Table 6 Re-classification of known genes to Gene Ontology biological process terms

GENE SYMBOL	GENE NAME	PROBE NO (Iyer et. al.)	ACCESSION NUMBER	PREDICTIONS FOR THE 23 BROAD CELLULAR PROCESSES USED FOR LEARNING	ANNOTATIONS TO THE 23 BROAD CELLULAR PROCESSES USED FOR LEARNING
SEPP1	selenoprotein P, plasma, 1	2	AA045003	transport, stress response	stress response, transport
EPB41L2	erythrocyte membrane protein band 4.1-like 2	4	W88572	cell proliferation	cell proliferation
OA48-18	acid-inducible phosphoprotein	5	AA029909	cell proliferation	cell proliferation
CTSK	cathepsin K (pycnodysostosis)	8	AA044619	cell proliferation, protein metabolism and modification	protein metabolism and modification
CPT1B	carnitine palmitoyltransferase I, muscle	9	W89012	lipid metabolism	lipid metabolism
CLDN11	claudin 11 (oligodendrocyte transmembrane protein)	11	N22392	cell proliferation, cell motility, cell adhesion, developmental processes	cell adhesion, cell motility, cell proliferation, developmental processes
RPL5	ribosomal protein L5	12	AA027277	protein metabolism and modification, cell organization and biogenesis	protein metabolism and modification, cell organization and biogenesis
	Homo sapiens clone 23785 mRNA sequence	14	N32247	lipid metabolism, cell adhesion, developmental processes	cell adhesion
	ESTs, Weakly similar to A45082 neurotrophic receptor ror1 precursor [H.sapiens]	15	T62968	cell surface receptor linked signal transduction, cell death, oncogenesis	cell surface receptor linked signal transduction
CCNG1	cyclin G1	19	R45687	cell death, cell cycle, oncogenesis	cell cycle, cell death
CDKN1C	cyclin-dependent kinase inhibitor 1C (p57, Kip2)	21	R81336	cell cycle, oncogenesis	cell cycle, cell proliferation
GRIA1	glutamate receptor, ionotropic, AMPA 1	22	N47974	developmental processes, cell surface receptor linked signal transduction, cell death	cell death, cell surface receptor linked signal transduction
	Homo sapiens mRNA for KIAA1888 protein, partial cds	25	H26264	transport, cell surface receptor linked signal transduction, cell death, intracellular signalling cascade	transport
FMOD	fibromodulin	33	AA029408	transport, cell adhesion, cell organization and biogenesis, cell surface receptor linked signal transduction, cell cycle	cell adhesion
CDK5R1	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	36	R49183	cell proliferation, lipid metabolism, cell cycle	cell proliferation, cell cycle
CAT	catalase	37	W89002	stress response, transcription, oncogenesis	stress response
	Homo sapiens, clone MGC:16131 IMAGE:3628944, mRNA, complete cds	47	R71462	transport, intracellular signalling cascade	transport, intracellular signalling cascade
	ESTs, Moderately similar to JX0336 succinate dehydrogenase [H.sapiens]	48	R60996	lipid metabolism, intracellular signalling cascade, energy pathways	energy pathways, lipid metabolism
GBAS	glioblastoma amplified sequence	50	T90846	lipid metabolism, cell surface receptor linked signal transduction	cell surface receptor linked signal transduction
MME	membrane metallo-endopeptidase (neutral endopeptidase, enkephalinase, CALLA, CD10)	53	H65598	cell proliferation, protein metabolism and modification, cell motility	protein metabolism and modification, cell proliferation, defense (immune) response, cell motility
DPP4	dipeptidylpeptidase IV (CD26, adenosine deaminase complexing protein 2)	55	H61694	protein metabolism and modification, cell motility, developmental processes	cell motility, protein metabolism and modification
FBN2	fibrillin 2 (congenital contractural arachnodactyly)	59	AA025721	lipid metabolism, cell motility, cell adhesion	cell motility, cell adhesion
	Homo sapiens cDNA: FLJ23176 fis, clone LNG10452	60	AA034939	lipid metabolism, cell adhesion, developmental processes	developmental processes, cell adhesion
ANXA3	annexin A3	61	W45327	lipid metabolism, blood coagulation	blood coagulation
HFL1	H factor (complement)-like 1	64	W88788	stress response, defense (immune) response	defense (immune) response
SQLE	squalene epoxidase	66	W80742	lipid metabolism	lipid metabolism
WNT2	wingless-type MMTV integration site family member 2	70	W80746	cell adhesion, developmental processes	developmental processes
ASNS	asparagine synthetase	72	AA053461	lipid metabolism, amino-acid and derivative metabolism	amino-acid and derivative metabolism
SMARCB1	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1	73	AA026808	cell proliferation, DNA metabolism, transcription	DNA metabolism, cell proliferation, transcription
DHCR24	24-dehydrocholesterol reductase	74	W91979	lipid metabolism	lipid metabolism
OSBP2	oxysterol binding protein 2	76	H52219	lipid metabolism, cell death	cell death, lipid metabolism
SC5DL	sterol-C5-desaturase (fungal ERG3, delta-5-desaturase)-like	80	N91268	lipid metabolism	lipid metabolism
	Homo sapiens cDNA FLJ13700 fis, clone PLACE2000216, highly similar to SPECTRIN BETA CHAIN, BRAIN	82	AA055558	transport, DNA metabolism	transport
HMGCR	3-hydroxy-3-methylglutaryl-Coenzyme A reductase	85	AA053028	lipid metabolism, cell adhesion	lipid metabolism
CYP1B1	cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)	86	AA040872	lipid metabolism	lipid metabolism
MID1	midline 1 (Opitz/BBB syndrome)	89	W90080	developmental processes, cell organization and biogenesis	developmental processes, cell organization and biogenesis
ELF2	E74-like factor 2 (ets domain transcription factor)	92	N32165	cell proliferation, cell cycle, transcription	transcription, cell proliferation
HBP1	HMG-box containing protein 1	93	AA043938	lipid metabolism, DNA metabolism, transcription, oncogenesis	DNA metabolism, transcription, oncogenesis
