Table 3.

Identification of genes differentially expressed under B-regulated development ordered by KOG group

Regulation, KOG groupa: (gene name) protein function/biological process/cellular component	Protein ID	Fold change in expression
Upregulated
M: chitinase	231665	14.7
O: molecular chaperone (DnaJ superfamily), heat shock protein DnaJ	231463	18.1
O: AAA+-type ATPase	109412	8.6
O: nuclear AAA ATPase, peptidase S16, Lon protease	58751	8.2
O: HSP90 cochaperone CPR7/cyclophilin, peptidyl-prolyl cis-trans isomerase, cyclophilin type	55359	6.1
T: indoleamine 2,3-dioxygenase	33516	198.5
T: signaling protein RIC-8/synembryn (regulates neurotransmitter secretion)	62504	20.1
T: G protein beta WD-40 repeat	104106	18.6
T: GTPase activator protein, Rab GTPase activator activity	108327	13.8
T: serine/threonine protein kinase	111639	13.5
T: casein kinase (serine/threonine/tyrosine protein kinase), protein kinase	106153	13.5
T: 3′,5′-cyclic nucleotide phosphodiesterase, 3′,5′-cyclic AMP phosphodiesterase activity, similar to S. cerevisiae Pde1	105393	10.6
T: serine/threonine protein kinase	103735	10.5
T: armadillo/beta-catenin/plakoglobin, uridine kinase, phosphoribulokinase	71870	10.2
T: signal transduction serine/threonine kinase with PAS/PAC sensor domain, protein kinase	16935	6.2
U: translocase of outer mitochondrial membrane complex, subunit TOM37/metaxin 1	83604	13.9
U: G-protein beta WD-40 repeat, prolactin regulatory element-binding protein/protein transport protein SEC12p	49920	9.3
U: endoplasmic reticulum-Golgi vesicle-tethering protein p115	110288	7.9
U: peptide exporter, ABC superfamily	51416	7.4
U: vacuolar sorting protein VPS24, Snf7, protein transport	47850	5.8
V: predicted transporter (major facilitator superfamily), tetracycline resistance protein TetB, hydrogen antiporter activity	41682	12.2
V: Von Willebrand factor and related coagulation proteins, various SH3 domains (protein destination)	255861	11.4
V: predicted transporter (major facilitator superfamily), tetracycline resistance protein TetB, similar to Mfs1.1	233429b	5.2
Y: nucleolar GTPase/ATPase p130	51001	12.2
Y: nucleolar GTPase/ATPase p130	256072	6.3
Z: spindle pole body protein Sad1p, peptidase C19, ubiquitin carboxyl-terminal hydrolase 2	80616	25.6
Z: myosin class V heavy chain, myosin head, motor region	70377	11.0
A: splicing coactivator SRm160/300, subunit SRm300	232813	33.0
A: splicing coactivator SRm160/300, subunit SRm300	113731	25.4
A: polyadenylation factor I complex, subunit, Yth1 (cleavage and polyadenylation specific factor [CPSF] subunit), Zn finger	13540	15.6
A: splicing coactivator SRm160/300, subunit SRm300	256249	7.9
A: tuftelin-interacting protein TIP39, contains G-patch domain, D111/G patch (mouse protein)	36337	5.7
B: SWI-SNF chromatin remodeling complex, Snf5 subunit, SNF5/SMARCB1/INI1, chromatin remodeling	53495	18.2
B: chromatin remodeling protein, contains PHD (plant homeodomain) Zn finger	233026	14.9
B: histone acetyltransferase SAGA, TRRAP/TRA1 component, phosphatidylinositol 3 and 4 kinases	12680	14.7
B: SWI/SNF chromatin-remodeling complex protein, prion protein, aminoacyl-tRNA synthetase	106231	6.9
J: 60s acidic ribosomal protein P1, structural constituent of ribosome	233634	11.5
J: tRNA methyltransferase, N2,N2-dimethylguanosine tRNA methyltransferase, tRNA (guanine-N2-)-methyltransferase	81492	10.0
J: pseudouridylate synthase, tRNA pseudouridine synthase	42694	8.9
J: translation initiation factor 2C (eIF-2C) and related proteins, argonaute and dicer protein, PAZ domain	257069	6.1
K: RNA polymerase II, large subunit, DNA-directed RNA polymerase	105543	16.8
K: RNA polymerase I, large subunit, DNA-directed RNA polymerase	255115	14.8
K: transcription regulator XNP/ATRX, DEAD box superfamily, shugoshin, N terminal	256320	13.8
