SZGR2

Summary ?

GeneID	6950
Symbol	TCP1
Synonyms	CCT-alpha\|CCT1\|CCTa\|D6S230E\|TCP-1-alpha
Description	t-complex 1
Reference	MIM:186980\|HGNC:HGNC:11655\|Ensembl:ENSG00000120438\|HPRD:01748\|Vega:OTTHUMG00000015937
Gene type	protein-coding
Map location	6q25.3-q26
Pascal p-value	0.019
Sherlock p-value	0.293
Fetal beta	1.674
DMG	1 (# studies)
Support	STRUCTURAL PLASTICITY G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS G2Cdb.humanPSD G2Cdb.humanPSP CompositeSet

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Jaffe_2016	Genome-wide DNA methylation analysis	This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05.	1
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Association	A combined odds ratio method (Sun et al. 2008), association studies	1	Link to SZGene
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg20673506	6	160210888	TCP1	2.1E-9	-0.017	1.67E-6	DMG:Jaffe_2016

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
VPS4A	0.90	0.86
PSMC4	0.89	0.86
ALAS1	0.88	0.85
VPS26B	0.88	0.85
PPP2R5D	0.87	0.83
PPP2R2D	0.86	0.83
SARS	0.86	0.80
MLX	0.86	0.83
PHF23	0.86	0.84
TOX4	0.86	0.82

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
MT-CO2	-0.78	-0.72
AF347015.8	-0.78	-0.73
AF347015.31	-0.77	-0.73
AF347015.2	-0.76	-0.71
MT-CYB	-0.76	-0.71
AF347015.21	-0.75	-0.72
AF347015.15	-0.74	-0.71
AF347015.27	-0.74	-0.73
AF347015.33	-0.74	-0.70
AF347015.26	-0.73	-0.69