	Homo sapiens cDNA: FLJ22189 fis, clone HRC01043	95	AA029774	transport, transcription	transport, transcription
PDE8A	phosphodiesterase 8A	96	N66765	cell surface receptor linked signal transduction, intracellular signalling cascade, transcription	intracellular signalling cascade
SSPN	sarcospan (Kras oncogene-associated gene)	99	N21470	lipid metabolism, cell adhesion, transcription, oncogenesis	oncogenesis, cell adhesion
ZNF161	zinc finger protein 161	101	AA034054	lipid metabolism, defense (immune) response, transcription	transcription, defense (immune) response
VDUP1	upregulated by 1,25-dihydroxyvitamin D-3	102	AA044633	stress response, cell proliferation, cell death	cell death, stress response, cell proliferation
RABIF	RAB interacting factor	103	AA011218	transport, stress response, cell death	transport
TRIP7	thyroid hormone receptor interactor 7	104	AA029205	cell cycle, DNA metabolism, transcription	transcription
	ESTs, Highly similar to 1715335A Wee1-like gene [H.sapiens]	109	AA039640	cell cycle	cell cycle
SMARCA3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3	110	W70150	cell organization and biogenesis, cell cycle, blood coagulation, DNA metabolism, transcription	cell motility, defense (immune) response, blood coagulation, DNA metabolism, transcription
	Homo sapiens clone 24889 mRNA sequence	123	R82488	cell organization and biogenesis, cell cycle	cell organization and biogenesis
ALDH3A2	aldehyde dehydrogenase 3 family, member A2	124	H63779	lipid metabolism, oncogenesis	lipid metabolism
MEIS1	Meis1 (mouse) homolog	125	R15989	lipid metabolism, transcription, oncogenesis	transcription, oncogenesis
F2R	coagulation factor II (thrombin) receptor	128	N70450	cell surface receptor linked signal transduction, intracellular signalling cascade, blood coagulation	cell surface receptor linked signal transduction, blood coagulation
THBS3	thrombospondin 3	130	AA025310	cell proliferation, cell adhesion, cell death, circulation	cell adhesion, cell death, cell proliferation, circulation
KIT	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	132	W93694	cell motility, cell surface receptor linked signal transduction, cell death, defense (immune) response, oncogenesis	cell surface receptor linked signal transduction, defense (immune) response, cell proliferation, cell motility, cell death, oncogenesis
ECM2	extracellular matrix protein 2, female organ and adipocyte specific	135	N79778	cell proliferation, cell motility, cell adhesion, defense (immune) response	cell adhesion, cell proliferation
HMG2	high-mobility group (nonhistone chromosomal) protein 2	139	AA019203	cell motility, cell cycle, DNA metabolism, transcription	cell cycle, transcription, DNA metabolism, cell organization and biogenesis
GTF2I	general transcription factor II, i	141	AA057771	cell cycle, DNA metabolism, transcription	transcription
B4-2	proline-rich protein with nuclear targeting signal	142	AA045742	cell motility, defense (immune) response	cell motility, defense (immune) response
TGFBR3	transforming growth factor, beta receptor III (betaglycan, 300kD)	145	H62473	cell proliferation, cell surface receptor linked signal transduction, cell death	cell death, cell proliferation, defense (immune) response, cell surface receptor linked signal transduction
FYN	FYN oncogene related to SRC, FGR, YES	146	W45726	cell proliferation, intracellular signalling cascade, transcription, oncogenesis	cell proliferation, intracellular signalling cascade, oncogenesis
PRKCL2	protein kinase C-like 2	148	AA035285	transport, intracellular signalling cascade	intracellular signalling cascade
DDIT3	DNA-damage-inducible transcript 3	150	AA001025	cell cycle, transcription	transcription, cell cycle
ACF7	actin cross-linking factor	152	AA059074	transport, cell organization and biogenesis, cell cycle	transport, cell organization and biogenesis, cell cycle
TAX1BP1	Tax1 (human T-cell leukemia virus type I) binding protein 1	153, 78	N67978, AA012996	cell death, transcription, cell proliferation, cell cycle	transcription, cell death
PDE8B	phosphodiesterase 8B	155	H17482	cell death, intracellular signalling cascade, transcription, oncogenesis	intracellular signalling cascade
DKFZP564D0764	DKFZP564D0764 protein	156	N93862	cell organization and biogenesis, intracellular signalling cascade, transcription, oncogenesis	transcription
AHR	aryl hydrocarbon receptor	157	W67226	lipid metabolism, transcription	lipid metabolism, transcription
ACACA	acetyl-Coenzyme A carboxylase alpha	158	AA011388	lipid metabolism, transcription, oncogenesis	lipid metabolism
CAMK2D	calcium/calmodulin-dependent protein kinase (CaM kinase) II delta	159, 160	W45465, AA010624	cell cycle, intracellular signalling cascade	intracellular signalling cascade, cell cycle
KIAA0456	KIAA0456 protein	163	N31484	cell organization and biogenesis, cell cycle, intracellular signalling cascade	cell organization and biogenesis, cell cycle, intracellular signalling cascade
DDB2	damage-specific DNA binding protein 2 (48kD)	167	H63374	lipid metabolism, DNA metabolism	DNA metabolism
KIAA0203	likely ortholog of mouse coiled coil forming protein 1	168	R44177	cell proliferation, cell organization and biogenesis, intracellular signalling cascade, oncogenesis	cell organization and biogenesis
ADD3	adducin 3 (gamma)	173	AA054129	cell proliferation, cell organization and biogenesis, intracellular signalling cascade, transcription, oncogenesis	cell organization and biogenesis
DDX17	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 17 (72kD)	177, 221	AA010407, R09377	lipid metabolism, transcription, cell surface receptor linked signal transduction	transcription
KIAA1536	KIAA1536 protein	179	AA058747	DNA metabolism, transcription, oncogenesis	DNA metabolism, transcription, oncogenesis
