SZGR2

Summary ?

GeneID	896
Symbol	CCND3
Synonyms	-
Description	cyclin D3
Reference	MIM:123834\|HGNC:HGNC:1585\|Ensembl:ENSG00000112576\|HPRD:00452\|Vega:OTTHUMG00000014690
Gene type	protein-coding
Map location	6p21
Pascal p-value	0.073
Sherlock p-value	0.998
Fetal beta	-1.124
DMG	1 (# studies)

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Wockner_2014	Genome-wide DNA methylation analysis	This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24).	1
GSMA_I	Genome scan meta-analysis	Psr: 0.033
GSMA_IIE	Genome scan meta-analysis (European-ancestry samples)	Psr: 0.04433
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.3258

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg04111789	6	41908262	CCND3	4.008E-4	0.571	0.044	DMG:Wockner_2014

Section II. Transcriptome annotation

General gene expression (GTEx)

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
POLR1B	0.94	0.93
ADNP	0.94	0.92
RBM12	0.93	0.94
EPC2	0.93	0.93
ZNF564	0.93	0.91
RSPRY1	0.93	0.93
ZNF709	0.93	0.89
TCEB3	0.93	0.90
NCOA5	0.93	0.91
ZNF518B	0.93	0.91

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AIFM3	-0.76	-0.81
MT-CO2	-0.74	-0.86
S100B	-0.73	-0.83
HLA-F	-0.73	-0.76
HSD17B14	-0.73	-0.82
FXYD1	-0.73	-0.86
AF347015.31	-0.73	-0.84
AF347015.27	-0.72	-0.82
AF347015.33	-0.72	-0.83
MT-CYB	-0.71	-0.84

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004693	cyclin-dependent protein kinase activity	IEA	neuron (GO term level: 8)	-
GO:0005515	protein binding	IEA		-
GO:0005515	protein binding	IPI		11896535 \|15232106 \|17274640 \|17517622
GO:0019901	protein kinase binding	IPI		8114739
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0001934	positive regulation of protein amino acid phosphorylation	IDA		8114739
GO:0007165	signal transduction	IEA		-
GO:0007049	cell cycle	IEA		-
GO:0042098	T cell proliferation	IEA		-
GO:0051301	cell division	IEA		-
GO:0045737	positive regulation of cyclin-dependent protein kinase activity	IDA		8114739
GO:0051726	regulation of cell cycle	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000307	cyclin-dependent protein kinase holoenzyme complex	IDA		8114739
GO:0005634	nucleus	IEA		-
GO:0005737	cytoplasm	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
AKAP8	AKAP95 \| DKFZp586B1222	A kinase (PRKA) anchor protein 8	-	HPRD,BioGRID	14641107
AREG	AR \| CRDGF \| MGC13647 \| SDGF	amphiregulin	-	HPRD	11469683
ATP5C1	ATP5C \| ATP5CL1	ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1	Two-hybrid	BioGRID	16169070
CASP2	CASP-2 \| ICH-1L \| ICH-1L/1S \| ICH1 \| NEDD2	caspase 2, apoptosis-related cysteine peptidase	-	HPRD,BioGRID	12011445
CDC2L1	CDC2L2 \| CDK11 \| CDK11-p110 \| CDK11-p46 \| CDK11-p58 \| CLK-1 \| FLJ59152 \| PK58 \| p58 \| p58CDC2L1 \| p58CLK-1	cell division cycle 2-like 1 (PITSLRE proteins)	-	HPRD,BioGRID	12082095
CDK4	CMM3 \| MGC14458 \| PSK-J3	cyclin-dependent kinase 4	-	HPRD,BioGRID	10342870
CDK6	MGC59692 \| PLSTIRE \| STQTL11	cyclin-dependent kinase 6	-	HPRD,BioGRID	8114739 \|11360184
CDKN1A	CAP20 \| CDKN1 \| CIP1 \| MDA-6 \| P21 \| SDI1 \| WAF1 \| p21CIP1	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	Two-hybrid	BioGRID	16189514
CDKN1B	CDKN4 \| KIP1 \| MEN1B \| MEN4 \| P27KIP1	cyclin-dependent kinase inhibitor 1B (p27, Kip1)	Affinity Capture-Western Reconstituted Complex Two-hybrid	BioGRID	10342870 \|11360184 \|16189514
CRABP2	CRABP-II \| RBP6	cellular retinoic acid binding protein 2	in vitro in vivo Two-hybrid	BioGRID	12482873
DMTF1	DMP1 \| DMTF \| FLJ41265 \| hDMP1	cyclin D binding myb-like transcription factor 1	-	HPRD	8887674
DTNBP1	DBND \| DKFZp564K192 \| FLJ30031 \| HPS7 \| MGC20210 \| My031 \| SDY	dystrobrevin binding protein 1	Two-hybrid	BioGRID	16189514
EFEMP2	FBLN4 \| MBP1 \| UPH1	EGF-containing fibulin-like extracellular matrix protein 2	Two-hybrid	BioGRID	16189514
EIF3K	ARG134 \| EIF3-p28 \| EIF3S12 \| HSPC029 \| M9 \| MSTP001 \| PLAC-24 \| PLAC24 \| PRO1474 \| PTD001	eukaryotic translation initiation factor 3, subunit K	-	HPRD,BioGRID	15327989
MAF1	MGC20332 \| MGC31779 \| MGC39758	MAF1 homolog (S. cerevisiae)	Two-hybrid	BioGRID	16189514
MCM10	CNA43 \| DNA43 \| MGC126776 \| PRO2249	minichromosome maintenance complex component 10	Affinity Capture-Western	BioGRID	16189514
MCM10	CNA43 \| DNA43 \| MGC126776 \| PRO2249	minichromosome maintenance complex component 10	-	HPRD	15232106
NPDC1	CAB \| CAB- \| CAB-1 \| CAB1 \| DKFZp586J0523	neural proliferation, differentiation and control, 1	-	HPRD,BioGRID	11042687
PCNA	MGC8367	proliferating cell nuclear antigen	-	HPRD,BioGRID	7908906
RARA	NR1B1 \| RAR	retinoic acid receptor, alpha	in vitro in vivo Two-hybrid	BioGRID	12482873
RB1	OSRC \| RB \| p105-Rb \| pRb \| pp110	retinoblastoma 1	Two-hybrid	BioGRID	17972097
RBX1	BA554C12.1 \| MGC13357 \| MGC1481 \| RNF75 \| ROC1	ring-box 1	Affinity Capture-Western	BioGRID	11311237
TSC2	FLJ43106 \| LAM \| TSC4	tuberous sclerosis 2	Affinity Capture-Western	BioGRID	16357142

