SZGR2

Summary ?

GeneID	203068
Symbol	TUBB
Synonyms	CDCBM6\|CSCSC1\|M40\|OK/SW-cl.56\|TUBB1\|TUBB5
Description	tubulin beta class I
Reference	MIM:191130\|HGNC:HGNC:20778\|Ensembl:ENSG00000196230\|Vega:OTTHUMG00000031059
Gene type	protein-coding
Map location	6p21.33
Pascal p-value	4.885E-14
Fetal beta	1.148
DMG	2 (# studies)
Support	STRUCTURAL PLASTICITY

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.	4
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).	4
GSMA_I	Genome scan meta-analysis	Psr: 0.033
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.2161

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg25742745	6	30689865	TUBB	2.457E-4	0.337	0.037	DMG:Wockner_2014
cg00783730	6	30689216	TUBB	3.533E-4	-0.161	0.042	DMG:Wockner_2014
cg12915947	6	30691623	TUBB	4.903E-4	0.161	0.047	DMG:Wockner_2014
cg26259575	6	30687946	TUBB	4.65E-9	-0.011	2.7E-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.

No co-expressed genes in brain regions

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000166	nucleotide binding	IEA		-
GO:0003924	GTPase activity	IEA		-
GO:0005525	GTP binding	IEA		-
GO:0005200	structural constituent of cytoskeleton	IEA		-
GO:0042288	MHC class I protein binding	IDA		11120798
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0051225	spindle assembly	IEA		-
GO:0007018	microtubule-based movement	IEA		-
GO:0006928	cell motion	TAS		16130169
GO:0042267	natural killer cell mediated cytotoxicity	NAS		11120798
GO:0051258	protein polymerization	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005856	cytoskeleton	TAS		16130169
GO:0005874	microtubule	IEA		-
GO:0005737	cytoplasm	IEA		-
GO:0043234	protein complex	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ARL8B	ARL10C \| FLJ10702 \| Gie1	ADP-ribosylation factor-like 8B	Affinity Capture-Western	BioGRID	15331635
ASCL2	ASH2 \| HASH2 \| MASH2 \| bHLHa45	achaete-scute complex homolog 2 (Drosophila)	Affinity Capture-Western	BioGRID	12482968
MARK4	FLJ90097 \| KIAA1860 \| MARKL1 \| Nbla00650	MAP/microtubule affinity-regulating kinase 4	Affinity Capture-MS	BioGRID	14594945
NCOA6	AIB3 \| ANTP \| ASC2 \| HOX1.1 \| HOXA7 \| KIAA0181 \| NRC \| PRIP \| RAP250 \| TRBP	nuclear receptor coactivator 6	Affinity Capture-MS Co-purification	BioGRID	12482968
NPHP1	FLJ97602 \| JBTS4 \| NPH1 \| SLSN1	nephronophthisis 1 (juvenile)	Affinity Capture-Western	BioGRID	12872123
RAB8B	FLJ38125	RAB8B, member RAS oncogene family	Affinity Capture-Western	BioGRID	12639940
RASSF1	123F2 \| NORE2A \| RASSF1A \| RDA32 \| REH3P21	Ras association (RalGDS/AF-6) domain family member 1	Reconstituted Complex	BioGRID	14603253
RBBP5	RBQ3 \| SWD1	retinoblastoma binding protein 5	Co-purification	BioGRID	12482968
SDC3	N-syndecan \| SDCN \| SYND3	syndecan 3	Reconstituted Complex	BioGRID	9553134
SIRT2	SIR2 \| SIR2L \| SIR2L2	sirtuin (silent mating type information regulation 2 homolog) 2 (S. cerevisiae)	Biochemical Activity	BioGRID	12620231
SMC3	BAM \| BMH \| CDLS3 \| CSPG6 \| HCAP \| SMC3L1	structural maintenance of chromosomes 3	Affinity Capture-Western	BioGRID	11590136
SYT9	FLJ45896	synaptotagmin IX	Affinity Capture-Western Reconstituted Complex	BioGRID	12966166

