SZGR2

Summary ?

GeneID	1948
Symbol	EFNB2
Synonyms	EPLG5\|HTKL\|Htk-L\|LERK5
Description	ephrin-B2
Reference	MIM:600527\|HGNC:HGNC:3227\|Ensembl:ENSG00000125266\|HPRD:02754\|Vega:OTTHUMG00000017324
Gene type	protein-coding
Map location	13q33
Pascal p-value	0.247
Sherlock p-value	0.303
Fetal beta	1.958
DMG	1 (# studies)
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
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.
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenias	Click to show details
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: 0.0172

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg24929737	13	107188614	EFNB2	1.98E-9	-0.008	1.63E-6	DMG:Jaffe_2016

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs4646491	chr1	47280883	EFNB2	1948		0.1		trans
rs521173	chr4	169244628	EFNB2	1948		0.19		trans

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
EGR2	0.84	0.86
FBXL16	0.82	0.84
ADRB1	0.82	0.77
NR4A1	0.80	0.81
EGR1	0.80	0.86
C2orf55	0.78	0.91
CYP46A1	0.77	0.87
DDN	0.77	0.90
RAB40B	0.77	0.80
INF2	0.76	0.73

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
TUBB2B	-0.43	-0.68
HEBP2	-0.43	-0.76
KIAA1949	-0.42	-0.60
RBMX2	-0.42	-0.71
DYNLT1	-0.41	-0.72
TRAF4	-0.41	-0.67
GTF3C6	-0.41	-0.56
UBE2L6	-0.41	-0.54
IDH1	-0.40	-0.58
YBX1	-0.40	-0.59

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005515	protein binding	IEA		-
GO:0046875	ephrin receptor binding	TAS		8559144
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007399	nervous system development	IEA	neurite (GO term level: 5)	-
GO:0001945	lymph vessel development	IEA		-
GO:0007267	cell-cell signaling	TAS		8559144
GO:0009887	organ morphogenesis	IEA		-
GO:0007275	multicellular organismal development	IEA		-
GO:0030154	cell differentiation	IEA		-
GO:0044419	interspecies interaction between organisms	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005886	plasma membrane	TAS		8660976
GO:0005887	integral to plasma membrane	TAS		8660976