CLCN3	chloride channel 3	188	N72130	transport, cell cycle	transport
TIA1	TIA1 cytotoxic granule-associated RNA-binding protein	189	N79013	cell death, defense (immune) response	cell death, defense (immune) response
CDKN1B	cyclin-dependent kinase inhibitor 1B (p27, Kip1)	192	R44858	cell surface receptor linked signal transduction, cell cycle	cell cycle
HSF2	heat shock transcription factor 2	196	N39221	lipid metabolism, transcription	transcription
CDKN2C	cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4)	204	N72115	cell proliferation, cell cycle	cell cycle, cell proliferation
TFDP2	transcription factor Dp-2 (E2F dimerization partner 2)	206	W46792	cell organization and biogenesis, intracellular signalling cascade, transcription, oncogenesis	transcription
OXR1	oxidation resistance 1	207	W47204	stress response	stress response
HNMT	histamine N-methyltransferase	208	N67806	cell organization and biogenesis, amino-acid and derivative metabolism, oncogenesis	amino-acid and derivative metabolism
RFX5	regulatory factor X, 5 (influences HLA class II expression)	211	AA040156	cell surface receptor linked signal transduction, transcription	defense (immune) response, transcription
NDR	serine threonine protein kinase	215	AA043103	protein metabolism and modification, cell organization and biogenesis, cell cycle	protein metabolism and modification
ROR2	receptor tyrosine kinase-like orphan receptor 2	217	AA024845	cell surface receptor linked signal transduction, transcription	cell surface receptor linked signal transduction
CEBPG	CCAAT/enhancer binding protein (C/EBP), gamma	218	AA035360	cell cycle, DNA metabolism, transcription	transcription
KIAA0092	KIAA0092 gene product	219	AA046042	cell motility, cell cycle	cell motility
PLSCR1	phospholipid scramblase 1	220	AA056199	lipid metabolism, cell death, blood coagulation	lipid metabolism, cell death, blood coagulation
ATRX	alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)	229	N22858	DNA metabolism, transcription, oncogenesis	DNA metabolism, transcription
NARS	asparaginyl-tRNA synthetase	231	AA044425	protein metabolism and modification	protein metabolism and modification
SDC3	syndecan 3 (N-syndecan)	233	R39117	cell adhesion, cell surface receptor linked signal transduction, cell cycle	cell adhesion, cell motility, cell surface receptor linked signal transduction
NR1D2	nuclear receptor subfamily 1, group D, member 2	234	AA013256	cell proliferation, intracellular signalling cascade, transcription, oncogenesis	transcription
FOXF2	forkhead box F2	237	N98485	cell organization and biogenesis, cell cycle, transcription	transcription
ZFP36L2	zinc finger protein 36, C3H type-like 2	238	AA039882	cell proliferation	cell proliferation
PPM1B	protein phosphatase 1B (formerly 2C), magnesium-dependent, beta isoform	241	W73157	protein metabolism and modification	protein metabolism and modification
GARP	glycoprotein A repetitions predominant	242	AA026909	lipid metabolism, cell surface receptor linked signal transduction, intracellular signalling cascade	cell surface receptor linked signal transduction
TMOD	tropomodulin	243	AA026182	cell organization and biogenesis, cell death	cell organization and biogenesis
PSPH	phosphoserine phosphatase	245	R00824	lipid metabolism, amino-acid and derivative metabolism, transcription	amino-acid and derivative metabolism
DAPK1	death-associated protein kinase 1	247	AA025275	cell death, intracellular signalling cascade	cell death
TRABID	TRAF-binding protein domain	248	AA005212	cell death, intracellular signalling cascade	intracellular signalling cascade
D5S346	DNA segment, single copy probe LNS-CAI/LNS-CAII (deleted in polyposis	250	R05666	oncogenesis	oncogenesis
CPT1A	carnitine palmitoyltransferase I, liver	253	H12318	lipid metabolism, cell cycle, DNA metabolism	lipid metabolism
FBN1	fibrillin 1 (Marfan syndrome)	255	T91093	cell motility, cell adhesion	cell adhesion, cell motility
PBX3	pre-B-cell leukemia transcription factor 3	257	T91871	lipid metabolism, transcription	transcription
EPS15	epidermal growth factor receptor pathway substrate 15	258	N78949	cell proliferation, cell surface receptor linked signal transduction, DNA metabolism, oncogenesis	cell proliferation, cell surface receptor linked signal transduction
PLA2R1	phospholipase A2 receptor 1, 180kD	259	W04525	cell cycle, DNA metabolism, transcription	cell surface receptor linked signal transduction, defense (immune) response
PACE4	paired basic amino acid cleaving system 4	260	R55773	stress response, protein metabolism and modification, blood coagulation	protein metabolism and modification
PDGFRB	platelet-derived growth factor receptor, beta polypeptide	264	AA046654	cell proliferation, cell surface receptor linked signal transduction, oncogenesis	cell surface receptor linked signal transduction, cell proliferation, oncogenesis
PAPPA	pregnancy-associated plasma protein A	267	R37986	cell proliferation, protein metabolism and modification, lipid metabolism	cell proliferation, protein metabolism and modification
CYP2C9	cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 9	268	T40987	protein metabolism and modification, lipid metabolism, developmental processes	lipid metabolism, developmental processes
FADS2	fatty acid desaturase 2	269	R12563	lipid metabolism	lipid metabolism
SCD	stearoyl-CoA desaturase (delta-9-desaturase)	270, 280, 295	H70783, AA039466, AA054956	lipid metabolism, transcription	lipid metabolism
	Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 248114	271	W86869	developmental processes, oncogenesis	developmental processes, oncogenesis
C1S	complement component 1, s subcomponent	272	AA055521	cell motility, defense (immune) response	cell motility, defense (immune) response
