# Table S1, Hall & Wallace 2022
# 78 mRNAs bound by at least 4 of 6 RNA-binding proteins in Saccharomyces cerevisiae
# Together with false discovery rates for RNA-protein binding
# Data were processed by Edward Wallace from Dataset S2 of:
#   Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System
#   Daniel J Hogan, Daniel P Riordan, André P Gerber, Daniel Herschlag ,Patrick O Brown 
# https://doi.org/10.1371/journal.pbio.0060255
# 
YBR029C	CDS1 Phosphatidate cytidylyltransferase (CDP-diglyceride synthetase); an enzyme that catalyzes that conversion of CTP + phosphate into diphosphate + CDP-diaclglyerol, a critical step in the synthesis of all major yeast phospholipids	98.200000000000003	0	0	0.94489480000000003	0	82.493329000000003
YBR078W	ECM33 GPI-anchored protein of unknown function, has a possible role in apical bud growth; GPI-anchoring on the plasma membrane crucial to function; phosphorylated in mitochondria; similar to Sps2p and Pst1p	0	NA	0	0	0	49.397630999999997
YBR162C	TOS1 Covalently-bound cell wall protein of unknown function; identified as a cell cycle regulated SBF target gene; deletion mutants are highly resistant to treatment with beta-1,3-glucanase; has sequence similarity to YJL171C	0	0	0	0	12.47511652	84.904486000000006
YBR212W	NGR1 RNA binding protein that negatively regulates growth rate; interacts with the 3' UTR of the mitochondrial porin (POR1) mRNA and enhances its degradation; overexpression impairs mitochondrial function; expressed in stationary phase	-72.3523	0	0	0	0	-54.132930000000002
YBR238C	Mitochondrial membrane protein with similarity to Rmd9p; not required for respiratory growth but causes a synthetic respiratory defect in combination with rmd9 mutations; transcriptionally up-regulated by TOR; deletion increases life span	98.099999999999994	0.040039922999999998	0	0	0	-78.002719999999997
YDL160C	DHH1 Cytoplasmic DExD/H-box helicase, stimulates mRNA decapping, coordinates distinct steps in mRNA function and decay, interacts with both the decapping and deadenylase complexes, may have a role in mRNA export and translation	-97.609089999999995	0	0	0	0	-44.3309
YDR077W	SED1 Major stress-induced structural GPI-cell wall glycoprotein in stationary-phase cells, associates with translating ribosomes, possible role in mitochondrial genome maintenance; ORF contains two distinct variable minisatellites	-92.026449999999997	0	0	0	0	0
YDR233C	RTN1 ER membrane protein that interacts with exocyst subunit Sec6p and with Yip3p; also interacts with Sbh1p; null mutant has an altered (mostly cisternal) ER morphology; member of the RTNLA (reticulon-like A) subfamily	-94.199129999999997	0.083645435000000004	0	0.51884850000000005	0	-78.002719999999997
YDR293C	SSD1 Protein with a role in maintenance of cellular integrity, interacts with components of the TOR pathway; ssd1 mutant of a clinical S. cerevisiae strain displays elevated virulence	8.7899999999999991	0	0	0	0	-82.49333
YDR309C	GIC2 Protein of unknown function involved in initiation of budding and cellular polarization, interacts with Cdc42p via the Cdc42/Rac-interactive binding (CRIB) domain	0	0	0	0	0	84.263171999999997
YDR441C	APT2 Apparent pseudogene, not transcribed or translated under normal conditions; encodes a protein with similarity to adenine phosphoribosyltransferase, but artificially expressed protein exhibits no enzymatic activity	0	26.498575630000001	0	0	-24.399999999999999	0
YDR492W	IZH1 Membrane protein involved in zinc metabolism, member of the four-protein IZH family; transcription is regulated directly by Zap1p, expression induced by zinc deficiency and fatty acids; deletion increases sensitivity to elevated zinc	91.700000000000003	0	0	0	0	-81.100589999999997
YDR504C	SPG3 Protein required for survival at high temperature during stationary phase; not required for growth on nonfermentable carbon sources	-86.934550000000002	0	0	0	0.14726311	0