K: transcription coactivator, double-stranded RNA binding	104274	11.5
K: DNA-directed RNA polymerase subunit E′, RNA polymerase Rpb7, N terminal	234509	7.6
K: transcription initiation factor IIF, small subunit (RAP30); transcription initiation factor IIF, beta subunit	78184	6.5
K: transcription factor XBP-1, basic leucine zipper (bZIP) transcription factor	236086	5.7
K: GCN5-related N-acetyltransferase, transferring groups other than amino acyl groups	52412	5.5
L: DNA repair protein, SNF2 family, helicase, C terminal, SNF2 related	81511	306.0
L: CDC45 (cell division cycle 45)-like protein, DNA replication initiation	50273	11.7
L: origin recognition complex, subunit 4	46745	8.2
C: mitochondrial carnitine-acylcarnitine carrier protein, adenine nucleotide translocator 1	58334	17.4
D: halotolerance protein HAL3 (contains flavoprotein domain), peptidyl-prolyl cis-trans isomerase activity	113841	26.5
D: halotolerance protein HAL3 (contains flavoprotein domain), phosphopantothenoylcysteine decarboxylase	15072	24.3
D: Mis12, chromosome, pericentric region	14071	15.9
D: mitotic spindle checkpoint protein BUB3, WD repeat superfamily, G-protein beta WD-40 repeat	86026	5.5
E: oxoprolinase, hydantoinase/oxoprolinase, glutathione metabolism	82383	7.3
E: serine carboxypeptidases (lysosomal cathepsin A), peptidase S10, serine carboxypeptidase	40585	5.8
E: Xaa-Pro aminopeptidase, peptidase M24	58445	5.2
G: glucose-6-phosphate/phosphate and phosphoenolpyruvate/phosphate antiporter	36941	22.9
G: general substrate transporter, sugar transporter superfamily	66123	14.4
G: esterase, poly-β-hydroxybutyrate depolymerase, esterase/lipase/thioesterase, carbohydrate esterase family 1 protein	47380	12.1
G: inositol monophosphatase	47747	7.7
G: beta-1,6-N-acetylglucosaminyltransferase, contains WSC domain	110551c	7.5
G: glycoside hydrolase, family 43	232782	6.6
I: acyl coenzyme A:diacylglycerol acyltransferase (DGAT)	53861	21.1
I: S-adenosylmethionine-dependent methyltransferases, generic methyltransferase	14559	13.5
I: cytochrome P450 CYP4/CYP19/CYP26 subfamilies, E-class P450, group I, gamma-hexachlorocyclohexane degradation, ascorbate and aldarate metabolism	233430	11.6
I: cytochrome P450 CYP4/CYP19/CYP26 subfamilies, unspecific monooxygenase, tryptophan metabolism, fatty acid metabolism	76871	6.0
P: Ca2+/H+ antiporter VCX1 and related proteins, sodium/calcium exchanger membrane region, calcium/proton exchanger	27729	9.4
P: Ca2+ transporting ATPase, potassium/sodium efflux P-type ATPase, fungal type	53464	5.4
Q: multidrug/pheromone exporter, ABC superfamily	113902	53.4
Q: multidrug/pheromone exporter, ABC superfamily	258386	5.0
R: Zn finger, C2H2 type, similar to vegetative cell wall protein gp1 precursor (hydroxyproline-rich glycoprotein 1)	113591	19.2
R: WD-40 repeat-containing protein	84316	9.0
R: Zn finger, cytochrome c heme-binding site, electron transport activity	233610	5.7
S: UbiA prenyltransferase, prenyltransferase activity	238827	23.8
S: chloroperoxidase, peroxidase activity, electron transport	57566	21.7
S: cyclin-like F-box domain	111277	18.4
S: cyclin-like F box, Zn finger, C2H2 type	104797	8.7
S: glutathione S-transferase, N terminal	111982	8.3
S: bucentaur or craniofacial development	112020	8.2
S: protein binding, BTB/POZ domain	236141	7.8
S: bacterial extracellular solute-binding protein, family 3, transporter activity	105400	7.7
S: predicted membrane protein	108226	7.7
S: Zn finger, MYND type	231200	7.1
S: target SNARE coiled-coil region	56068	6.5
S: cyclin-like F box, Zn finger, C2H2 type	234065	6.3
S: Zn finger, CCHC type	237097	6.0
S: notchless-like WD-40 repeat-containing protein, 2-acetyl-1-alkylglycerophosphocholine esterase, G-protein beta WD-40 repeat	37220	5.2
Downregulated
O: alkyl hydroperoxide reductase/peroxiredoxin	56996	−20.1