C1R	complement component 1, r subcomponent	273	AA041382	cell motility, defense (immune) response	defense (immune) response, cell motility
LPL	lipoprotein lipase	276	AA043362	transport, lipid metabolism, cell adhesion	cell adhesion, lipid metabolism, transport
	Homo sapiens, clone IMAGE:4296901, mRNA	277	AA026678	cell motility	cell motility, cell cycle
P8	p8 protein (candidate of metastasis 1)	279	AA025313	cell proliferation, developmental processes	cell proliferation
PSA	phosphoserine aminotransferase	282	AA025800	protein metabolism and modification, cell organization and biogenesis, amino-acid and derivative metabolism	cell organization and biogenesis, amino-acid and derivative metabolism, protein metabolism and modification
FDFT1	farnesyl-diphosphate farnesyltransferase 1	283	AA053173	lipid metabolism, developmental processes	lipid metabolism
MLN64	steroidogenic acute regulatory protein related	287	AA045181	transport, lipid metabolism	lipid metabolism, transport
RPL39	ribosomal protein L39	288	AA045480	protein metabolism and modification, cell organization and biogenesis, intracellular signalling cascade, oncogenesis	protein metabolism and modification, cell organization and biogenesis
IDI1	isopentenyl-diphosphate delta isomerase	289	AA045372	cell proliferation, lipid metabolism, intracellular signalling cascade, transcription, oncogenesis	lipid metabolism
OSR1	oxidative-stress responsive 1	290	AA039663	stress response, cell proliferation, lipid metabolism, cell cycle	stress response
INSIG1	insulin induced gene 1	291	AA046719	cell proliferation, cell cycle	cell cycle, cell proliferation
PPAP2B	phosphatidic acid phosphatase type 2B	297	AA045283	lipid metabolism, cell cycle, DNA metabolism	lipid metabolism
AKAP12	A kinase (PRKA) anchor protein (gravin) 12	299	W68000	cell motility, cell organization and biogenesis, cell cycle, intracellular signalling cascade	cell motility, intracellular signalling cascade, cell organization and biogenesis, cell cycle
HEF1	enhancer of filamentation 1 (cas-like docking; Crk-associated substrate related)	300	H65122	cell adhesion, developmental processes, cell organization and biogenesis, cell surface receptor linked signal transduction, cell cycle	cell organization and biogenesis, cell surface receptor linked signal transduction, cell cycle, cell adhesion
PRIM2A	primase, polypeptide 2A (58kD)	304	N68268	cell cycle, DNA metabolism	DNA metabolism, cell cycle
CIC	capicua (Drosophila) homolog	305	AA025540	cell surface receptor linked signal transduction, defense (immune) response	defense (immune) response, cell surface receptor linked signal transduction
LBR	lamin B receptor	306	N93426	cell organization and biogenesis, cell cycle	cell organization and biogenesis, cell cycle
CENPE	centromere protein E (312kD)	308	W90493	cell organization and biogenesis, cell cycle	cell cycle, cell organization and biogenesis
MSH2	mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)	311	R43551	cell cycle, DNA metabolism, oncogenesis	oncogenesis, DNA metabolism, cell cycle
XPO1	exportin 1 (CRM1, yeast, homolog)	312	W93537	transport, cell cycle, DNA metabolism, transcription, protein targeting	transcription, transport, protein targeting
POLD3	polymerase (DNA directed), delta 3	313	W93122	cell cycle, DNA metabolism	DNA metabolism, cell cycle
FAF1	Fas (TNFRSF6) associated factor 1	314	R51770	cell death, cell cycle, intracellular signalling cascade, DNA metabolism	cell death, intracellular signalling cascade
ADAMTS1	a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1	315	AA057170	cell proliferation, cell adhesion, developmental processes, defense (immune) response, circulation	cell proliferation, defense (immune) response, cell adhesion, circulation
ARF4L	ADP-ribosylation factor 4-like	316	AA045331	transport, stress response, protein metabolism and modification, intracellular signalling cascade	stress response, protein metabolism and modification, transport, intracellular signalling cascade
BMP1	bone morphogenetic protein 1	320	AA029677	protein metabolism and modification, developmental processes, cell death, circulation	developmental processes, circulation, cell death, cell motility, protein metabolism and modification, cell proliferation
PCNA	proliferating cell nuclear antigen	321	W73785	cell cycle, DNA metabolism	DNA metabolism, cell cycle
LOC51053	geminin	322	N55327	developmental processes, cell cycle, DNA metabolism, transcription	cell cycle, transcription, DNA metabolism, developmental processes
	Homo sapiens cDNA: FLJ22783 fis, clone KAIA1993	323	W79392	developmental processes	developmental processes
GPC1	glypican 1	324	W72759	cell proliferation, protein metabolism and modification, cell adhesion	cell adhesion, cell proliferation, protein metabolism and modification
TOP2A	topoisomerase (DNA) II alpha (170kD)	325	N53767	transport, cell cycle, DNA metabolism, transcription, protein targeting	cell cycle, DNA metabolism, transcription
ANLN	anillin (Drosophila Scraps homolog), actin binding protein	327	R40626	cell cycle, transcription	cell cycle
MAD2L1	MAD2 (mitotic arrest deficient, yeast, homolog)-like 1	328	R10992	cell cycle	cell cycle
C20orf1	chromosome 20 open reading frame 1	329	H68298	cell proliferation, cell cycle	cell proliferation, cell cycle
CENPF	centromere protein F (350/400kD, mitosin)	331	T48153	cell organization and biogenesis, cell cycle, DNA metabolism	cell cycle, cell organization and biogenesis
RRM1	ribonucleotide reductase M1 polypeptide	332	N93479	cell cycle, DNA metabolism	DNA metabolism, cell cycle
CCNA2	cyclin A2	333	AA001916	cell cycle, DNA metabolism	cell cycle