YDR508C	GNP1 High-affinity glutamine permease, also transports Leu, Ser, Thr, Cys, Met and Asn; expression is fully dependent on Grr1p and modulated by the Ssy1p-Ptr3p-Ssy5p (SPS) sensor of extracellular amino acids	-64.580590000000001	0.78555900000000001	0.013185769999999999	0	0	-78.002719999999997
YEL017W	GTT3 Protein of unknown function with a possible role in glutathione metabolism, as suggested by computational analysis of large-scale protein-protein interaction data; GFP-fusion protein localizes to the nuclear periphery	96.599999999999994	0	0.013185769999999999	0.51884850000000005	0	-81.100589999999997
YER070W	RNR1 Ribonucleotide-diphosphate reductase (RNR), large subunit; the RNR complex catalyzes the rate-limiting step in dNTP synthesis and is regulated by DNA replication and DNA damage checkpoint pathways via localization of the small subunits	-40.64526	0.79754521099999998	0	0	0	84.904486000000006
YER158C	Protein of unknown function, has similarity to Afr1p; potentially phosphorylated by Cdc28p	6.8799999999999999	0	0	0	0.055673380000000001	-72.177289999999999
YGL014W	PUF4 Member of the PUF protein family, which is defined by the presence of Pumilio homology domains that confer RNA binding activity; preferentially binds mRNAs encoding nucleolar ribosomal RNA-processing factors	-74.578500000000005	0	0	0.51884850000000005	0	81.100584999999995
YGL028C	SCW11 Cell wall protein with similarity to glucanases; may play a role in conjugation during mating based on its regulation by Ste12p	-50.275779999999997	0	0	0	0	-78.002719999999997
YGL032C	AGA2 Adhesion subunit of a-agglutinin of a-cells, C-terminal sequence acts as a ligand for alpha-agglutinin (Sag1p) during agglutination, modified with O-linked oligomannosyl chains, linked to anchorage subunit Aga1p via two disulfide bonds	96.599999999999994	0	0	0	-13.800000000000001	0
YGL178W	MPT5 Member of the Puf family of RNA-binding proteins; binds to mRNAs encoding chromatin modifiers and spindle pole body components; involved in longevity, maintenance of cell wall integrity, and sensitivity to and recovery from pheromone arrest	0	-48.100000000000001	0	0	0	82.493329000000003
YGR014W	MSB2 Mucin family member involved in the Cdc42p- and MAP kinase-dependent filamentous growth signaling pathway; also functions as an osmosensor in parallel to the Sho1p-mediated pathway; potential Cdc28p substrate	0.076600000000000001	0	0	NA	0	84.904486000000006
YGR258C	RAD2 Single-stranded DNA endonuclease, cleaves single-stranded DNA during nucleotide excision repair to excise damaged DNA; subunit of Nucleotide Excision Repair Factor 3 (NEF3); homolog of human XPG protein	0	46.980531650000003	0	0	0.96984554999999995	39.787239999999997
YGR279C	SCW4 Cell wall protein with similarity to glucanases; scw4 scw10 double mutants exhibit defects in mating	0	0	0	0	2.0960994899999998	0
YHR143W	DSE2 Daughter cell-specific secreted protein with similarity to glucanases, degrades cell wall from the daughter side causing daughter to separate from mother; expression is repressed by cAMP	0	0	0	0	0.094823580000000005	27.093131
YIL056W	VHR1 Transcriptional activator, required for the vitamin H-responsive element (VHRE) mediated induction of VHT1 (Vitamin H transporter) and BIO5 (biotin biosynthesis intermediate transporter) in response to low biotin concentrations	-62.44444	0	0	0	0	-62.851819999999996
YIL123W	SIM1 Protein of the SUN family (Sim1p, Uth1p, Nca3p, Sun4p) that may participate in DNA replication, promoter contains SCB regulation box at -300 bp indicating that expression may be cell cycle-regulated	0.0166	0.051173218999999999	0	0	0	-66.827089999999998
YIL162W	SUC2 Invertase, sucrose hydrolyzing enzyme; a secreted, glycosylated form is regulated by glucose repression, and an intracellular, nonglycosylated enzyme is produced constitutively	98.099999999999994	-48.200000000000003	0	0	0	0
YJL079C	PRY1 Protein of unknown function, has similarity to Pry2p and Pry3p and to the plant PR-1 class of pathogen related proteins	11.699999999999999	0	0	0	0	62.851821999999999
