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Table 1 GO Terms enriched in REMc clusters

From: A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin

Media INT GTA HLEG GTA HLD Clust GO term name p value Genes
Resp Enh 5.0 2.8 1-0-7 nucleosome organization 1.1E−07 VPS71 RSC2 SWR1 LDB7 HHF1 RSC4 IES1 ISW1 ARP6 RTT106 HIR3 SWC3 HPC2 YAF9 HIR1 HIR2 HTB1 NHP6A SWC5 NHP10
Resp Enh 7.1 0.1 1-0-7 Set1C/COMPASS complex 5.5E−04 SPP1 SDC1 SWD1 SWD3 BRE2
Resp Enh 3.9 − 0.6 1-0-7 histone methylation 4.1E−03 SPP1 SDC1 LGE1 NOP1 SWD3 HHF1 SWD1 BRE2
Resp Enh 3.4 3.0 1-0-7 protein import into mitochondrial matrix 6.4E−03 MGR2 TOM7 YME1 TOM70 PAM17 TIM17 TIM23 TOM6
Resp Enh 0.6 0.8 2-0.7-1 ER membrane protein complex 4.6E−06 EMC6 EMC4 EMC3 EMC5
Resp Enh 4.6 0.2 2-0.7-2 Sin3-type complex 1.5E−05 RCO1 RXT2 SAP30 PHO23 DEP1 UME1
Resp Enh 5.2 − 0.1 2-0.7-2 Rpd3L complex 7.1E−05 RXT2 SAP30 PHO23 DEP1 UME1
Resp Enh 7.3 1.6 2-0.7-2 Swr1 complex 1.2E−06 SWC3 SWC5 VPS71 YAF9 SWR1 ARP6
Resp Enh 5.9 2.1 2-0.7-2 histone exchange 5.7E−06 SWC3 SWC5 VPS71 YAF9 SWR1 ARP6
Resp Enh 5.0 3.4 2-0.7-2 ATP-dependent chromatin remodeling 2.4E−04 SWC3 SWC5 VPS71 YAF9 SWR1 LDB7 ARP6
Resp Enh 11.9 0.2 2-0.7-2 HIR complex 6.6E−06 HPC2 HIR1 HIR3 HIR2
Resp Enh 11.4 3.2 2-0.7-2 DNA replication-independent nucleosome assembly 4.5E−04 HPC2 HIR1 HIR3 HIR2
Resp Enh 11.0 1.7 1-0-8 respiratory chain complex III assembly 4.2E−02 QCR9 CBP4 FMP25
Resp Enh 7.9 0.7 2-0.8-0 DNA topological change 2.6E−02 TOP3 MUS81
Resp Enh 14.9 − 0.4 2-0.8-1 NatC complex 5.6E−03 MAK31 MAK3
Resp Sup − 2.6 − 1.5 2-0.3-1 regulation of fatty acid beta-oxidation 2.1E−02 ADR1 OAF1 PIP2
Resp Sup − 0.3 6.7 2-0.3-5 translation reinitiation 2.0E−02 TMA20 TIF34 TMA22
Glyc Enh 1.1 0.5 2-0.2-2 ribonucleoprotein complex subunit organization 1.9E−02 RSA4 HBS1 BRR1 SDO1 RPS17A DHH1 CLF1 RRP7 TIF6 RPS14A RPS27B PRP9
Glyc Sup − 2.2 − 3.0 2-0.4-0 7-methylguanosine cap hypermethylation 5.6E−03 SWM2 TGS1
Glyc Sup 1.5 − 0.4 2-0.4-2 mRNA 3'-end processing 8.6E−04 MPE1 CDC73 YSH1 KIN28 RNA14 NRD1
Glyc Sup 1.3 0.9 2-0.4-2 mRNA cleavage 3.3E−02 MPE1 YSH1 POP8 RNA14
Glyc Sup − 0.8 − 2.9 2-0.4-2 meiotic chromosome condensation 3.4E−03 SMC2 YCG1 YCS4
Glyc Sup − 1.0 − 2.7 2-0.4-2 condensin complex 2.8E−03 SMC2 YCG1 YCS4
Both Enh 2.9 2.3 1-0-6 cellular response to DNA damage stimulus 4.1E−08 CTK3 SIT4 RTT109 RVB1 RAD54 MMS22 CDC1 RAD55 PSF3 RAD50 BUD25 RAD51 MRE11 ARP8 ARP4 RAD57 TFB1 CDC7 RAD52 NPL6
Both Enh 5.0 5.0 1-0-6 double-strand break repair via homologous recombination 2.9E−07 PSF3 RAD50 RAD51 MRE11 RAD54 MMS22 RAD57 CDC7 RAD52 RAD55
Both Enh 7.7 9.7 1-0-6 double-strand break repair via synthesis-dependent strand annealing 4.3E−06 RAD54 RAD57 RAD51 RAD52 MRE11 RAD55
Both Enh 9.2 5.0 2-0.6-1 ATP-dependent 3'-5' DNA helicase activity 1.9E−04 RVB1 ARP5 ARP8 ARP4
Both Enh 9.0 2.5 2-0.6-1 Ino80 complex 2.1E−05 RVB1 IES6 ARP5 ARP8 ARP4
Both Enh 3.4 1.6 2-0.6-1 histone acetylation 4.1E−02 RTT109 RVB1 NGG1 SPT20 ARP4
Resp Enh 7.4 1.1 2-0.2-1 protein urmylation 1.1E−03 URM1 URE2 UBA4 ELP2
Both Enh 9.9 3.9 2-0.2-1 Lst4-Lst7 complex 3.1E−02 LST7 LST4
Both Sup − 4.5 − 2.3 2-0.4-1 cellular sphingolipid homeostasis 9.6E−05 VPS53 VPS52 VPS54 VPS51
Both Sup − 12.2 − 7.0 2-0.4-1 fatty acid elongase activity 2.9E−02 ELO3 ELO2
Both Sup − 3.0 − 1.3 2-0.4-1 actin cortical patch localization 8.1E−03 RVS167 LSB3 RVS161 VRP1
Both Sup − 9.0 − 3.5 2-0.4-1 Rvs161p-Rvs167p complex 1.7E−02 RVS167 RVS161
Both Sup − 4.4 − 0.6 2-0.4-1 telomere tethering at nuclear periphery 1.8E−02 NUP60 MLP1 NUP120 NUP133
  1. The table headers are defined as follows: For the column, “Media,” “Resp,” “Glyc,” and “Both” refer to whether the gene interaction type observed for the REMc cluster associated with the term was prominent in HLEG, HLD, or both media (see Additional file 1: Figure S3). For the column, “INT,” “Enh,” and “Sup” indicate deletion-enhancing or deletion-suppressing. The column “GTA” refers to GO term average. The column “Clust” refers to REMc ID