PMSCL1	polymyositis/scleroderma autoantigen 1 (75kD)	334	R43728	protein metabolism and modification, cell organization and biogenesis	cell organization and biogenesis
FEN1	flap structure-specific endonuclease 1	335	H29274	cell cycle, DNA metabolism	cell cycle, DNA metabolism
KPNA2	karyopherin alpha 2 (RAG cohort 1, importin alpha 1)	336	W86618	transport, protein targeting	transport, protein targeting
RRM2	ribonucleotide reductase M2 polypeptide	338	AA053076	cell cycle, DNA metabolism	cell cycle, DNA metabolism
CDC2	cell division cycle 2, G1 to S and G2 to M	339	W74500	cell cycle, DNA metabolism	cell cycle, DNA metabolism
OCLN	occludin	340	H94471	cell adhesion, cell cycle, DNA metabolism	cell adhesion
CKS2	CDC28 protein kinase 2	341	AA010065	cell cycle, DNA metabolism, transcription	cell cycle, transcription
CCNB1	cyclin B1	342	N90191	cell cycle	cell cycle
	Homo sapiens clone 23605 mRNA sequence	343	R39436	cell cycle, transcription	transcription
PPP4C	protein phosphatase 4 (formerly X), catalytic subunit	345	AA041370	cell proliferation, protein metabolism and modification, intracellular signalling cascade, transcription, oncogenesis	protein metabolism and modification, intracellular signalling cascade
FOS	v-fos FBJ murine osteosarcoma viral oncogene homolog	348	R20750	cell proliferation, transcription, oncogenesis	transcription, cell proliferation, oncogenesis
EGR1	early growth response 1	349	H27557	cell proliferation, transcription, oncogenesis	cell proliferation, transcription
NR4A2	nuclear receptor subfamily 4, group A, member 2	350	N22386	cell cycle, transcription, oncogenesis	cell cycle, transcription
GRO2	GRO2 oncogene	351	T70079	cell motility, defense (immune) response	defense (immune) response, cell motility
GEM	GTP-binding protein overexpressed in skeletal muscle	352	R40776	cell surface receptor linked signal transduction, intracellular signalling cascade	intracellular signalling cascade
PBEF	pre-B-cell colony-enhancing factor	354, 507	AA045438, AA047266	cell proliferation, defense (immune) response, cell motility	cell proliferation, defense (immune) response
ZNF295	zinc finger protein 295	355	T50056	cell proliferation, transcription	transcription
DUSP6	dual specificity phosphatase 6	356, 384	W72836, R59865	protein metabolism and modification, intracellular signalling cascade	protein metabolism and modification, intracellular signalling cascade
TNFAIP3	tumor necrosis factor, alpha-induced protein 3	357	AA053239	cell death, defense (immune) response, transcription	transcription, cell death, defense (immune) response
HIVEP2	human immunodeficiency virus type I enhancer-binding protein 2	358	R39209	defense (immune) response, transcription	transcription, defense (immune) response
SCYA2	small inducible cytokine A2 (monocyte chemotactic protein 1, homologous to mouse Sig-je)	360	T77817	cell motility, defense (immune) response	cell motility, defense (immune) response
IL1B	interleukin 1, beta	362	W47101	cell proliferation, defense (immune) response	cell proliferation, defense (immune) response
IL8	interleukin 8	363	W45324	cell motility, defense (immune) response	cell motility, defense (immune) response
ETS2	v-ets avian erythroblastosis virus E26 oncogene homolog 2	364, 365	R26543, H52671	cell proliferation, cell motility, developmental processes, cell death, defense (immune) response, oncogenesis	oncogenesis, cell proliferation, cell death, transcription, developmental processes
CLDN4	claudin 4	367	W74492	developmental processes, circulation	circulation, cell adhesion
	ESTs, Highly similar to S03700 nonhistone chromosomal protein HMG-17 [H.sapiens]	368	AA057727	defense (immune) response, blood coagulation, DNA metabolism	DNA metabolism, transcription
VEGF	vascular endothelial growth factor	370	AA045836	developmental processes, circulation	developmental processes, circulation, cell proliferation
	Homo sapiens clone IMAGE:451939, mRNA sequence	371	H11257	cell surface receptor linked signal transduction, defense (immune) response, circulation	circulation, cell surface receptor linked signal transduction
MAT2A	methionine adenosyltransferase II, alpha	372	AA039310	cell proliferation, defense (immune) response, amino-acid and derivative metabolism	amino-acid and derivative metabolism
THBD	thrombomodulin	375	AA057068	cell surface receptor linked signal transduction, defense (immune) response, blood coagulation	defense (immune) response, cell surface receptor linked signal transduction, blood coagulation
BMPR2	bone morphogenetic protein receptor, type II (serine/threonine kinase)	376	H96519	cell proliferation, developmental processes, circulation	developmental processes, cell proliferation, circulation
STC1	stanniocalcin 1	378	R48580	transport, circulation, ion homeostasis	transport, ion homeostasis, circulation
RGS4	regulator of G-protein signalling 4	379	AA007419	cell surface receptor linked signal transduction	cell surface receptor linked signal transduction
FCGR2B	Fc fragment of IgG, low affinity IIb, receptor for (CD32)	380	R78403	cell surface receptor linked signal transduction, defense (immune) response	defense (immune) response, cell surface receptor linked signal transduction
ICAM1	intercellular adhesion molecule 1 (CD54), human rhinovirus receptor	382	T62835	cell motility, cell adhesion, defense (immune) response	cell motility, defense (immune) response, cell adhesion
TMEM2	transmembrane protein 2	386	N79533	cell surface receptor linked signal transduction, defense (immune) response, transcription	transcription
FGF7	fibroblast growth factor 7 (keratinocyte growth factor)	387	AA009609	cell proliferation, defense (immune) response, circulation	cell proliferation, circulation