YJL091C	GWT1 Protein involved in the inositol acylation of glucosaminyl phosphatidylinositol (GlcN-PI) to form glucosaminyl(acyl)phosphatidylinositol (GlcN(acyl)PI), an intermediate in the biosynthesis of glycosylphosphatidylinositol (GPI) anchors	-97.297870000000003	0	0	0	0	62.851821999999999
YJL159W	HSP150 O-mannosylated heat shock protein that is secreted and covalently attached to the cell wall via beta-1,3-glucan and disulfide bridges; required for cell wall stability; induced by heat shock, oxidative stress, and nitrogen limitation	75.5	0	0	0	0	0
YKL032C	IXR1 Protein that binds DNA containing intrastrand cross-links formed by cisplatin, contains two HMG (high mobility group box) domains, which confer the ability to bend cisplatin-modified DNA; mediates aerobic transcriptional repression of COX5b	-77.456559999999996	0.013744948999999999	0	0	0	-72.177289999999999
YKL051W	SFK1 Plasma membrane protein that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, at least partially mediates proper localization of Stt4p to the plasma membrane	-53.775970000000001	0	0	0	0	-72.177289999999999
YKL164C	PIR1 O-glycosylated protein required for cell wall stability; attached to the cell wall via beta-1,3-glucan; mediates mitochondrial translocation of Apn1p; expression regulated by the cell integrity pathway and by Swi5p during the cell cycle	-97.587260000000001	0	0	0	0	0
YKR042W	UTH1 Mitochondrial outer membrane and cell wall localized SUN family member required for mitochondrial autophagy; involved in the oxidative stress response, life span during starvation, mitochondrial biogenesis, and cell death	0	0	0	0	3.9245841299999999	0
YLL013C	PUF3 Protein of the mitochondrial outer surface, links the Arp2/3 complex with the mitochore during anterograde mitochondrial movement; also binds to and promotes degradation of mRNAs for select nuclear-encoded mitochondrial proteins	73.5	0	0	0	0.19796871999999999	83.857618000000002
YLR056W	ERG3 C-5 sterol desaturase, catalyzes the introduction of a C-5(6) double bond into episterol, a precursor in ergosterol biosynthesis; mutants are viable, but cannot grow on non-fermentable carbon sources	97.799999999999997	0	0	0	0	57.886611000000002
YLR064W	Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the endoplasmic reticulum; YLR064W is not an essential gene	97.200000000000003	0.13178986500000001	0	0	0.021650760000000002	57.886611000000002
YLR089C	ALT1 Putative alanine transaminase (glutamic pyruvic transaminase); the authentic, non-tagged protein is detected in highly purified mitochondria in high-throughput studies	-95.066649999999996	0	0.013185769999999999	0.37734440000000002	0	-66.827089999999998
YLR286C	CTS1 Endochitinase, required for cell separation after mitosis; transcriptional activation during late G and early M cell cycle phases is mediated by transcription factor Ace2p	0	0	0	0	0.38339684000000002	0
YLR413W	Putative protein of unknown function; YLR413W is not an essential gene	-44.08034	0.031672383999999998	0	0	0	-78.002719999999997
YLR459W	GAB1 GPI transamidase subunit, involved in attachment of glycosylphosphatidylinositol (GPI) anchors to proteins; may have a role in recognition of the attachment signal or of the lipid portion of GPI	97.700000000000003	0	0	0	0	72.177285999999995
YML027W	YOX1 Homeodomain-containing transcriptional repressor, binds to Mcm1p and to early cell cycle boxes (ECBs) in the promoters of cell cycle-regulated genes expressed in M/G1 phase; expression is cell cycle-regulated; potential Cdc28p substrate	-51.369950000000003	0	0.036489460000000001	0	0.27084109000000001	-66.827089999999998
YML058W	SML1 Ribonucleotide reductase inhibitor involved in regulating dNTP production; regulated by Mec1p and Rad53p during DNA damage and S phase	-89.049369999999996	0	0	0	0	1.2571209999999999
YMR011W	HXT2 High-affinity glucose transporter of the major facilitator superfamily, expression is induced by low levels of glucose and repressed by high levels of glucose	95.5	0	0	0.19566	0	-78.002719999999997
YMR015C	ERG5 C-22 sterol desaturase, a cytochrome P450 enzyme that catalyzes the formation of the C-22(23) double bond in the sterol side chain in ergosterol biosynthesis; may be a target of azole antifungal drugs	-83.294049999999999	0	0	0	0	83.857618000000002
