Table I. GO enrichment of each module.
The top five overrepresented GO terms in the Biological Process (BP) subcategory and corresponding q values are listed. Associated genes are also provided. The BP keywords are the vocabularies in GO terms (only the BP subcategory) shared by at least 5% of genes in a module.
| Module | GO Accession No. | GO Term | q Value | Gene |
| MP | GO:0022904 | Respiratory electron transport chain | 1.17 × 10−6 | CI51, At3g52730, SDH1-1, SDH2-2, At2g02050, At5g25450 |
| GO:0045005 | Maintenance of fidelity during DNA-dependent DNA replication | 2.03 × 10−6 | MSH6, MSH2, MSH7, ATMLH3, MSH3 | |
| GO:0009693 | Ethylene biosynthetic process | 4.88 × 10−6 | ACS8, ACS7, ACS11, ETO3, ACS4 | |
| GO:0009960 | Endosperm development | 1.87 × 10−3 | AGL62, FIS2, MEA | |
| GO:0006417 | Regulation of translation | 2.94 × 10−3 | ATAUX2-11, MPC, ETO3 | |
| VP | GO:0009658 | Chloroplast organization | 4.96 × 10−7 | PHOT1, PDE120, CLPR2, ADL2, GLK2, ATMINE1, FTSZ2-1, STH3, ARC6 |
| GO:0000096 | Sulfur amino acid metabolic process | 6.23 × 10−6 | ACS5, OASC, ATHMT-1, ATCYSD1, PIL6, AtSerat2;2, AtSera1;1 | |
| GO:0000097 | Sulfur amino acid biosynthetic process | 6.48 × 10−5 | OASC, ATHMT-1, ATCYSD1, AtSerat2;2, AtSera1;1 | |
| GO:0006534 | Cys metabolic process | 1.28 × 10−4 | OASC, ATCYSD1, AtSerat2;2, AtSera1;1 | |
| GO:0009813 | Flavonoid biosynthetic process | 1.28 × 10−4 | DFR, ATOMT1, TT8, STH3, PAP1, ATMYBL2 | |
| BP keyword | Signaling | ABF1, RCD1, CBL6, JAZ1, ATMPK4, ATMPK3, CBL2, CAM9, WOL, ARR5, ABF3, ATNAC3, ARR7, CBL1, ATMYC2 | ||
| BP keyword | Biosynthetic process | DFR, ABI5, MYB113, ATOMT1, CESA8, FAH1, PAP1, TT8, STH3, ATMYBL2, GLK2, ATMYC2 | ||
| MR | GO:0009966 | Regulation of signal transduction | 1.52 × 10−8 | SLY1, TMAC2, ERS1, FTA, RGL2, SLY2, ATGID1C, ATGGT-IB, TAF12B, CTR1 |
| GO:0009968 | Negative regulation of signal transduction | 1.97 × 10−5 | TMAC2, ERS1, FTA, RGL2, ATGGT-IB, CTR1 | |
| GO:0009909 | Regulation of flower development | 1.97 × 10−5 | FY, CO, COL1, ELF8, FIE, VIP4, EMF2, FCA | |
| GO:0009937 | Regulation of gibberellic acid-mediated signaling | 1.83 × 10−4 | SLY1, RGL2, SLY2, ATGID1C | |
| GO:0006605 | Protein targeting | 2.03 × 10−4 | MAG2, ATVTI1A, MAG1, ATVTI12, SYP121, TOC159, PEX5 | |
| BP keyword | Signaling | TMAC2, AFP1, TTL, PAD4, EEL, HY5, PIF3, TAF12B, SLY1, BIM1, ATGGT-IB, RGL2, CPK32, CTR1, ATGID1C, FTA, BIN2, CO, ERS1, OBF5, SYP121 | ||
| SU | GO:0045333 | Cellular respiration | 7.65 × 10−3 | NAD6, COB, NAD7 |
| GO:0050832 | Defense response to fungus | 7.65 × 10−3 | PRL1, BAK1, NPR1, COI1 | |
