SZGR2

Summary ?

GeneID	26960
Symbol	NBEA
Synonyms	BCL8B\|LYST2
Description	neurobeachin
Reference	MIM:604889\|HGNC:HGNC:7648\|Ensembl:ENSG00000172915\|HPRD:05352\|Vega:OTTHUMG00000016724
Gene type	protein-coding
Map location	13q13
Pascal p-value	0.701
Sherlock p-value	0.597
Fetal beta	1.168
DMG	1 (# studies)
Support	G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS G2Cdb.humanPSD G2Cdb.humanPSP CompositeSet Darnell FMRP targets Ascano FMRP targets Potential synaptic genes

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).	2
DNM:Fromer_2014	Whole Exome Sequencing analysis	This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.1835

Section I. Genetics and epigenetics annotation

DNM table

Gene	Chromosome	Position	Ref	Alt	Transcript	AA change	Mutation type	Sift	CG46	Trait	Study
NBEA	chr13	35683436	G	A	NM_015678	p.564V>I	missense			Schizophrenia	DNM:Fromer_2014

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg19557340	13	35516445	NBEA	2.292E-4	-0.302	0.036	DMG:Wockner_2014
cg13652338	13	36172439	MIR548F5;NBEA	3.852E-4	-0.679	0.043	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.

No co-expressed genes in brain regions

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005488	binding	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0012505	endomembrane system	ISS		-
GO:0005802	trans-Golgi network	ISS		-
GO:0005829	cytosol	ISS		-
GO:0005737	cytoplasm	IEA		-
GO:0005886	plasma membrane	ISS		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
SENGUPTA NASOPHARYNGEAL CARCINOMA DN	349	157	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA UP	1821	933	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN	1781	1082	All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER BASAL VS LULMINAL	330	215	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN	428	306	All SZGR 2.0 genes in this pathway
PASQUALUCCI LYMPHOMA BY GC STAGE UP	283	177	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL LONG TERM	302	191	All SZGR 2.0 genes in this pathway
XU GH1 AUTOCRINE TARGETS DN	142	94	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN	701	446	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA C D DN	252	155	All SZGR 2.0 genes in this pathway
MCMURRAY TP53 HRAS COOPERATION RESPONSE DN	67	46	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA PCA1 UP	101	66	All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE	721	492	All SZGR 2.0 genes in this pathway
LU EZH2 TARGETS DN	414	237	All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 6HR DN	91	56	All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 24HR DN	505	328	All SZGR 2.0 genes in this pathway
GABRIELY MIR21 TARGETS	289	187	All SZGR 2.0 genes in this pathway
BILANGES SERUM AND RAPAMYCIN SENSITIVE GENES	68	35	All SZGR 2.0 genes in this pathway
TORCHIA TARGETS OF EWSR1 FLI1 FUSION UP	271	165	All SZGR 2.0 genes in this pathway
RATTENBACHER BOUND BY CELF1	467	251	All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY	1839	928	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-129-5p	1712	1718	1A	hsa-miR-129^brain	CUUUUUGCGGUCUGGGCUUGC
miR-129-5p	1712	1718	1A	hsa-miR-129-5p	CUUUUUGCGGUCUGGGCUUGCU
miR-130/301	672	678	m8	hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
miR-135	736	742	m8	hsa-miR-135a	UAUGGCUUUUUAUUCCUAUGUGA
miR-135	736	742	m8	hsa-miR-135b	UAUGGCUUUUCAUUCCUAUGUG
miR-137	1536	1543	1A,m8	hsa-miR-137	UAUUGCUUAAGAAUACGCGUAG
miR-138	184	190	m8	hsa-miR-138^brain	AGCUGGUGUUGUGAAUC
miR-148/152	1442	1448	1A	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-153	1731	1737	1A	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-17-5p/20/93.mr/106/519.d	674	680	m8	hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU
				hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU
miR-181	1282	1288	1A	hsa-miR-181a^brain	AACAUUCAACGCUGUCGGUGAGU
				hsa-miR-181b^SZ	AACAUUCAUUGCUGUCGGUGGG
				hsa-miR-181c^brain	AACAUUCAACCUGUCGGUGAGU
				hsa-miR-181d^brain	AACAUUCAUUGUUGUCGGUGGGUU
miR-188	453	460	1A,m8	hsa-miR-188	CAUCCCUUGCAUGGUGGAGGGU
miR-19	1368	1374	m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
				hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
				hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
				hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-190	1380	1387	1A,m8	hsa-miR-190	UGAUAUGUUUGAUAUAUUAGGU
miR-194	336	342	1A	hsa-miR-194	UGUAACAGCAACUCCAUGUGGA
miR-203.1	1598	1604	1A	hsa-miR-203	UGAAAUGUUUAGGACCACUAG
miR-204/211	452	458	m8	hsa-miR-204^brain	UUCCCUUUGUCAUCCUAUGCCU
miR-204/211	452	458	m8	hsa-miR-211	UUCCCUUUGUCAUCCUUCGCCU
miR-21	1646	1652	1A	hsa-miR-21^brain	UAGCUUAUCAGACUGAUGUUGA
miR-21	1646	1652	1A	hsa-miR-590	GAGCUUAUUCAUAAAAGUGCAG
miR-218	38	44	1A	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-330	351	357	1A	hsa-miR-330^brain	GCAAAGCACACGGCCUGCAGAGA
miR-331	1178	1184	m8	hsa-miR-331^brain	GCCCCUGGGCCUAUCCUAGAA
miR-342	1697	1703	m8	hsa-miR-342^brain	UCUCACACAGAAAUCGCACCCGUC
miR-377	1696	1702	m8	hsa-miR-377	AUCACACAAAGGCAACUUUUGU
miR-381	1212	1218	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-381	1212	1218	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-409-5p	1655	1661	1A	hsa-miR-409-5p	AGGUUACCCGAGCAACUUUGCA
miR-421	1266	1273	1A,m8	hsa-miR-421	GGCCUCAUUAAAUGUUUGUUG
miR-448	1730	1737	1A,m8	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-485-5p	379	385	m8	hsa-miR-485-5p	AGAGGCUGGCCGUGAUGAAUUC
miR-488	1582	1588	1A	hsa-miR-488	CCCAGAUAAUGGCACUCUCAA
miR-493-5p	1241	1247	m8	hsa-miR-493-5p	UUGUACAUGGUAGGCUUUCAUU
miR-494	1201	1207	m8	hsa-miR-494^brain	UGAAACAUACACGGGAAACCUCUU
miR-496	1677	1683	1A	hsa-miR-496	AUUACAUGGCCAAUCUC
miR-496	1677	1683	1A	hsa-miR-496	AUUACAUGGCCAAUCUC
miR-500	562	568	m8	hsa-miR-500	AUGCACCUGGGCAAGGAUUCUG
miR-539	1291	1297	1A	hsa-miR-539	GGAGAAAUUAUCCUUGGUGUGU

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: NBEA