Table 1. Selected GO terms associated with clusters with the largest number of proteins (stSILAC dataset).
| Cluster | Model | Class | GO term | Description | FDR q-value | Enrichment | #genes | Examples |
| 2 | [0,1,2] | GOBP | 0006986 | response to unfolded protein | 5.21E-004 | 7.59 | 11 | Hsp70, Grp94, Hsp40 (DNAJB1) |
| 2 | [0,1,2] | GOBP | 0006457 | protein folding | 1.97E-003 | 4.62 | 14 | PDIA's, BAG2, Hsp70, Grp94, Hsp40 (DNAJB1) |
| 2 | [0,1,2] | GOCC | 0005788 | endoplasmic reticulum lumen | 6.76E-008 | 11.64 | 12 | PDIA's, PPI's, CANX, CALU, SERPINH1 |
| 2 | [0,1,2] | GOCC | 0031982 | vesicle | 3.24E-005 | 3.69 | 20 | GABARAPL2, MAP1LC3B, PDI's, CANX, SEC's |
| 6 | [0,0,1] | GOBP | 0006457 | protein folding | 4.48E-004 | 3.09 | 22 | CCT chaperonins, Hsp90 & cofactors, HSPD1 |
| 6 | [0,0,1] | GOBP | 0051493 | regulation of cytoskeleton organization | 4.70E-004 | 3.6 | 18 | Arp2/3 subunits, AURKA, RAC1 |
| 6 | [0,0,1] | GOBP | 0016192 | vesicle-mediated transport | 1.43E-003 | 2.33 | 31 | RAB's, Sec proteins, vacuolar proteins, coatomer |
| 6 | [0,0,1] | GOBP | 0019882 | antigen processing and presentation | 4.78E-003 | 2.9 | 18 | Proteasome subunits |
| 6 | [0,0,1] | GOBP | 0007264 | small GTPase mediated signal transduction | 6.00E-003 | 2.83 | 18 | RAB's, RAC1, NRAS |
| 6 | [0,0,1] | GOBP | 0006986 | response to unfolded protein | 3.74E-002 | 3.23 | 11 | Hsp70, Hsp90 families, |
| 6 | [0,0,1] | GOBP | 0043069 | negative regulation of programmed cell death | 4.25E-002 | 2.11 | 22 | Hsp60, Hsp90, Proteasome, PRDX's, NRAS, USP47 |
| 6 | [0,0,1] | GOMF | 0008092 | cytoskeletal protein binding | 3.19E-003 | 2.64 | 25 | CAPG, CAPZ, ARL3, Arp2/3 proteins, spindle-associated proteins |
| 6 | [0,0,1] | GOCC | 0000139 | Golgi membrane | 1.68E-005 | 3.6 | 21 | ARL3,Sec proteins, GOLGB1, coatomer, RAB's |
| 6 | [0,0,1] | GOCC | 0005839 | proteasome core complex | 3.67E-003 | 5.78 | 7 | Proteasome |
| 7 | [0,0, –1] | GOBP | 0016072 | rRNA metabolic process | 7.69E-004 | 3.87 | 17 | BOP1, processome, ribosomal proteins, DDX56 |
| 7 | [0,0, –1] | GOBP | 0006364 | rRNA processing | 1.64E-003 | 3.74 | 16 | BOP1, DDX56, processome, RRP1 |
| 7 | [0,0, –1] | GOBP | 0000723 | telomere maintenance | 2.68E-003 | 6.31 | 9 | RFC5, XRCC5, POLD1,POLD2, POLA1, PRIM1 |
| 7 | [0,0, –1] | GOBP | 0006271 | DNA strand elongation involved in DNA replication | 4.68E-002 | 5.58 | 7 | RFC5, XRCC5,POLD1,POLD2, POLA1, MCM4 |
| 7 | [0,0, –1] | GOCC | 0005730 | nucleolus | 1.52E-009 | 3.08 | 43 | RNA Helicases, processome subunits |
| 7 | [0,0, –1] | GOCC | 0030684 | preribosome | 4.86E-002 | 7.3 | 5 | Small subunit processome |
| 11 | [0, –1, –2] | GOBP | 0006998 | nuclear envelope organization | 2.56E-002 | 6.57 | 8 | Nucleoporins, CDK1 |
| 11 | [0, –1, –2] | GOMF | 0004672 | protein kinase activity | 1.29E-002 | 3.86 | 11 | CDK1, PRKDC,ILK, LCK, CHEK1 |
| 11 | [0, –1, –2] | GOMF | 0004674 | protein serine/threonine kinase activity | 1.30E-002 | 4.24 | 10 | MAP4K4 ; PRKDC ; CDK11B ; ILK ; CDK1 ; TAOK3 ; MAP2K4 ; CHEK1 ; NEK9 ; ADRBK1 |
| 11 | [0, –1, –2] | GOMF | 0005524 | ATP binding | 2.06E-002 | 2.16 | 31 | Helicases, Kinases |
Model refers to the theoretical evolution of the ratio over 3 time points (t = 0,6,20h) of GA treatment. Each model defines a cluster. PDI : protein disulphide isomerase A; PPI : peptidylprolyl isomerase; CCT : Chaperonin-Containing-TCP-1 complex. All others are standard gene names or usual protein names. GO terms in bold were analysed in more detail (Figures 6,7).Abbreviations for GO term categories are : CC = cellular compartment; MF = molecular function; BP = biological process