O: E3 ubiquitin ligase interacting with arginine methyltransferase, Zn finger, CCHC type	83759	−19.5
O: peptidase M28, transferrin receptor and related proteins containing the protease-associated (PA) domain	17256	−11.3
T: serine/threonine protein kinase	108101	−8.5
T: (brl3) fungal pheromone STE3 6-protein-coupled receptor, mating-type alpha-factor pheromone receptor activity	258344	−5.6
T: (bbp2) pheromone precursor	12028	−14.2
U: nuclear pore complex, Nup98 component (sc Nup145/Nup100/Nup116), ribosomal protein L9 N-terminal like	112737	−5.9
U: clathrin adaptor complex, medium chain, adaptor complexes medium subunit family	61803	−5.2
K: fungal transcriptional regulatory protein, N-terminal, fungus-specific transcription factor, DNA binding, zinc ion binding	65707	−12.8
K: transcription factor activity, similar to Cu-dependent DNA-binding protein, copper fist DNA binding	61956	−9.4
K: fungus-specific transcription factor, DNA binding, zinc ion binding	35685	−7.3
K: peptidase M, neutral zinc metallopeptidases, zinc-binding site, selective LIM domain binding factor	114395	−6.9
K: GATA-4/5/6 transcription factors, Zn finger, GATA type	256713	−6.2
C: aldehyde dehydrogenase, tyrosine metabolism, glycolysis/gluconeogenesis	258124	−7.7
C: kynurenine 3-monooxygenase and related flavoprotein monooxygenases, salicylate 1-monooxygenase	238637	−6.5
G: gluconate transport-inducing protein	108884	−25.9
G: predicted short-chain-type dehydrogenase, glucose/ribitol dehydrogenase	236244	−20.5
G: predicted short-chain-type dehydrogenase, glucose/ribitol dehydrogenase	110470	−10.0
G: general substrate transporter, permease of the major facilitator superfamily	55688	−9.6
G: dTDP-glucose 4-6-dehydratase/UDP-glucuronic acid decarboxylase, erythromycin biosynthesis	13089	−6.8
G: permease of the major facilitator superfamily	13397	−6.0
G: glycoside hydrolase family 23 protein, candidate beta-glycosidase distantly related to N-acetylmuramidases	31488	−5.4
G: alpha-amylase	70398	−5.2
G: predicted transporter (major facilitator superfamily), sugar:hydrogen symporter activity	109961	−5.1
I: esterase/lipase/thioesterase, hormone-sensitive lipase (HSL)	85341	−8.1
I: fatty acid desaturase, Cytochrome b5	43089	−5.1
Q: laccase, multicopper oxidase, type 1	111478	−5.2
R: Zn finger, C2H2 type, cytochrome c heme-binding site, electron transport	111555	−19.5
R: transposon-encoded proteins with TyA, reverse transcriptase, integrase domains in various combinations	41205	−11.2
R: oxidoreductase, electron transport	16666	−7.5
R: transposon-encoded proteins with TyA, reverse transcriptase, integrase domains in various combinations	40072	−7.4
R: reductases with broad range of substrate specificities, oxidoreductase activity	61612	−6.5
R: O-methyltransferase, family 2, hydroxyindole-O-methyltransferase, S-adenosylmethionine-dependent methyltransferase (SAM) activity	238432c	−5.5
R: monodehydroascorbate/ferredoxin reductase, flavin adenine dinucleotide-dependent pyridine nucleotide-disulfide oxidoreductase, electron transport	62520	−5.1
S: pyridoxamine 5′-phosphate oxidase-related, flavin mononucleotide binding	42417	−17.7
S: S-adenosylmethionine-dependent methyltransferase, S-adenosylmethionine (and some other nucleotide) binding motif	80619	−9.9
S: d-alanyl–d-alanine endopeptidase activity, peptidase A22B, minor histocompatibility antigen H13, aspartic-type endopeptidase activity	58664	−8.5
S: cell growth regulatory protein CGR11	238935	−7.9
S: cyclin-like F box	110269	−7.7
S: thaumatin, pathogenesis related	111995	−6.3
S: variant SH3 domain	65138	−6.1
S: cyclin-like F box	114268	−5.7

^aKOG groups are defined in the legend to Fig. 10.

^bAdditionally downregulated in thin phenotype.

^cAdditionally upregulated in thin phenotype.