FGF2	fibroblast growth factor 2 (basic)	389	W44678	cell proliferation, cell motility, circulation	cell proliferation, cell motility, circulation
ADRA2C	adrenergic, alpha-2C-, receptor	391	T40595	protein metabolism and modification, cell surface receptor linked signal transduction	cell surface receptor linked signal transduction
FOSL1	FOS-like antigen-1	392	T89996	cell proliferation, transcription	transcription, cell proliferation
SDC2	syndecan 2 (heparan sulfate proteoglycan 1, cell surface-associated, fibroglycan)	393	T79471	cell proliferation, protein metabolism and modification, cell adhesion	cell proliferation, cell adhesion
MKI67	antigen identified by monoclonal antibody Ki-67	394	AA053556	cell proliferation, cell cycle	cell cycle, cell proliferation
RPS2	ribosomal protein S2	395	AA057638	protein metabolism and modification	protein metabolism and modification
SDF1	stromal cell-derived factor 1	396, 446	AA056414, W84538	cell proliferation, cell motility, defense (immune) response	defense (immune) response, cell motility, cell proliferation
RAN	RAN, member RAS oncogene family	397	H23544	transport, cell cycle, oncogenesis, protein targeting	transport, transcription, cell organization and biogenesis, intracellular signalling cascade, cell cycle, protein targeting, oncogenesis
ITGA6	integrin, alpha 6	398	N22383	cell motility, cell adhesion, cell organization and biogenesis, cell surface receptor linked signal transduction	cell organization and biogenesis, cell adhesion, cell motility, cell surface receptor linked signal transduction
ACP1	acid phosphatase 1, soluble	399	AA056583	protein metabolism and modification, intracellular signalling cascade	intracellular signalling cascade, protein metabolism and modification
CDK7	cyclin-dependent kinase 7 (homolog of Xenopus MO15 cdk-activating kinase)	400	AA031961	cell cycle, DNA metabolism, transcription	cell cycle, transcription, DNA metabolism, cell proliferation
SLC25A5	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 5	402	AA028950	transport, cell proliferation, cell motility, energy pathways	energy pathways, transport
RANBP1	RAN binding protein 1	403	N91825	transport, cell organization and biogenesis, cell cycle, intracellular signalling cascade, protein targeting	intracellular signalling cascade, cell organization and biogenesis, transport, protein targeting, cell cycle, transcription
FKBP1A	FK506-binding protein 1A (12kD)	404	AA056621	transport, cell proliferation, protein metabolism and modification, cell motility, defense (immune) response	protein metabolism and modification, transport
NOP56	nucleolar protein (KKE/D repeat)	405	AA056338	stress response, protein metabolism and modification, cell organization and biogenesis	cell organization and biogenesis
	Homo sapiens mRNA; cDNA DKFZp434N1221 (from clone DKFZp434N1221)	406	N71362	protein metabolism and modification	protein metabolism and modification
HSPA8	heat shock 70kD protein 8	407	AA052965	stress response, protein metabolism and modification, cell motility	protein metabolism and modification, stress response
CKAP1	cytoskeleton-associated protein 1	408	AA055578	protein metabolism and modification, cell organization and biogenesis, cell cycle	cell cycle, cell organization and biogenesis, protein metabolism and modification
B4GALT1	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 1	409	AA043796	protein metabolism and modification, lipid metabolism	protein metabolism and modification, lipid metabolism
ESM1	endothelial cell-specific molecule 1	412	W46577	stress response, protein metabolism and modification, cell adhesion, defense (immune) response	defense (immune) response, cell adhesion
DSP	desmoplakin (DPI, DPII)	413	AA056401	stress response, protein metabolism and modification, cell organization and biogenesis	cell organization and biogenesis
HNT	neurotrimin	414, 415	N63308, AA037351	cell adhesion, cell surface receptor linked signal transduction, cell motility	cell adhesion, cell surface receptor linked signal transduction
DNAJB9	DnaJ (Hsp40) homolog, subfamily B, member 9	416	N40987	cell surface receptor linked signal transduction, circulation	circulation
OXTR	oxytocin receptor	421	AA029292	cell proliferation, cell motility, cell surface receptor linked signal transduction	cell proliferation, cell motility, cell surface receptor linked signal transduction
LOC51660	HSPC040 protein	422	N74406	stress response, cell cycle	stress response
EBNA1BP2	EBNA1-binding protein 2	423	AA052986	cell proliferation, protein metabolism and modification, cell organization and biogenesis	cell organization and biogenesis, cell proliferation
COL4A1	collagen, type IV, alpha 1	424	R78226	cell motility, cell adhesion, cell organization and biogenesis	cell adhesion, cell motility
HSPB7	heat shock 27kD protein family, member 7 (cardiovascular)	426	AA044617	stress response, protein metabolism and modification	stress response, protein metabolism and modification
TIMP3	tissue inhibitor of metalloproteinase 3 (Sorsby fundus dystrophy, pseudoinflammatory)	428	AA043969	protein metabolism and modification, cell motility, cell adhesion	cell adhesion, protein metabolism and modification, cell motility
DDX21	DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21	429	AA026141	cell proliferation, cell organization and biogenesis, cell surface receptor linked signal transduction, transcription	cell organization and biogenesis, cell proliferation, transcription
ANPEP	alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)	430	H72904	protein metabolism and modification, cell motility, circulation	protein metabolism and modification, cell motility, circulation