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG AXON GUIDANCE	129	103	All SZGR 2.0 genes in this pathway
PID EPHB FWD PATHWAY	40	38	All SZGR 2.0 genes in this pathway
PID EPHRINB REV PATHWAY	30	25	All SZGR 2.0 genes in this pathway
FRASOR TAMOXIFEN RESPONSE UP	51	36	All SZGR 2.0 genes in this pathway
SENGUPTA NASOPHARYNGEAL CARCINOMA UP	294	178	All SZGR 2.0 genes in this pathway
DOANE RESPONSE TO ANDROGEN DN	241	146	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN	1375	806	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
PROVENZANI METASTASIS UP	194	112	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION KRAS UP	126	72	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION CDC25 UP	120	73	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION UP	552	347	All SZGR 2.0 genes in this pathway
VANHARANTA UTERINE FIBROID UP	45	26	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN UP	1142	669	All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN UP	612	367	All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA UP	536	340	All SZGR 2.0 genes in this pathway
KAN RESPONSE TO ARSENIC TRIOXIDE	123	80	All SZGR 2.0 genes in this pathway
KOBAYASHI RESPONSE TO ROMIDEPSIN	19	14	All SZGR 2.0 genes in this pathway
DAUER STAT3 TARGETS UP	49	35	All SZGR 2.0 genes in this pathway
SEITZ NEOPLASTIC TRANSFORMATION BY 8P DELETION UP	73	47	All SZGR 2.0 genes in this pathway
DACOSTA ERCC3 ALLELE XPCS VS TTD UP	28	19	All SZGR 2.0 genes in this pathway
WU CELL MIGRATION	184	114	All SZGR 2.0 genes in this pathway
GEORGES TARGETS OF MIR192 AND MIR215	893	528	All SZGR 2.0 genes in this pathway
HADDAD B LYMPHOCYTE PROGENITOR	293	193	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 STEM CELL LONG TERM	302	191	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN	830	547	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 8HR UP	105	73	All SZGR 2.0 genes in this pathway
HAN JNK SINGALING UP	35	21	All SZGR 2.0 genes in this pathway
DAZARD RESPONSE TO UV NHEK DN	318	220	All SZGR 2.0 genes in this pathway
TSENG IRS1 TARGETS UP	113	71	All SZGR 2.0 genes in this pathway
XU GH1 AUTOCRINE TARGETS DN	142	94	All SZGR 2.0 genes in this pathway
TSENG ADIPOGENIC POTENTIAL UP	30	19	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 5	482	296	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION UP	461	298	All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS PTEN DN	353	226	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP	863	514	All SZGR 2.0 genes in this pathway
BONCI TARGETS OF MIR15A AND MIR16 1	91	75	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL DN	216	143	All SZGR 2.0 genes in this pathway
VART KSHV INFECTION ANGIOGENIC MARKERS UP	165	118	All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS DN	435	289	All SZGR 2.0 genes in this pathway
LEE DOUBLE POLAR THYMOCYTE	27	17	All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 60HR UP	293	203	All SZGR 2.0 genes in this pathway
YAGI AML WITH T 9 11 TRANSLOCATION	130	87	All SZGR 2.0 genes in this pathway
CAIRO LIVER DEVELOPMENT UP	166	105	All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE	721	492	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 6	75	48	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 4HR UP	55	41	All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 24HR DN	505	328	All SZGR 2.0 genes in this pathway
THILLAINADESAN ZNF217 TARGETS DN	9	5	All SZGR 2.0 genes in this pathway
WIERENGA STAT5A TARGETS DN	213	127	All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS NOT VIA AKT1 DN	88	61	All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS VIA AKT1 DN	82	51	All SZGR 2.0 genes in this pathway
DELPUECH FOXO3 TARGETS DN	41	27	All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS UP	682	433	All SZGR 2.0 genes in this pathway
IKEDA MIR1 TARGETS UP	53	39	All SZGR 2.0 genes in this pathway
LOPEZ TRANSLATION VIA FN1 SIGNALING	35	21	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE VIA P38 PARTIAL	160	106	All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM B	517	302	All SZGR 2.0 genes in this pathway
HOLLEMAN VINCRISTINE RESISTANCE B ALL UP	38	22	All SZGR 2.0 genes in this pathway
ZWANG CLASS 1 TRANSIENTLY INDUCED BY EGF	516	308	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-1/206	3227	3234	1A,m8	hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
miR-103/107	3027	3033	1A	hsa-miR-103^brain	AGCAGCAUUGUACAGGGCUAUGA
miR-103/107	3027	3033	1A	hsa-miR-107^brain	AGCAGCAUUGUACAGGGCUAUCA
miR-124.1	1865	1871	m8	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-124/506	1865	1871	1A	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	1865	1871	1A	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-129-5p	1717	1723	m8	hsa-miR-129^brain	CUUUUUGCGGUCUGGGCUUGC
				hsa-miR-129-5p	CUUUUUGCGGUCUGGGCUUGCU
				hsa-miR-129^brain	CUUUUUGCGGUCUGGGCUUGC
				hsa-miR-129-5p	CUUUUUGCGGUCUGGGCUUGCU
miR-130/301	2984	2990	m8	hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
miR-146	2116	2122	1A	hsa-miR-146a	UGAGAACUGAAUUCCAUGGGUU
miR-146	2116	2122	1A	hsa-miR-146b^brain	UGAGAACUGAAUUCCAUAGGCU
miR-148/152	2985	2991	m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-15/16/195/424/497	1125	1131	1A	hsa-miR-15a^brain	UAGCAGCACAUAAUGGUUUGUG
				hsa-miR-16^brain	UAGCAGCACGUAAAUAUUGGCG
				hsa-miR-15b^brain	UAGCAGCACAUCAUGGUUUACA
				hsa-miR-195^SZ	UAGCAGCACAGAAAUAUUGGC
				hsa-miR-424	CAGCAGCAAUUCAUGUUUUGAA
				hsa-miR-497	CAGCAGCACACUGUGGUUUGU
miR-153	2018	2025	1A,m8	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-182	3018	3025	1A,m8	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-188	1530	1537	1A,m8	hsa-miR-188	CAUCCCUUGCAUGGUGGAGGGU
miR-19	2983	2989	m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	2983	2989	m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-192/215	1216	1222	1A	hsa-miR-192	CUGACCUAUGAAUUGACAGCC
miR-192/215	1216	1222	1A	hsa-miR-215	AUGACCUAUGAAUUGACAGAC
miR-200bc/429	3101	3108	1A,m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-218	1426	1432	m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-324-3p	2967	2973	m8	hsa-miR-324-3p	CCACUGCCCCAGGUGCUGCUGG
miR-330	1096	1102	m8	hsa-miR-330^brain	GCAAAGCACACGGCCUGCAGAGA
miR-339	1154	1160	1A	hsa-miR-339	UCCCUGUCCUCCAGGAGCUCA
miR-369-3p	3103	3109	m8	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-375	959	965	1A	hsa-miR-375	UUUGUUCGUUCGGCUCGCGUGA
miR-381	2918	2924	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-448	2019	2025	1A	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-450	2141	2147	1A	hsa-miR-450	UUUUUGCGAUGUGUUCCUAAUA
miR-450	2141	2147	1A	hsa-miR-450	UUUUUGCGAUGUGUUCCUAAUA
miR-494	3239	3245	1A	hsa-miR-494^brain	UGAAACAUACACGGGAAACCUCUU
miR-503	1125	1131	1A	hsa-miR-503	UAGCAGCGGGAACAGUUCUGCAG
miR-96	3019	3025	1A	hsa-miR-96^brain	UUUGGCACUAGCACAUUUUUGC

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: EFNB2