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000166	nucleotide binding	IEA		-
GO:0005524	ATP binding	IEA		-
GO:0051082	unfolded protein binding	IEA		-
GO:0051082	unfolded protein binding	TAS		1630491
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006457	protein folding	IEA		-
GO:0006457	protein folding	TAS		1630491
GO:0007021	tubulin complex assembly	NAS		11532003
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005829	cytosol	TAS		1630491
GO:0005737	cytoplasm	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
CCT2	99D8.1 \| CCT-beta \| CCTB \| MGC142074 \| MGC142076 \| PRO1633 \| TCP-1-beta	chaperonin containing TCP1, subunit 2 (beta)	Affinity Capture-MS	BioGRID	16085932
CCT3	CCT-gamma \| CCTG \| PIG48 \| TCP-1-gamma \| TRIC5	chaperonin containing TCP1, subunit 3 (gamma)	Affinity Capture-MS	BioGRID	16085932
CCT3	CCT-gamma \| CCTG \| PIG48 \| TCP-1-gamma \| TRIC5	chaperonin containing TCP1, subunit 3 (gamma)	-	HPRD	7953530
CCT4	CCT-DELTA \| Cctd \| MGC126164 \| MGC126165 \| SRB	chaperonin containing TCP1, subunit 4 (delta)	Affinity Capture-MS	BioGRID	16085932
CCT5	CCT-epsilon \| CCTE \| KIAA0098 \| TCP-1-epsilon	chaperonin containing TCP1, subunit 5 (epsilon)	-	HPRD	9250675
CCT5	CCT-epsilon \| CCTE \| KIAA0098 \| TCP-1-epsilon	chaperonin containing TCP1, subunit 5 (epsilon)	Affinity Capture-MS	BioGRID	16085932
CCT6A	CCT-zeta \| CCT-zeta-1 \| CCT6 \| Cctz \| HTR3 \| MGC126214 \| MGC126215 \| MoDP-2 \| TCP-1-zeta \| TCP20 \| TCPZ \| TTCP20	chaperonin containing TCP1, subunit 6A (zeta 1)	Affinity Capture-MS	BioGRID	16085932
CCT7	CCT-ETA \| Ccth \| MGC110985 \| Nip7-1 \| TCP-1-eta	chaperonin containing TCP1, subunit 7 (eta)	-	HPRD	9250675
CCT7	CCT-ETA \| Ccth \| MGC110985 \| Nip7-1 \| TCP-1-eta	chaperonin containing TCP1, subunit 7 (eta)	Affinity Capture-MS	BioGRID	16085932
CCT8	C21orf112 \| Cctq \| D21S246 \| KIAA0002 \| PRED71	chaperonin containing TCP1, subunit 8 (theta)	Affinity Capture-MS	BioGRID	16085932
CTTNBP2	C7orf8 \| CORTBP2 \| FLJ34229 \| KIAA1758 \| MGC104579 \| Orf4	cortactin binding protein 2	Affinity Capture-MS	BioGRID	18782753
FANCA	FA \| FA-H \| FA1 \| FAA \| FACA \| FAH \| FANCH \| MGC75158	Fanconi anemia, complementation group A	Two-hybrid	BioGRID	14499622
HDAC3	HD3 \| RPD3 \| RPD3-2	histone deacetylase 3	Affinity Capture-Western Reconstituted Complex	BioGRID	12502735
HSPA8	HSC54 \| HSC70 \| HSC71 \| HSP71 \| HSP73 \| HSPA10 \| LAP1 \| MGC131511 \| MGC29929 \| NIP71	heat shock 70kDa protein 8	Reconstituted Complex	BioGRID	10075921
IGBP1	ALPHA-4 \| IBP1	immunoglobulin (CD79A) binding protein 1	Affinity Capture-MS	BioGRID	16085932
MOBKL3	2C4D \| CGI-95 \| MGC12264 \| MOB1 \| MOB3 \| PREI3	MOB1, Mps One Binder kinase activator-like 3 (yeast)	Affinity Capture-MS	BioGRID	18782753
PDCL	DKFZp564M1863 \| PhLP	phosducin-like	Phosducin-like protein (PhLP) binds to the CCT subunit TCP-1-alpha. This interaction was modeled on a demonstrated interaction between Rat PhLP and human TCP-1-alpha.	BIND	12060742
PPP2CA	PP2Ac \| PP2CA \| RP-C	protein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoform	Affinity Capture-MS	BioGRID	18782753
PPP2CB	PP2CB	protein phosphatase 2 (formerly 2A), catalytic subunit, beta isoform	Affinity Capture-MS	BioGRID	18782753
PPP2R2C	B55-GAMMA \| IMYPNO \| IMYPNO1 \| MGC33570 \| PR52 \| PR55G	protein phosphatase 2 (formerly 2A), regulatory subunit B, gamma isoform	Affinity Capture-MS	BioGRID	18782753
PPP4C	PP4 \| PPH3 \| PPX	protein phosphatase 4 (formerly X), catalytic subunit	Affinity Capture-MS	BioGRID	16085932 \|18715871
STK24	MST-3 \| MST3 \| MST3B \| STE20 \| STK3	serine/threonine kinase 24 (STE20 homolog, yeast)	Affinity Capture-MS	BioGRID	18782753
STK25	DKFZp686J1430 \| SOK1 \| YSK1	serine/threonine kinase 25 (STE20 homolog, yeast)	Affinity Capture-MS	BioGRID	18782753
STRN	MGC125642 \| SG2NA	striatin, calmodulin binding protein	Affinity Capture-MS	BioGRID	18782753
STRN3	SG2NA	striatin, calmodulin binding protein 3	Affinity Capture-MS	BioGRID	18782753
TRAF3IP3	DJ434O14.3 \| FLJ44151 \| MGC117354 \| MGC163289 \| T3JAM	TRAF3 interacting protein 3	Affinity Capture-MS	BioGRID	18782753