PPIF	peptidylprolyl isomerase F (cyclophilin F)	432	N49296	transport, protein metabolism and modification, cell motility, oncogenesis, circulation	protein metabolism and modification
FDPS	farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase)	434	AA053331	lipid metabolism	lipid metabolism
TM4SF1	transmembrane 4 superfamily member 1	435	N47476	transport, stress response	stress response, transport
HXB	hexabrachion (tenascin C, cytotactin)	436	AA045473	cell motility, cell adhesion, oncogenesis	oncogenesis, cell motility, cell adhesion
DSCR1	Down syndrome critical region gene 1	439	AA058543	transport, cell adhesion, developmental processes, intracellular signalling cascade, circulation	circulation, developmental processes, transcription, intracellular signalling cascade
HSPA1A	heat shock 70kD protein 1A	440	N67200	stress response, protein metabolism and modification, intracellular signalling cascade, protein targeting	protein metabolism and modification, protein targeting, stress response, intracellular signalling cascade
MYO10	myosin X	441	W86798	transport, cell motility, cell adhesion, cell organization and biogenesis	transport, cell motility, cell adhesion, cell organization and biogenesis
TGM2	transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)	443	AA045437	stress response, protein metabolism and modification	protein metabolism and modification, stress response
SSR3	signal sequence receptor, gamma (translocon-associated protein gamma)	444	N73309	cell proliferation, cell motility, defense (immune) response, protein targeting	protein targeting
EDG1	endothelial differentiation, sphingolipid G-protein-coupled receptor, 1	445	N93476	stress response, protein metabolism and modification, cell surface receptor linked signal transduction	cell surface receptor linked signal transduction
WDR1	WD repeat domain 1	448	W19191	stress response, protein metabolism and modification, cell adhesion	cell adhesion
PLOD2	procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2	449	N98463	protein metabolism and modification	protein metabolism and modification
ATP5G1	ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9), isoform 1	450	AA046701	stress response, lipid metabolism, energy pathways	energy pathways, lipid metabolism
PFKP	phosphofructokinase, platelet	452	AA044444	energy pathways	energy pathways
SLC20A1	solute carrier family 20 (phosphate transporter), member 1	453	AA039313	transport, protein metabolism and modification, circulation	circulation, transport
MT1L	metallothionein 1L	456	N80129	stress response, ion homeostasis	stress response, ion homeostasis
MT2A	metallothionein 2A	457	AA037443	stress response, ion homeostasis	stress response, ion homeostasis
ACY1	aminoacylase 1	458	N35315	amino-acid and derivative metabolism	amino-acid and derivative metabolism
CCND1	cyclin D1 (PRAD1: parathyroid adenomatosis 1)	459	T89175	cell cycle, oncogenesis	cell cycle, oncogenesis, cell proliferation
GPM6B	glycoprotein M6B	460	N23200	developmental processes	developmental processes
MT1H	metallothionein 1H	463	H77597	stress response, ion homeostasis	stress response, ion homeostasis
KIAA0165	extra spindle poles, S. cerevisiae, homolog of	465	R42883	cell organization and biogenesis, cell cycle, blood coagulation	cell organization and biogenesis, cell cycle
CDH2	cadherin 2, type 1, N-cadherin (neuronal)	467	W49619	transport, stress response, protein metabolism and modification, cell adhesion, protein targeting	cell adhesion
SERPIND1	serine (or cysteine) proteinase inhibitor, clade D (heparin cofactor), member 1	468	N69996	cell motility, defense (immune) response, blood coagulation	defense (immune) response, cell motility, blood coagulation
GPD1	glycerol-3-phosphate dehydrogenase 1 (soluble)	470	AA007629	energy pathways	energy pathways
TFPI2	tissue factor pathway inhibitor 2	473	AA017446	cell proliferation, cell adhesion, defense (immune) response, blood coagulation	blood coagulation, cell adhesion, cell proliferation, defense (immune) response
PKM2	pyruvate kinase, muscle	474	AA057761	transport, cell organization and biogenesis, cell surface receptor linked signal transduction, energy pathways, circulation	energy pathways
CCT5	chaperonin containing TCP1, subunit 5 (epsilon)	475	AA053249	protein metabolism and modification, cell organization and biogenesis, cell cycle	cell organization and biogenesis, cell cycle, protein metabolism and modification
CLTC	clathrin, heavy polypeptide (Hc)	476	AA058324	transport, cell organization and biogenesis, cell surface receptor linked signal transduction	cell organization and biogenesis, transport
RGS12	regulator of G-protein signalling 12	477	W67134	transport, cell organization and biogenesis, cell surface receptor linked signal transduction	cell surface receptor linked signal transduction
ACLY	ATP citrate lyase	478	AA001722	lipid metabolism	lipid metabolism
FLNB	filamin B, beta (actin-binding protein-278)	479	AA059125	cell organization and biogenesis, cell cycle	cell organization and biogenesis, cell cycle
TPM1	tropomyosin 1 (alpha)	480	AA046749	cell motility	cell motility
SERPINE1	serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1	481	AA046659	cell motility, cell adhesion, defense (immune) response, blood coagulation	cell motility, cell adhesion, blood coagulation, defense (immune) response
FLNA	filamin A, alpha (actin-binding protein-280)	482	AA046721	cell organization and biogenesis, cell cycle, defense (immune) response	cell organization and biogenesis, cell cycle
MAP2K3	mitogen-activated protein kinase kinase 3	483	AA035527	intracellular signalling cascade, defense (immune) response	intracellular signalling cascade, defense (immune) response
