I. Clusters matched with GRID protein complexes: +1) 4 elements matched T=1.000, Corrected p-value=7.975284e-008 YGR092W YIL106W YNR052C YAL021C +2) 5 elements matched T=0.710, Corrected p-value=3.414434e-014 YJL124C YNL147W YLR438C-A YER112W YER146W +3) 3 elements matched T=1.000, Corrected p-value=1.494359e-006 YAR007C YML032C YJL173C +4) 3 elements matched T=1.000, Corrected p-value=1.170933e-024 YBR254C YKR068C YDR472W +5) 3 elements matched T=1.000, Corrected p-value=3.148983e-005 YHR166C YKL022C YBL084C +6) 4 elements matched T=1.000, Corrected p-value=8.612823e-009 YIL109C YPL085W YPR181C YDL195W +7) 3 elements matched T=1.000, Corrected p-value=9.390059e-006 YIR017C YJR060W YNL103W +8) 3 elements matched T=1.000, Corrected p-value=4.323076e-009 YJR006W YJR043C YDL102W +9) 4 elements matched T=1.000, Corrected p-value=4.042196e-012 YLR103C YLR274W YBR202W YEL032W +10) 3 elements matched T=1.000, Corrected p-value=1.006675e-006 YML098W YDR167W YML015C +11) 4 elements matched T=1.000, Corrected p-value=2.352382e-015 YLR200W YNL153C YEL003W YML094W YGR078C +12) 3 elements matched T=1.000, Corrected p-value=1.265024e-006 YPR072W YCR093W YIL038C +13) 4 elements matched T=1.000, Corrected p-value=1.167256e-008 YDR356W YHR172W YNL126W YLR212C +14) 4 elements matched T=1.000, Corrected p-value=7.867440e-022 YBR126C YDR074W YMR261C YML100W +15) 4 elements matched T=0.800, Corrected p-value=1.975909e-005 YBL016W YDR103W YDL159W YLR362W +16) 3 elements matched T=1.000, Corrected p-value=9.147192e-010 YDR429C YOR361C YMR146C +17) 3 elements matched T=1.000, Corrected p-value=3.625088e-004 (higher than 1*10^{-4}) YHL019C YPR029C YKL135C +18) 4 elements matched T=1.000, Corrected p-value=1.917961e-010 YGL237C YOR358W YKL109W YBL021C +19) 3 elements matched T=1.000, Corrected p-value=6.723367e-004 (higher than 1*10^{-4}) YFR037C YLR321C YIL126W +20) 3 elements matched T=0.750, Corrected p-value=3.399418e-008 YGR113W YKR037C YDR016C +21) 3 elements matched T=1.000, Corected p-value=6.439383e-006 YEL015W YLR264W YOL149W +22) 4 elements matched T=1.000, Corrected p-value=3.358551e-006 YDR477W YGL115W YGL208W YER027C II. Functional Modules supported by co-expression or co-citation: +1) 3 elements, Functional module (possible complex), co-location cytoplasm, co-expressed. Corrected p-value=1.529413e-006 YBL078C YHR171W YNR007C YBL078C - essential for autophagy YHR171W - component of the autophagic system YNR007C - essential for autophagocytosis +2) 3 elements, Functional module (possible complex) of tubulin and tubulin associated proteins, co-location : cytoplasm, cytoskeleton; co-citation. Corrected p-value=1.803673e-010 YCL029C YER016W YML085C YCL029C - microtubule-associated protein required for microtubule function during mating and mitosis YER016W - Binding to microtubules YML085C - Alpha-1 tubulin +3) 4 elements, Functional Module (possible complex), co-location nucleus, co-citation. Corrected p-value=3.415077e-008 YPR135W YML069W YNL102W YGL207W YPR135W - DNA-directed DNA polymerase alpha-binding protein, DNA repare, DNA binding. YML069W - Protein that binds to DNA polymerase I (PolI), DNA repare, DNA recombination. YNL102W - DNA-directed DNA polymerase alpha, 180 KD subunit, DNA repare. YGL207W - General chromatin factor, DNA modification, transcription control. +4) 3 elements, Functional module (possible complex), co-location-nucleus, co-citation. Corrected p-value=3.155784e-008 YGR048W YKR002W YDR390C YGR048W - Ubiquitin fusion degradation protein, mRNA processing (splicing, 5'-, 3'-end processing), proteasomal degradation (ubiquitin/proteasomal pathway). YKR002W - Poly(A) polymerase, mRNA processing (3' end processing), mRNA stability. YDR390C - E1-like (ubiquitin-activating) enzyme, mRNA processing (splicing, 5'-, 3'-end processing). +5) 3 elements, Functional module (probable complex), location : cytoplasm, cell perifery; co-citation. Corrected p-value=5.094002e-004 (higher than 1*10^{-4}) YDR264C YBR200W YLR229C YDR264C - ankyrin