Table 2 Biological Process GO terms significally enriched in the clusters of the gene co-expression network ChlamyNET and the Metabolic and Signalling Pathways contained in each cluster
Cluster | Functional Annotation | Representative Genes | Metabolic/Signalling Pathways |
|---|---|---|---|
Cluster 2 (Brown) 535 genes Silhoutte 0.44 | DNA replication (GO:0006260) | Cre01.g015250 - POLD1 Cre16.g651000 - RFA1 | Pyrimidine deoxyribonucleotides de novo biosynthesis pathway Cre16.g667850 - DUT Cre17.g715900 - THY Cre03.g190800 - TMPK |
Chromosome organization (GO:00051276) | Cre02.g086650 - SMC2 Cre12.g4 934 00 - SMC4 | ||
Regulation of Cell Cycle (GO:0010564) | Cre10.g466200 - CYCAB1 Cre03.g207900 - CYCA1 | ||
Cluster 9 (Blue) 1058 genes Silhouette 0.40 | protein phosphorylation (GO:0006468) | Cre17.g742400 - PTK17 Cre12.g537400 - CrAUR3 | Starch Biosynthetic Pathway Cre04.g215150 - SSS Sucrose Biosynthetic Pathway Cre06.g283400 - SPP Nitrogen Assimilation Pathway Cre09.g410750 - NII1 |
carbohydrate metabolic process (GO:0005975) | Cre08.g384750 - AMY Cre10.g444700 - SBE3 | ||
transmembrane transport (GO:0055085) | Cre09.g396000 - NRT2.3 Cre13.g564650 - MRS5 | ||
Cluster 1 (Orange) 824 genes Silhouette 0.38 | vesicle-mediated transport (GO:0016192) | Cre17.g728150 - Yky6 Cre16.g676650 - AP1G1 | TAG Biosynthetic Pathway Cre02.g106400 - PDAT Phospholipid Biosynthetic Pathway Cre01.g035500 - PI3K Coenzyme A Biosynthetic Pathway Cre01.g048050 - COAB |
GTPase activity (GO:0043087) | Cre12.g532600 - CGL44 Cre07.g315350 - RABGAP | ||
Autophagy (GO:0006914) | Cre09.g391500 - APG9 | ||
Cluster 3 (Red) 1723 genes Silhouette 0.28 | protein phosphorylation (GO:0006468) | Cre02.g145500 - PTK24 Cre12.g498650 - ALK3 | TAG Biosynthetic Pathway g9572 - DGAT1 Hydrogen production Cre09.g396600 - HYDA2 MAP kinase cascade Cre10.g461150 - CrMAPKKK |
ribosome biogenesis (GO:0042254) | Cre12.g532550 - RPL13a Cre09.g400650 - RPS6 | ||
macromolecule biosynthesis (GO:0009059) | Cre03.g207250 - GLN4 | ||
Cluster 4 (Purple) 1174 genes Silhouette 0.26 | translation (GO:0006412) | Cre03.g199900 - EIF4E Cre02.g117900 - RH | tRNA Charging Pathway g2951 - TrpS Amino Acid Biosynthesis Cre03.g161400 - WSN2 Pentose Phosphate Non-oxydative Cre12.g511900 - RPE1 TAG Biosynthetic Pathway Cre03.g205050 - DGAT2 |
RNA processing (GO:0006396) | Cre16.g653050 - SpoU Cre10.g421600 - ThrRS g4 679 - RNase P | ||
lipid metabolism (GO:0006629) | Cre09.g397250 - FAD5 Cre06.g295250 - PAP | ||
Cluster 7 (Green) 909 genes Silhouette 0.25 | protein complex assembly (GO:0006461) | g9912 - CSN5 Cre16.g663500 - CrRPN10 | Aerobic Respiration Pathway Cre15.g638500 - CYC1 COP9 Signalling g11578 - CSN6 |
response to misfolded protein (GO:0051788) | Cre06.g280850 - PSMB4 Cre12.g501200 - SKP1 | ||
Cluster 6 (Yellow) 1351 genes Silhouette 0.24 | chromatin organization (GO:0006325) | g11636 - HDA Cre13.g590750 - HTB37 | Chromatin Remodelling Cre13.g591200 - HTB38 Cre13.g562400 - ABI3 |
posttranscriptional regulation (GO:0010608) | g7250 - DCL | ||
Cluster 5 (Dark Green) 567 genes Silhouette 0.21 | response to heat (GO:0009408) | Cre14.g617400 - HSP22F Cre08.g372100 - HSP70A | Stress Response Cre02.g098800 - ERP29 g9861 - TOR |
protein folding (GO:0006457) | g9881 - FKBP Cre01.g047700 - CYP40 | ||
Cluster 8 (Turquoise) 1030 genes Silhouette 0.10 | photosynthesis (GO:0015979) | Cre09.g412100 - PSAF Cre10.g44 04 50 - PSB28 | Calvin Cycle Cre12.g554800 - PRK1 TCA Cycle Cre02.g143250 - IDH2 |
hexose metabolic process (GO:0019318) | Cre17.g725550 - GLD1 Cre02.g093450 - FBA2 |