YMR215W	GAS3 Putative 1,3-beta-glucanosyltransferase, has similarity to Gas1p; localizes to the cell wall	-89.408199999999994	0	0	0.51884850000000005	0	84.579728000000003
YMR305C	SCW10 Cell wall protein with similarity to glucanases; may play a role in conjugation during mating based on mutant phenotype and its regulation by Ste12p	0	0	0	0	0.040348479999999999	83.222423000000006
YNL066W	SUN4 Cell wall protein related to glucanases, possibly involved in cell wall septation; member of the SUN family	0.044999999999999998	0.037650553000000003	0	0.19566	13.83937076	84.904486000000006
YNL074C	MLF3 Serine-rich protein of unknown function; overproduction suppresses the growth inhibition caused by exposure to the immunosuppressant leflunomide	98.200000000000003	0	0	0	0	23.416965000000001
YNL145W	MFA2 Mating pheromone a-factor, made by a cells; interacts with alpha cells to induce cell cycle arrest and other responses leading to mating; biogenesis involves C-terminal modification, N-terminal proteolysis, and export; also encoded by MFA1	94.599999999999994	0	0	0	0.021650760000000002	-81.100589999999997
YNL160W	YGP1 Cell wall-related secretory glycoprotein; induced by nutrient deprivation-associated growth arrest and upon entry into stationary phase; may be involved in adaptation prior to stationary phase entry; has similarity to Sps100p	-97.59272	0	0	0	0.021650760000000002	0
YNL167C	SKO1 Basic leucine zipper (bZIP) transcription factor of the ATF/CREB family, forms a complex with Tup1p and Ssn6p to both activate and repress transcription; cytosolic and nuclear protein involved in osmotic and oxidative stress responses	97.900000000000006	0.040158269000000003	0	0	0.69883002999999999	-72.177289999999999
YNL176C	Cell cycle-regulated gene of unknown function, promoter bound by Fkh2p	86.900000000000006	0.00061373799999999996	0.13990361000000001	0	0.19796871999999999	84.904486000000006
YNL190W	Cell wall protein of unknown function; proposed role as a hydrophilin induced by osmotic stress; contains a putative GPI-attachment site	98.099999999999994	0.043908390999999998	0	0	8.7496704899999997	0
YNL197C	WHI3 RNA binding protein that sequesters CLN3 mRNA in cytoplasmic foci; cytoplasmic retention factor for Cdc28p and associated cyclins; regulates cell fate and dose-dependently regulates the critical cell size required for passage through Start	-91.116659999999996	0.073346418999999996	0	0	0	-72.177289999999999
YNL283C	WSC2 Partially redundant sensor-transducer of the stress-activated PKC1-MPK1 signaling pathway involved in maintenance of cell wall integrity and recovery from heat shock; secretory pathway Wsc2p is required for the arrest of secretion response	0	0.038165597000000002	0	0	23.615292910000001	-72.177289999999999
YNL288W	CAF40 Evolutionarily conserved subunit of the CCR4-NOT complex involved in controlling mRNA initiation, elongation and degradation; binds Cdc39p	-96.876729999999995	0	0	0	0	-72.177289999999999
YNL300W	Glycosylphosphatidylinositol-dependent cell wall protein, expression is periodic and decreases in respone to ergosterol perturbation or upon entry into stationary phase; depletion increases resistance to lactic acid	0	0	0	0	24.373229779999999	-72.177289999999999
YNL327W	EGT2 Glycosylphosphatidylinositol (GPI)-anchored cell wall endoglucanase required for proper cell separation after cytokinesis, expression is activated by Swi5p and tightly regulated in a cell cycle-dependent manner	-80.513919999999999	0.054177835000000001	0	0	0	54.132928
YNR009W	NRM1 Transcriptional co-repressor of MBF (MCB binding factor)-regulated gene expression; Nrm1p associates stably with promoters via MBF to repress transcription upon exit from G1 phase	95.099999999999994	0	0	0	0.040348479999999999	-72.177289999999999
YNR030W	ALG12 Alpha-1,6-mannosyltransferase localized to the ER; responsible for the addition of the alpha-1,6 mannose to dolichol-linked Man7GlcNAc2, acts in the dolichol pathway for N-glycosylation	-93.068669999999997	0	0	0.37734440000000002	0	-72.177289999999999