repeat-containing protein, pheromone response, mating-type determination, sex-specific proteins. YBR200W - bud emergence mediator, mitotic cell cycle and cell cycle control, cytoskeleton, pheromone response, mating-type determination, sex-specific protein. YLR229C - GTP-binding protein of RAS superfamily, mitotic cell cycle and cell cycle control, cytoskeleton, pheromone response, mating-type determination, sex-specific protein. +6) 5 elements matched T=1.000 with the extra protein. Corrected p-value=2.459701e-010 YDL140C YOR116C YOR341W YBR154C YOR224C YDL140C - an additional member (DNA-directed RNA polymerase II,transcription, DNA-binding, location nucleus. participate in the same cell process as other proteins in the cluster, same co-location nucleus) III. Functional Modules, without co-expression or co-citation evidence available +1) 4 elements, Functional Module, co-location cytoplasm. Corrected p-value=1.995208e-011 YJR102C YMR077C YPL002C YLR417W YJR102C - Vacuolar protein sorting (putative) YMR077C - Vaculolar protein sorting (putative) YPL002C - Protein involved in glucose derepression, vacuolor transport YLR417W - Defective in vacuolar protein sorting +2) 3 elements, Functional module, co-location : cytoplasm, nucleus. Corrected p-value=5.600935e-006 YCL055W YGL192W YBR057C YCL055W - Regulatory protein required for pheromone induction of karyogamy genes mitosis, meiosis, nuclear division, for the efficient transit from G1 during mitosis, and for essential functions during meiosis. YGL192W - Positive transcription factor for IME2 required early in meiosis for IME1 transcript accumulation and sporulation. YBR057C - Meiotic protein. +3) 3 elements, Functional module, co-location : vacuole,vacuolar membrane. Corrected p-value=6.480036e-005 YKR007W YML121W YGR163W YKR007W - Multicopy suppressor of Ers1 Hygromycin B sensitivity, vacuolar protein degradation, homeostasis of protons. YML121W - GTP-binding protein, phosphate transport, cellular transport. YGR163W - Cytoplasmic GTP binding protein, functions as a negative regulator of the Ran/Tc4 GTPase cycle, GTP-binding protein. +4) 5 elements Functional module, co-location: cytoplasm, nucleus; Corrected p-value=4.016907e-008 YNL273W YPR078C YLR368W YMR048W YDL081C YNL273W - DNA topology and repair, cell cycle checkpoints (checkpoints of morphogenesis, DNA-damage,-replication, mitotic phase and spindle) YPR078C -DNA degradation, DNA processing, meiosis. YLR368W -Cell cycle control YMR048W - Cell cycle checkpoints (checkpoints of morphogenesis, DNA-damage,-replication, mitotic phase and spindle), meiosis, DNA synthesis and replication YDL081C - translation elongation. (YDL081C is a candidate for cell cycle control and DNA processing functional module) +5) 4 elements - Functional module, co-location nucleus, ER. Corrected p-value=8.619965e-004 (higher than 1*10^{-4}) YAL032C YBL102W YOR036W YPL151C YAL032C - Pre-mRNA splicing factor, transcriptional activator, probaby RNA metaabolism, nucleus YBL102W - Suppressor of sed5 ts mutants, vesicular transport (Golgi network, etc.), the ER to Golgi Subfamily complex, location golgi membrane, golgy YOR036W - Syntaxin (T-SNARE), vacuolar, vesicular transport (Golgi network, etc.), protein targeting, sorting and translocation, location vacuole, nuclear envelope YPL151C - Splicing factor that is found in the Cef1p subcomplex of the spliceosome, mRNA processing, RNA metabolism, location cytoplasm, nucleus YAL032C and YPL151C are from the same complex. +6) 3 elements, Functional module, not enough location evidence. Corrected p-value=6.080315e-006 YFL059W YNL333W YNL334C YFL059W - strong similarity to Para rubber tree ethylene-responsive protein1 (Class II). YNL333W - putative pyridoxine (vitamin B6) biosynthetic enzyme. YNL334C - strong similarity to hypothetical proteins YFL060C and YMR095C (Class IV). +7) 3 elements, Functional module, co-location nuclear pore. Corrected p-value=1.280724e-007 YDR192C YMR255W YDL207W YDR192C - Nuclear pore