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG CELL CYCLE	128	84	All SZGR 2.0 genes in this pathway
KEGG P53 SIGNALING PATHWAY	69	45	All SZGR 2.0 genes in this pathway
KEGG WNT SIGNALING PATHWAY	151	112	All SZGR 2.0 genes in this pathway
KEGG FOCAL ADHESION	201	138	All SZGR 2.0 genes in this pathway
KEGG JAK STAT SIGNALING PATHWAY	155	105	All SZGR 2.0 genes in this pathway
BIOCARTA CELLCYCLE PATHWAY	23	15	All SZGR 2.0 genes in this pathway
WNT SIGNALING	89	71	All SZGR 2.0 genes in this pathway
PID E2F PATHWAY	74	48	All SZGR 2.0 genes in this pathway
PID AR PATHWAY	61	46	All SZGR 2.0 genes in this pathway
PID IL2 STAT5 PATHWAY	30	23	All SZGR 2.0 genes in this pathway
PID RB 1PATHWAY	65	46	All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY	396	292	All SZGR 2.0 genes in this pathway
REACTOME CELL CYCLE	421	253	All SZGR 2.0 genes in this pathway
REACTOME CELL CYCLE MITOTIC	325	185	All SZGR 2.0 genes in this pathway
REACTOME G1 PHASE	38	23	All SZGR 2.0 genes in this pathway
REACTOME MITOTIC G1 G1 S PHASES	137	79	All SZGR 2.0 genes in this pathway
REACTOME TRANSCRIPTIONAL REGULATION OF WHITE ADIPOCYTE DIFFERENTIATION	72	53	All SZGR 2.0 genes in this pathway
LIU SOX4 TARGETS DN	309	191	All SZGR 2.0 genes in this pathway
BASAKI YBX1 TARGETS UP	290	177	All SZGR 2.0 genes in this pathway
OSMAN BLADDER CANCER UP	404	246	All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY DN	362	238	All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 1 UP	380	236	All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 UP	418	263	All SZGR 2.0 genes in this pathway
TONKS TARGETS OF RUNX1 RUNX1T1 FUSION HSC DN	187	115	All SZGR 2.0 genes in this pathway
ELVIDGE HYPOXIA DN	146	94	All SZGR 2.0 genes in this pathway
ELVIDGE HYPOXIA BY DMOG DN	59	40	All SZGR 2.0 genes in this pathway
ELVIDGE HIF1A TARGETS UP	67	40	All SZGR 2.0 genes in this pathway
ELVIDGE HIF1A AND HIF2A TARGETS UP	41	22	All SZGR 2.0 genes in this pathway
NUNODA RESPONSE TO DASATINIB IMATINIB UP	29	20	All SZGR 2.0 genes in this pathway
BAKER HEMATOPOIESIS STAT3 TARGETS	16	12	All SZGR 2.0 genes in this pathway
BAKER HEMATOPOESIS STAT5 TARGETS	7	7	All SZGR 2.0 genes in this pathway
MYLLYKANGAS AMPLIFICATION HOT SPOT 15	13	9	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 UP	309	199	All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK	1652	1023	All SZGR 2.0 genes in this pathway
PUJANA BRCA2 PCC NETWORK	423	265	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN	637	377	All SZGR 2.0 genes in this pathway
GUENTHER GROWTH SPHERICAL VS ADHERENT DN	26	19	All SZGR 2.0 genes in this pathway
HE PTEN TARGETS UP	16	15	All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 480 HELA	164	118	All SZGR 2.0 genes in this pathway
SHIN B CELL LYMPHOMA CLUSTER 3	28	23	All SZGR 2.0 genes in this pathway
MORI IMMATURE B LYMPHOCYTE DN	90	55	All SZGR 2.0 genes in this pathway
MORI MATURE B LYMPHOCYTE DN	75	43	All SZGR 2.0 genes in this pathway
ROSS ACUTE MYELOID LEUKEMIA CBF	82	57	All SZGR 2.0 genes in this pathway
