TABLE 3 .
Transcriptional analysis of functionally related gene families that exhibit a nonrandom genomic distribution in S. cerevisiae
| Description | GO no. | Gene set size | No. clustered | P value | PCC fora: |
|
|---|---|---|---|---|---|---|
| Singletons | Clusters | |||||
| Vitamin metabolic process | GO:0006766 | 43 | 11 | 9.06E−13 | 0.1005 | 0.507 |
| Cell wall organization or biogenesis | GO:0071554 | 198 | 38 | 8.35E−10 | 0.044 | 0.155 |
| Sporulation | GO:0043934 | 133 | 20 | 5.09E−07 | 0.043 | 0.4626 |
| Meiotic cell cycle | GO:0051321 | 282 | 49 | 8.53E−06 | 0.0354 | 0.2281 |
| Phosphatase activity | GO:0016791 | 95 | 12 | 1.10E−05 | 0.0406 | 0.5193 |
| Ribosome | GO:0005840 | 343 | 62 | 7.90E−05 | 0.1153 | 0.264 |
| Structural constituent of ribosome | GO:0003735 | 236 | 35 | 1.01E−04 | 0.1667 | 0.0907 |
| Monocarboxylic acid metabolic process | GO:0032787 | 141 | 17 | 1.29E−04 | 0.0523 | 0.5586 |
| Amino acid transport | GO:0006865 | 46 | 4 | 7.34E−04 | 0.1148 | 0.2534 |
| Lipid transport | GO:0006869 | 68 | 6 | 9.55E−04 | 0.0429 | −0.1973 |
| DNA replication | GO:0006260 | 139 | 14 | 2.21E−03 | 0.0991 | 0.2963 |
| Chromatin organization | GO:0006325 | 318 | 49 | 2.61E−03 | 0.0718 | 0.1108 |
| Translational initiation | GO:0006413 | 54 | 4 | 3.00E−03 | 0.1375 | 0.0586 |
| Peptidase activity | GO:0008233 | 94 | 8 | 3.01E−03 | 0.1 | 0.3957 |
| Pseudohyphal growth | GO:0007124 | 56 | 4 | 4.16E−03 | 0.0126 | 0.6038 |
| Extracellular region | GO:0005576 | 31 | 2 | 4.17E−03 | 0.0413 | −0.5761 |
| Telomere organization | GO:0032200 | 78 | 6 | 4.51E−03 | 0.0565 | 0.7413 |
| Methyltransferase activity | GO:0008168 | 90 | 7 | 6.10E−03 | 0.119 | 0.6294 |
| tRNA aminoacylation for protein translation | GO:0006418 | 36 | 2 | 9.57E−03 | 0.0966 | 0.7101 |
| Protein glycosylation | GO:0006486 | 62 | 4 | 9.69E−03 | 0.1917 | 0.6667 |
| rRNA processing | GO:0006364 | 236 | 28 | 1.12E−02 | 0.3511 | 0.338 |
| Helicase activity | GO:0004386 | 86 | 6 | 1.26E−02 | 0.1096 | 0.6232 |
| Regulation of cell cycle | GO:0051726 | 232 | 27 | 1.28E−02 | 0.0411 | 0.047 |
| Cytoskeleton organization | GO:0007010 | 238 | 28 | 1.39E−02 | 0.0662 | 0.0753 |
| Regulation of DNA metabolic process | GO:0051052 | 107 | 8 | 1.54E−02 | 0.0584 | 0.4021 |
| Nucleus organization | GO:0006997 | 66 | 4 | 1.60E−02 | 0.0906 | 0.1009 |
| Cytoskeletal protein binding | GO:0008092 | 67 | 4 | 1.79E−02 | 0.0539 | −0.2497 |
| Lyase activity | GO:0016829 | 90 | 6 | 1.98E−02 | 0.0545 | 0.5955 |
| Nuclease activity | GO:0004518 | 92 | 6 | 2.44E−02 | 0.0788 | 0.0358 |
| DNA-templated transcription, initiation | GO:0006352 | 73 | 4 | 3.43E−02 | 0.106 | 0.3507 |
| Hydrolase activity, acting on glycosyl bonds | GO:0016798 | 47 | 2 | 3.88E−02 | 0.0515 | −0.0869 |
| Cofactor metabolic process | GO:0051186 | 179 | 16 | 4.09E−02 | 0.0928 | 0.1328 |
| Guanyl-nucleotide exchange factor activity | GO:0005085 | 48 | 2 | 4.30E−02 | 0.0662 | −0.6026 |
| DNA repair | GO:0006281 | 256 | 29 | 4.63E−02 | 0.05 | 0.2181 |
| Transmembrane transport | GO:0055085 | 235 | 25 | 4.69E−02 | 0.0869 | 0.4296 |
| Exocytosis | GO:0006887 | 47 | 2 | 4.77E−02 | 0.6251 | 0.0608 |
| Nuclear transport | GO:0051169 | 181 | 16 | 4.85E−02 | 0.1614 | 0.2033 |
| Cellular bud | GO:0005933 | 241 | 26 | 4.92E−02 | 0.047 | 0.1037 |
a
PCC, Pearson’s correlation coefficient following expression throughout the cell cycle (24).