protein. YMR255W - Protein of the nuclear pore complex ,RNA transport, nuclear transport. YDL207W -RNA export mediator, RNA transport, nuclear transport, nuclear pore complex. +8) 3 elements, Functional Module, co-location cytoplasm, Corrected p-value=1.278755e-009 YMR068W YIL105C YNL047C YMR068W - Component of a complex containing the Tor2p kinase, regulation of cell growth, regulation of cell size, -weak similarity to mouse transcription factor NF-kappa B (Class III) YIL105C - Phosphoinositide PI4,5P(2) binding protein, required for actin cytoskeleton polarization, actin cytoskeleton, -weak similarity to probable transcription factor ASK10P (Class III) YNL047C - Phosphoinositide PI4,5P(2) binding protein, required for actin cytoskeleton polarization and viability, actin cytoskeleton, - hypothetical protein YPR115W, and strong similarity to hypothetical protein YIL105C (Class III) +9) 3 elements, Functional module, no location information. Corrected p-value=1.920600e-007 YCL019W YDR261W-A YDR261W-B YCL019W - TY2B protein, TRANSPOSABLE ELEMENTS, VIRAL AND PLASMID PROTEINS YDR261W-A - TY2A protein, TRANSPOSABLE ELEMENTS, VIRAL AND PLASMID PROTEINS YDR261W-B - TY2B protein, TRANSPOSABLE ELEMENTS, VIRAL AND PLASMID PROTEINS +10) 3 elements, Functional module, co-location : cytoplasm, nucleus, Corrected p-value=9.394184e-006 YLR257W YGR246C YGR047C YLR257W - unclassified, unknown function. YGR246C - TFIIIB subunit, 70 kD, rRMA and TRNA synthesis, general transcription activities. YGR047C - TFIIIC (transcription initiation factor) subunit, 131 kD, r-RNA, t-RNA synthesis, general transcription activities. +11) 3 elements , Functional module, possible protein ccompex with YOR275C as a new protein involved in the complex of YLR025W and YPR173C, co-location: endosome, vacuole, cytoplasm. Corrected p-value=1.828720e-011 YLR025W YOR275C YPR173C YLR025W - Class E Vps protein, regulation of C-compound and carbohydrate utilization, vacuolar transport, development of asco- basidio- or zygospore. YOR275C - Regulator of IME2, development of asco- basidio- or zygospore. YPR173C - Vacuolar sorting protein, vacuole or lysosome, protein targeting, sorting and translocation intra Golgi transport ,ATP binding, involved in both the internalization and delivery steps of endocytosis. YLR025W and YPR173C participate in the same cell complex. +12) 5 elements, possible Functional module, co-location nucleus (not all locations available). Corrected p-value=5.604836e-010 YDR078C YHL006C YKR034W YLR376C YNL021W YDR078C - Suppressor of hydroxy-urea sensitivity, promote resistance to killing by methyl methanesulfonate, unclassified, no location. YHL006C - Protein involved in recombination, unclassified, no location. YKR034W - Transcriptional repressor for allantoin and GABA catabolic genes, transcriptional control,regulation of nitrogen utiliztion, regulation of netrogen catabolic genes. also represses the urea catabolic pathway. YLR376C - Platinum SensitivitY protein, unclassified.. YNL021W -Histone deacetylase A, transcriptional control, subunit of the HDA complex involved in histone deacetylation. IV. Functional modules with limited information (various miscellaneous support) +1) 4 elements - Functional module, co-location :cytoplasm, mitochindria; co-expressed. Corrected p-value=1.058010e-011. YLL027W YGL189C YER131W YLR435W YLL027W - Mitochondrial protein required for normal iron metabolism, heavy metal ion transport. YGL189C - 40S small subunit ribosomal protein S26e.c7. YER131W - 40S small subunit ribosomal protein S26e-c5. YLR435W - Twenty S rRNA accumulation protein. +2) 4 elements, Corrected p-value=1.961503e-005 YLR078C YOL006C YMR257C YMR233W YLR078C - Secretory pathway protein, essential for vegetative cellular growth. YOL006C -extension/ polymerization activity, somatic / mitotic recombination, DNA processing, transcription cotrol. YMR257C - Protein required for tr anslation of COX2 mRNA, translational control. YMR233W - unknown function, unclassified