NET1	neuroepithelial cell transforming gene 1	484	AA042891	cell proliferation, intracellular signalling cascade, defense (immune) response, oncogenesis	cell cycle, oncogenesis, defense (immune) response, cell proliferation, intracellular signalling cascade, cell organization and biogenesis
PLAUR	plasminogen activator, urokinase receptor	486	W49706	cell adhesion, defense (immune) response, blood coagulation	defense (immune) response, cell adhesion, blood coagulation
ZNF222	zinc finger protein 222	489	R49309	cell motility, defense (immune) response, transcription	transcription
F3	coagulation factor III (thromboplastin, tissue factor)	490	R34833	cell surface receptor linked signal transduction, defense (immune) response, blood coagulation	blood coagulation, defense (immune) response, cell surface receptor linked signal transduction
PTGS2	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	491	R80217	intracellular signalling cascade, defense (immune) response	cell proliferation, lipid metabolism, intracellular signalling cascade, defense (immune) response
ID3	inhibitor of DNA binding 3, dominant negative helix-loop-helix protein	492	W46413	transcription	transcription
NR4A1	nuclear receptor subfamily 4, group A, member 1	493	N94487	cell proliferation, intracellular signalling cascade, transcription	transcription, intracellular signalling cascade, cell proliferation
TIEG	TGFB inducible early growth response	494	AA045731	cell proliferation, developmental processes, cell surface receptor linked signal transduction, transcription	transcription, developmental processes, cell proliferation, cell surface receptor linked signal transduction
CTGF	connective tissue growth factor	496	AA044993	cell proliferation, cell motility, cell surface receptor linked signal transduction	cell surface receptor linked signal transduction, cell motility, cell proliferation
CDKN1A	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	499	N23941	stress response, cell proliferation	cell cycle, cell proliferation, stress response
RPS5	ribosomal protein S5	500	AA057826	protein metabolism and modification, cell organization and biogenesis	protein metabolism and modification, cell organization and biogenesis
NR4A3	nuclear receptor subfamily 4, group A, member 3	501	W42606	cell proliferation, intracellular signalling cascade, transcription, oncogenesis	cell proliferation, transcription
BHLHB2	basic helix-loop-helix domain containing, class B, 2	502	AA026120	cell proliferation, intracellular signalling cascade, transcription, oncogenesis	transcription
JUNB	jun B proto-oncogene	504	N99070	cell proliferation, intracellular signalling cascade, transcription, oncogenesis	transcription, intracellular signalling cascade, cell proliferation, oncogenesis
MCL1	myeloid cell leukemia sequence 1 (BCL2-related)	505, 506	AA044235, R77289	cell death, intracellular signalling cascade, defense (immune) response	intracellular signalling cascade, cell death, defense (immune) response
EDN1	endothelin 1	508	H11003	defense (immune) response, circulation	circulation
IL6	interleukin 6 (interferon, beta 2)	509	N98591	cell proliferation, defense (immune) response	defense (immune) response, cell proliferation
SGK	serum/glucocorticoid regulated kinase	511	AA057359	protein metabolism and modification, intracellular signalling cascade, defense (immune) response	defense (immune) response, protein metabolism and modification, intracellular signalling cascade
COPEB	core promoter element binding protein	512	AA055585	transcription, oncogenesis	transcription

Table 6b Re-classification of known genes without annotations to the 23 broad cellular processes used for learning

GENE SYMBOL	GENE NAME	PROBE NO (Iyer et. al.)	ACCESSION NUMBER	PREDICTIONS FOR THE 23 BROAD CELLULAR PROCESSES USED FOR LEARNING	ANNOTATIONS AT THE MOST SPECIFIC LEVEL OF GO
PGRMC2	progesterone receptor membrane component 2	100	AA031314	cell motility, cell adhesion	signal transduction
FPGT	fucose-1-phosphate guanylyltransferase	107	R38619	transport, cell organization and biogenesis, cell cycle, DNA metabolism	fucose metabolism
DPYD	dihydropyrimidine dehydrogenase	164	N63511	cell surface receptor linked signal transduction, cell death	uridine catabolism, thymidine catabolism
SPR	sepiapterin reductase (7,8-dihydrobiopterin:NADP+ oxidoreductase)	278	AA026314	lipid metabolism, developmental processes, oncogenesis	tetrahydrobiopterin biosynthesistetrahydrobiopterin biosynthesistetrahydrobiopterin biosynthesis
GJB1	gap junction protein, beta 1, 32kD (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked)	286	AA041403	cell proliferation, lipid metabolism, transcription, oncogenesis	cell communication
GCH1	GTP cyclohydrolase 1 (dopa-responsive dystonia)	427	N32784	stress response, protein metabolism and modification, cell organization and biogenesis	tetrahydrobiopterin biosynthesistetrahydrobiopterin biosynthesistetrahydrobiopterin biosynthesis
CTPS	CTP synthase	433	W44416	cell adhesion	CTP biosynthesis, `de novo` pyrimidine biosynthesis
HCS	cytochrome c	454	AA037369	stress response, protein metabolism and modification, cell organization and biogenesis	oxidative phosphorylation
UAP1	UDP-N-acteylglucosamine pyrophosphorylase 1	485	AA040861	cell proliferation, defense (immune) response, blood coagulation	N-acetylglucosamine biosynthesis
SV2B	synaptic vesicle protein 2B homolog	513	AA016304	cell proliferation, intracellular signalling cascade, defense (immune) response	synaptic transmission
UROS	uroporphyrinogen III synthase (congenital erythropoietic porphyria)	515	W88807	cell proliferation, intracellular signalling cascade, defense (immune) response, transcription	heme biosynthesis, uroporphyrinogen III biosynthesis