| GO:0010043 | Response to zinc ion | 1.49 × 10−2 | CXIP4, At3g22460 | |
| GO:0031348 | Negative regulation of defense response | 1.49 × 10−2 | NPR1, COI1 | |
| GO:0048440 | Carpel development | 1.49 × 10−2 | SHP2, SHP1 | |
| PS | GO:0009658 | Chloroplast organization | 4.40 × 10−8 | CRB, GPRI1, PMI2, CLPP4, CLPC, FTSZ1-1, CLPP6, ATTIC110, CPN60A |
| GO:0019253 | Reductive pentose phosphate cycle | 5.69 × 10−7 | SBPASE, CP12-2, GAPBGAPB, TIM, At3g04790 | |
| GO:0045038 | Protein import into chloroplast thylakoid membrane | 3.74 × 10−6 | FFC, CAO, ALB3, PSB29 | |
| GO:0017038 | Protein import | 3.74 × 10−6 | FFC, CAO, ALB3, CLPC, PSB29, ATTIC110 | |
| GO:0010207 | PSII assembly | 2.74 × 10−5 | LPA2, PSBO1, PSBO-2, PSB29 | |
| BP keyword | Signaling | PKS1, ARR16, ARR4, ARR15, NDPK2, PIF4, ARR9, BRL2, ARR6, SGT1B | ||
| BP keyword | Light | PKS1, PSBO-2, JAR1, PMI2, PSBO1, ARR4, CAB2, PRN, NDPK2, RBCS1A, PIF4, KAT2, ROC4, CAO | ||
| DP | GO:0009908 | Flower development | 2.53 × 10−7 | ZTL, LUG, GCR1, MP, AP1, ARF8, HTA11, SEP1, SEP3, SEP2, DCL1 |
| GO:0048364 | Root development | 1.07 × 10−5 | NIP3;1, NPH4, HBT, XLG3, PIN7, AGG1, AGB1, LHW, MP, JKD | |
| GO:0009736 | Cytokinin-mediated signaling | 1.84 × 10−5 | AHP2, NIP3;1, AHP1, ARR1, KNAT2, ARR10, AHK2 | |
| GO:0048437 | Floral organ development | 2.62 × 10−5 | NUA, ROXY1, STM, ATPGP1, AFB3, AG, AP3 | |
| GO:0009909 | Regulation of flower development | 2.62 × 10−5 | ESD1, NUA, ELF3, UBC1, SEU, BRI1, CRY2, CIB5, CLV2 | |
| BP keyword | Response | NPH4, ATTRX3, CRY1, AGG1, HUB1, CAT2, RIN13, HD1, RPM1, BAG6, ATPGP1, PHYB, RPS2, ATMPK6, AGB1, NPR4, BZO2H1, PUB17, CRY2 | ||
| RP | GO:0009742 | Brassinosteroid-mediated signaling | 3.22 × 10−7 | GRF2, TTL3, GRF6, GRF8, BZR1, BES1, ASKdZeta |
| GO:0048827 | Phyllome development | 1.74 × 10−5 | RPN12A, TCP10, HSP81-2, AN3, AtGRF5, AtGRF1, CDC2B, NHX1, RBR1 | |
| GO:0007126 | Meiosis | 2.45 × 10−5 | ATDMC1, BRCA2V, BRCA2, ATRAD51C, SKP1 | |
| GO:0009909 | Regulation of flower development | 5.65 × 10−5 | COL2, SEF, ATFYPP3, TFL1, SOC1, FD, FUL, CAL | |
| GO:0009966 | Regulation of signal transduction | 5.65 × 10−5 | ATCDPK2, RGL1, CIPK15, EBF2, RCN1, PLDALPHA1, GAI | |
| BP keyword | Signaling | GAI, At3g02880, RPT5B, RKL1, AT3G56370, ECT1, ETO1, RGL3, FLS2, RCN1, RAX2, CAM7, CIPK15, ATCDPK2, EDS1, ATHXK1, JAZ3, CAM8, PLDALPHA1, AHBP-1B, RGL1, LFY, ATCUL1, HFR1, PIL5, At1g68400 | ||
| BP keyword | Assembly | TAF4, EIF3E, TAF13, HTB2, TBP2, XPO1A, FUS6, NAP1;2, CSN6A, ATCUL1, FUS5, CSN6B, HTA2 |