zero growth) | RNA polymerase II regulatory region sequence-specific DNA binding (MF) | 0.00 |
| Cellular response to chemical stimulus (BP) | 0.00 | |
| Sequence-specific DNA binding (MF) | 0.00 | |
| Nucleic acid binding transcription factor activity (MF) | 0.00 | |
| Cell communication (BP) | 0.00 | |
| Regulatory region nucleic acid binding (MF) | 0.00 | |
| Response to chemical (BP) | 0.00 | |
| Regulatory region DNA binding (MF) | 0.00 | |
| RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (MF) | 0.01 | |
| Aldehyde dehydrogenase (NAD) activity (MF) | 0.01 | |
| Oxidoreductase activity, acting on the aldehyde or oxo group of donors (MF) | 0.01 | |
| Regulation of nitrogen utilization (BP) | 0.01 | |
| Oxidoreductase activity, acting on the aldehyde or oxo group of donors, with NAD or NADP as an acceptor (MF) | 0.04 | |
| B (genes downregulated toward zero growth) | Mitotic nuclear division (BP) | 0.00 |
| Organelle fission (BP) | 0.00 | |
| Chromosome segregation (BP) | 0.00 | |
| Cell cycle (BP) | 0.00 | |
| Cell division (BP) | 0.00 | |
| Microtubule-based process (BP) | 0.00 | |
| Cytoskeleton organization (BP) | 0.00 | |
| Structural constituent of cytoskeleton (MF) | 0.00 | |
| Tubulin binding (MF) | 0.00 | |
| Chromosome organization (BP) | 0.00 | |
| DNA-dependent DNA replication (BP) | 0.00 | |
| DNA conformation change (BP) | 0.00 | |
| DNA replication (BP) | 0.00 | |
| Single-organism cellular process (BP) | 0.00 | |
| Single-organism reproductive process (BP) | 0.00 | |
| Single-organism process (BP) | 0.00 | |
| Cytoskeletal protein binding (MF) | 0.00 | |
| DNA packaging (BP) | 0.00 | |
| Nuclear migration (BP) | 0.00 | |
| Double-strand break repair (BP) | 0.00 | |
| Substrate-specific transmembrane transporter activity (MF) | 0.01 | |
| Organic acid transmembrane transporter activity (MF) | 0.01 | |
| DNA metabolic process (BP) | 0.01 | |
| Small-molecule metabolic process (BP) | 0.01 | |
| Sterol metabolic process (BP) | 0.02 | |
| Reproduction (BP) | 0.02 | |
| Reproductive process (BP) | 0.03 |
a
Redundant GO terms were excluded by using the Web-based tool REVIGO (73). For the full-length list as well as the number of significantly regulated genes per GO term and GO term size, see Data Set S2 in the supplemental material. BP, biological process; MF, molecular function.
b
Bonferroni correction.