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Table 1 Subnetwork organization of gene products whose disruption specifically affects nickel or cadmium tolerance

From: Membrane transporters and protein traffic networks differentially affecting metal tolerance: a genomic phenotyping study in yeast

Subnetworksa Nickel Cadmium
  Interacting gene products Functionally linked gene productsb Interacting gene products3 Functionally linked gene productsb,c
V-ATPase assembly/regulation (sn. 1) Rav1, Vma16, Vph1    
Proteasome (sn. 3) Cue1   Bre5, Cdc26, Doa1, Hlj1, Sel1, Ubi4, Ubp6, Ump1 Dia2
Chromatin assembly/remodelling (sn. 4)    SAGA complex (Ada2, Chd1, Gcn5, Hfi1, Ngg1, Spt7*, Spt20); Ino80 complex (Arp5, Arp8, Taf14); COMPASS complex (Bre2, Sdc1); Asf1, Ard1, Eaf7*, Esc2, Hda1*, Hmo1, Ioc2 Hmo1
Cell wall integrity pathway (sn. 5)   Whi3 Bem2, Dom34, Ecm33, Kcs1, Pin4, Pog1, Rvs161, Rvs167, Sic1, Sit4*, Sur7, Swi4, Swi6, Whi2  
CCR4 and other mRNA processing enzymes (sn. 6)    Dhh1 Paf1
Nuclear pore complex (sn. 7) Nup84, Sac3, Thp1    
Essential ion homeostasis (sn. 9) Pho88 Ccc2, Zap1 Smf3 Gef1, Pho89
AP-3 complex (sn. 10) Apl5, Apl6, Apm3, Aps3    
General transcription (sn. 11) Mft1, Rpb9, Rtt103, Thp2   Mediator complexes (Gal11, Med2, Pgd1, Spt21, Srb8*, Srb10); Cad1, Elp4, Tup1, Yap1 Mss11
DNA repair (sn. 12)    Ctf4, Him1, Met18, Mms22, Mre11, Pol32, Rad6, Rad27, Xrs2  
Antioxidant defense (sn. 13)    Atx2, Ccs1, Sod1, Sod2 Cad1, Glr1, Gsh1, Gsh2, Yap1, Zwf1
Hog1 pathway (sn. 14)    Fps1, Hog1, Pbs2, Rck2, Ste11 Gre2
Vesicle targeting to, from or within Golgi (sn. 15)    Erv41, Erv46, Get2, Sac1, Sec22, Sec66; Vps13; Cog5, Cog8; Pep7, Tlg2, Vps3, Vps9, Vps21, Vps45; Arl1, Arl3, Ent3, Gga2, Nhx1*, Rgp1, Ric1, Sys1, Yil039w*, Vps51, Vps54, Ypt6; Vam10*, Vps1*, Vps8*; Pep8*, Vps5*, Vps17*, Vps29*, Vps30*, Vps35*, Vps38* Apm2, Snx3*
Ubiquitin-dependent sorting to the multivesicular body pathway (sn. 16)    Vps27*; ESCRT I complex (Vps28*, Mvb12*, Srn2*, Stp22*); ESCRT II complex (Snf8*, Vps25*, Vps36*); ESCRT-III complex (Did4*, Snf7*, Vps20*, Vps24*); Bro1*, Did2*, Doa4*, Vps4* Bsd2*, Bul1*, Nhx1*, Tre1*
  1. aSubnetworks 1 to 9 are the same as those described in Figure 2 but include deletion mutants specifically sensitive to nickel or cadmium (no nickel or cadmium specific mutants were identified for subnetworks 2 and 8); subnetworks 10 to 16 are newly identified interaction networks comprised of gene products causing nickel-specific or cadmium-specific sensitivity when disrupted (also see Additional data files 3 and 4). bGene products for which no physical or genetic interaction is documented in the BioGRID database [22] but for which a functional relationship with the indicated subnetworks has been reported. cGene mutations causing cadmium sensitivity but nickel resistance are marked with an asterisk. AP-3, Adaptor Protein-3; CCR, Carbon Catabolite Repression; ESCRT, endosomal sorting complexes required for transport; sn., subnetwork.
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Genome Biology

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