GOLUB ALL VS AML UP	24	20	All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS B LYMPHOCYTE DN	38	25	All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK UP	87	58	All SZGR 2.0 genes in this pathway
POMEROY MEDULLOBLASTOMA DESMOPLASIC VS CLASSIC DN	59	35	All SZGR 2.0 genes in this pathway
TENEDINI MEGAKARYOCYTE MARKERS	66	48	All SZGR 2.0 genes in this pathway
CROMER METASTASIS UP	79	46	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR UP	240	152	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS MATURE CELL	293	160	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
DELASERNA MYOD TARGETS UP	89	51	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 2	72	52	All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY UP	487	303	All SZGR 2.0 genes in this pathway
BILD E2F3 ONCOGENIC SIGNATURE	246	153	All SZGR 2.0 genes in this pathway
GHO ATF5 TARGETS DN	16	10	All SZGR 2.0 genes in this pathway
HILLION HMGA1B TARGETS	92	68	All SZGR 2.0 genes in this pathway
LEIN CHOROID PLEXUS MARKERS	103	61	All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 STIMULATED	1022	619	All SZGR 2.0 genes in this pathway
MARZEC IL2 SIGNALING UP	115	80	All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS PTEN DN	353	226	All SZGR 2.0 genes in this pathway
AMBROSINI FLAVOPIRIDOL TREATMENT TP53	109	63	All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL OPTIMAL DEBULKING	246	152	All SZGR 2.0 genes in this pathway
BLUM RESPONSE TO SALIRASIB DN	342	220	All SZGR 2.0 genes in this pathway
GRESHOCK CANCER COPY NUMBER UP	323	240	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA D CLUSTER DN	40	26	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
LEE DIFFERENTIATING T LYMPHOCYTE	200	115	All SZGR 2.0 genes in this pathway
WOO LIVER CANCER RECURRENCE UP	105	75	All SZGR 2.0 genes in this pathway
YAGI AML WITH T 8 21 TRANSLOCATION	368	247	All SZGR 2.0 genes in this pathway
YAGI AML WITH 11Q23 REARRANGED	351	238	All SZGR 2.0 genes in this pathway
KOBAYASHI EGFR SIGNALING 24HR DN	251	151	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA PCA3 DN	69	38	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL IL3RA	9	6	All SZGR 2.0 genes in this pathway
MARTENS BOUND BY PML RARA FUSION	456	287	All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP	682	440	All SZGR 2.0 genes in this pathway
HIRSCH CELLULAR TRANSFORMATION SIGNATURE DN	103	67	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 DN	918	550	All SZGR 2.0 genes in this pathway
ZHU SKIL TARGETS DN	9	5	All SZGR 2.0 genes in this pathway
DORMOY ELAVL1 TARGETS	17	10	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION UP	570	339	All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN	784	464	All SZGR 2.0 genes in this pathway
BOUDOUKHA BOUND BY IGF2BP2	111	59	All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family	Target position			miRNA ID	miRNA seq
miRNA family	UTR start	UTR end	Match method	miRNA ID	miRNA seq
miR-130/301	157	163	1A	hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
miR-330	571	577	m8	hsa-miR-330^brain	GCAAAGCACACGGCCUGCAGAGA

SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.

Gene Page: CCND3