YOL030W	GAS5 1,3-beta-glucanosyltransferase, has similarity to Gas1p; localizes to the cell wall	-84.541839999999993	0	0	0	0	84.904486000000006
YOL051W	GAL11 Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; affects transcription by acting as target of activators and repressors	-44.700429999999997	0.0054667860000000004	0	0	0	-78.002719999999997
YOR002W	ALG6 Alpha 1,3 glucosyltransferase, involved in transfer of oligosaccharides from dolichyl pyrophosphate to asparagine residues of proteins during N-linked protein glycosylation; mutations in human ortholog are associated with disease	91.400000000000006	0	0	0	0.021650760000000002	66.827087000000006
YOR010C	TIR2 Putative cell wall mannoprotein of the Srp1p/Tip1p family of serine-alanine-rich proteins; transcription is induced by cold shock and anaerobiosis	29.399999999999999	49.391676099999998	0	0	0	0
YOR085W	OST3 Gamma subunit of the oligosaccharyltransferase complex of the ER lumen, which catalyzes asparagine-linked glycosylation of newly synthesized proteins; Ost3p is important for N-glycosylation of a subset of proteins	-96.238	0.040727513999999999	0	0	0	84.904486000000006
YOR140W	SFL1 Transcriptional repressor and activator; involved in repression of flocculation-related genes, and activation of stress responsive genes; negatively regulated by cAMP-dependent protein kinase A subunit Tpk2p	-86.588890000000006	0.084076465000000003	0	0	0	-66.827089999999998
YOR247W	SRL1 Mannoprotein that exhibits a tight association with the cell wall, required for cell wall stability in the absence of GPI-anchored mannoproteins; has a high serine-threonine content; expression is induced in cell wall mutants	0	0.067589581999999995	0	0.51884850000000005	23.615292910000001	-57.886609999999997
YOR248W	Dubious open reading frame, unlikely to encode a functional protein; based on available experimental and comparative sequence data	0	0	0	0	5.5185047000000003	-78.002719999999997
YOR267C	HRK1 Protein kinase implicated in activation of the plasma membrane H(+)-ATPase Pma1p in response to glucose metabolism; plays a role in ion homeostasis	-76.502769999999998	0.0094940700000000003	0	0.51884850000000005	0.27084109000000001	-62.851819999999996
YOR372C	NDD1 Transcriptional activator essential for nuclear division; localized to the nucleus; essential component of the mechanism that activates the expression of a set of late-S-phase-specific genes	-44.577860000000001	0.072489974999999998	0	0	0	84.904486000000006
YOR383C	FIT3 Mannoprotein that is incorporated into the cell wall via a glycosylphosphatidylinositol (GPI) anchor, involved in the retention of siderophore-iron in the cell wall	0.0062199999999999998	0	11.079685700000001	0	25.171815550000002	0
YPL076W	GPI2 Protein involved in the synthesis of N-acetylglucosaminyl phosphatidylinositol (GlcNAc-PI), the first intermediate in the synthesis of glycosylphosphatidylinositol (GPI) anchors; homologous to the human PIG-C protein	0	0	0	0	1.2526005899999999	84.263171999999997
YPL179W	PPQ1 Putative protein serine/threonine phosphatase; null mutation enhances efficiency of translational suppressors	-79.756330000000005	0.048963442000000003	0	0.37734440000000002	0.19796871999999999	81.100584999999995
YPL190C	NAB3 Single stranded RNA binding protein; acidic ribonucleoprotein; required for termination of non-poly(A) transcripts and efficient splicing; interacts with Nrd1p	-64.790469999999999	0	0	0	0	66.827087000000006
YPL256C	CLN2 G1 cyclin involved in regulation of the cell cycle; activates Cdc28p kinase to promote the G1 to S phase transition; late G1 specific expression depends on transcription factor complexes, MBF (Swi6p-Mbp1p) and SBF (Swi6p-Swi4p)	0	0.080377675999999995	0	0.51884850000000005	0.69883002999999999	66.827087000000006
YPR065W	ROX1 Heme-dependent repressor of hypoxic genes; contains an HMG domain that is responsible for DNA bending activity	-82.278760000000005	0	0	0	0	-72.177289999999999