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG GAP JUNCTION	90	68	All SZGR 2.0 genes in this pathway
KEGG PATHOGENIC ESCHERICHIA COLI INFECTION	59	36	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 RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES	66	43	All SZGR 2.0 genes in this pathway
REACTOME LOSS OF NLP FROM MITOTIC CENTROSOMES	59	38	All SZGR 2.0 genes in this pathway
REACTOME MITOTIC G2 G2 M PHASES	81	50	All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA DN	663	425	All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL DN	460	312	All SZGR 2.0 genes in this pathway
WANG LMO4 TARGETS UP	372	227	All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY DN	362	238	All SZGR 2.0 genes in this pathway
SCIBETTA KDM5B TARGETS DN	81	55	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN	1375	806	All SZGR 2.0 genes in this pathway
PROVENZANI METASTASIS UP	194	112	All SZGR 2.0 genes in this pathway
MARKEY RB1 ACUTE LOF DN	228	137	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
OUELLET OVARIAN CANCER INVASIVE VS LMP UP	117	85	All SZGR 2.0 genes in this pathway
TOMIDA METASTASIS UP	26	13	All SZGR 2.0 genes in this pathway
LI LUNG CANCER	41	30	All SZGR 2.0 genes in this pathway
MATTIOLI MGUS VS PCL	116	62	All SZGR 2.0 genes in this pathway
HERNANDEZ MITOTIC ARREST BY DOCETAXEL 1 DN	38	23	All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER	747	453	All SZGR 2.0 genes in this pathway
WANG METHYLATED IN BREAST CANCER	35	25	All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS UP	414	287	All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER UP	358	245	All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP	479	299	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN	637	377	All SZGR 2.0 genes in this pathway
WEI MYCN TARGETS WITH E BOX	795	478	All SZGR 2.0 genes in this pathway
CAFFAREL RESPONSE TO THC DN	31	23	All SZGR 2.0 genes in this pathway
CAFFAREL RESPONSE TO THC 24HR 5 UP	34	23	All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS	734	436	All SZGR 2.0 genes in this pathway
MORI PRE BI LYMPHOCYTE UP	80	54	All SZGR 2.0 genes in this pathway
MORI LARGE PRE BII LYMPHOCYTE UP	86	49	All SZGR 2.0 genes in this pathway
MORI IMMATURE B LYMPHOCYTE DN	90	55	All SZGR 2.0 genes in this pathway
RADAEVA RESPONSE TO IFNA1 UP	52	40	All SZGR 2.0 genes in this pathway
UEDA PERIFERAL CLOCK	169	111	All SZGR 2.0 genes in this pathway
SASAKI ADULT T CELL LEUKEMIA	176	122	All SZGR 2.0 genes in this pathway
PENG GLUTAMINE DEPRIVATION DN	337	230	All SZGR 2.0 genes in this pathway
BHATTACHARYA EMBRYONIC STEM CELL	89	60	All SZGR 2.0 genes in this pathway
HASLINGER B CLL WITH 13Q14 DELETION	24	18	All SZGR 2.0 genes in this pathway
LEI MYB TARGETS	318	215	All SZGR 2.0 genes in this pathway
IGLESIAS E2F TARGETS UP	151	103	All SZGR 2.0 genes in this pathway
ZAMORA NOS2 TARGETS UP	69	41	All SZGR 2.0 genes in this pathway
LEE CALORIE RESTRICTION NEOCORTEX UP	83	66	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 16HR DN	86	62	All SZGR 2.0 genes in this pathway
RHODES CANCER META SIGNATURE	64	47	All SZGR 2.0 genes in this pathway
MODY HIPPOCAMPUS NEONATAL	35	25	All SZGR 2.0 genes in this pathway
KRASNOSELSKAYA ILF3 TARGETS UP	38	24	All SZGR 2.0 genes in this pathway
RHODES UNDIFFERENTIATED CANCER	69	44	All SZGR 2.0 genes in this pathway
YAMAZAKI TCEB3 TARGETS DN	215	132	All SZGR 2.0 genes in this pathway
GERHOLD ADIPOGENESIS DN	64	44	All SZGR 2.0 genes in this pathway
LEE AGING NEOCORTEX UP	89	59	All SZGR 2.0 genes in this pathway
WELCSH BRCA1 TARGETS UP	198	132	All SZGR 2.0 genes in this pathway
HEDENFALK BREAST CANCER BRCA1 VS BRCA2	163	113	All SZGR 2.0 genes in this pathway
BRACHAT RESPONSE TO CAMPTOTHECIN DN	46	31	All SZGR 2.0 genes in this pathway
BACOLOD RESISTANCE TO ALKYLATING AGENTS DN	60	45	All SZGR 2.0 genes in this pathway
BANDRES RESPONSE TO CARMUSTIN MGMT 48HR UP	18	13	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 12HR DN	101	64	All SZGR 2.0 genes in this pathway
ZHONG SECRETOME OF LUNG CANCER AND ENDOTHELIUM	66	47	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 1	528	324	All SZGR 2.0 genes in this pathway
MARSON BOUND BY E2F4 UNSTIMULATED	728	415	All SZGR 2.0 genes in this pathway
SARRIO EPITHELIAL MESENCHYMAL TRANSITION UP	180	114	All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN DN	249	165	All SZGR 2.0 genes in this pathway
TOYOTA TARGETS OF MIR34B AND MIR34C	463	262	All SZGR 2.0 genes in this pathway
HONMA DOCETAXEL RESISTANCE	34	23	All SZGR 2.0 genes in this pathway
BLUM RESPONSE TO SALIRASIB DN	342	220	All SZGR 2.0 genes in this pathway
WANG TUMOR INVASIVENESS UP	374	247	All SZGR 2.0 genes in this pathway
PIONTEK PKD1 TARGETS DN	18	12	All SZGR 2.0 genes in this pathway
CHAUHAN RESPONSE TO METHOXYESTRADIOL DN	102	65	All SZGR 2.0 genes in this pathway
CHANG CYCLING GENES	148	83	All SZGR 2.0 genes in this pathway
HOFFMANN LARGE TO SMALL PRE BII LYMPHOCYTE UP	163	102	All SZGR 2.0 genes in this pathway
LEE EARLY T LYMPHOCYTE UP	107	59	All SZGR 2.0 genes in this pathway
CHEN METABOLIC SYNDROM NETWORK	1210	725	All SZGR 2.0 genes in this pathway
HSIAO HOUSEKEEPING GENES	389	245	All SZGR 2.0 genes in this pathway
ROME INSULIN TARGETS IN MUSCLE UP	442	263	All SZGR 2.0 genes in this pathway
KOBAYASHI EGFR SIGNALING 24HR DN	251	151	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
WHITFIELD CELL CYCLE G2	182	102	All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT	567	365	All SZGR 2.0 genes in this pathway
BAKKER FOXO3 TARGETS DN	187	109	All SZGR 2.0 genes in this pathway
BILANGES SERUM SENSITIVE GENES	90	54	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
KOINUMA TARGETS OF SMAD2 OR SMAD3	824	528	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
GUO TARGETS OF IRS1 AND IRS2	98	67	All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A	770	480	All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN	784	464	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-200bc/429	541	548	1A,m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU

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: TUBB