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
REACTOME ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS	27	15	All SZGR 2.0 genes in this pathway
REACTOME PREFOLDIN MEDIATED TRANSFER OF SUBSTRATE TO CCT TRIC	28	15	All SZGR 2.0 genes in this pathway
REACTOME PROTEIN FOLDING	53	30	All SZGR 2.0 genes in this pathway
REACTOME FORMATION OF TUBULIN FOLDING INTERMEDIATES BY CCT TRIC	22	11	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF PROTEINS	518	242	All SZGR 2.0 genes in this pathway
NAKAMURA CANCER MICROENVIRONMENT DN	46	29	All SZGR 2.0 genes in this pathway
LIU SOX4 TARGETS DN	309	191	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
TONKS TARGETS OF RUNX1 RUNX1T1 FUSION MONOCYTE UP	204	140	All SZGR 2.0 genes in this pathway
DITTMER PTHLH TARGETS DN	73	51	All SZGR 2.0 genes in this pathway
HUMMEL BURKITTS LYMPHOMA UP	43	27	All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP	1278	748	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN	1781	1082	All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN DN	770	415	All SZGR 2.0 genes in this pathway
DARWICHE SKIN TUMOR PROMOTER UP	142	96	All SZGR 2.0 genes in this pathway
DARWICHE PAPILLOMA RISK LOW UP	162	104	All SZGR 2.0 genes in this pathway
DARWICHE PAPILLOMA RISK HIGH DN	180	110	All SZGR 2.0 genes in this pathway
DARWICHE SQUAMOUS CELL CARCINOMA UP	146	104	All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS FETAL LIVER UP	227	137	All SZGR 2.0 genes in this pathway
DAIRKEE TERT TARGETS UP	380	213	All SZGR 2.0 genes in this pathway
YANG BREAST CANCER ESR1 LASER DN	50	38	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
PUJANA CHEK2 PCC NETWORK	779	480	All SZGR 2.0 genes in this pathway
STARK PREFRONTAL CORTEX 22Q11 DELETION DN	517	309	All SZGR 2.0 genes in this pathway
BASSO B LYMPHOCYTE NETWORK	143	96	All SZGR 2.0 genes in this pathway
PENG LEUCINE DEPRIVATION DN	187	122	All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST DN	309	206	All SZGR 2.0 genes in this pathway
PENG GLUTAMINE DEPRIVATION DN	337	230	All SZGR 2.0 genes in this pathway
TAKAO RESPONSE TO UVB RADIATION UP	86	55	All SZGR 2.0 genes in this pathway
SESTO RESPONSE TO UV C0	107	72	All SZGR 2.0 genes in this pathway
XU GH1 EXOGENOUS TARGETS DN	120	69	All SZGR 2.0 genes in this pathway
MARSON BOUND BY E2F4 UNSTIMULATED	728	415	All SZGR 2.0 genes in this pathway
DAIRKEE CANCER PRONE RESPONSE BPA E2	118	65	All SZGR 2.0 genes in this pathway
WEST ADRENOCORTICAL TUMOR UP	294	199	All SZGR 2.0 genes in this pathway
WANG TUMOR INVASIVENESS DN	210	128	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER POOR SURVIVAL A6	456	285	All SZGR 2.0 genes in this pathway
SAKAI CHRONIC HEPATITIS VS LIVER CANCER UP	83	63	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 17	181	101	All SZGR 2.0 genes in this pathway
KARLSSON TGFB1 TARGETS UP	127	78	All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE DN	841	431	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP	756	494	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
JOHNSTONE PARVB TARGETS 3 DN	918	550	All SZGR 2.0 genes in this pathway
BILANGES RAPAMYCIN SENSITIVE VIA TSC1 AND TSC2	73	37	All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS DN	553	343	All SZGR 2.0 genes in this pathway
JUBAN TARGETS OF SPI1 AND FLI1 DN	92	60	All SZGR 2.0 genes in this pathway
FU INTERACT WITH ALKBH8	13	8	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE VIA P38 COMPLETE	227	151	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-149	332	338	1A	hsa-miR-149^brain	UCUGGCUCCGUGUCUUCACUCC

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: TCP1