SZGR2

Summary ?

GeneID	627
Symbol	BDNF
Synonyms	ANON2\|BULN2
Description	brain-derived neurotrophic factor
Reference	MIM:113505\|HGNC:HGNC:1033\|Ensembl:ENSG00000176697\|HPRD:00214\|Vega:OTTHUMG00000178797
Gene type	protein-coding
Map location	11p13
Pascal p-value	0.002
Sherlock p-value	0.855
Fetal beta	-1.443
DMG	1 (# studies)
eGene	Nucleus accumbens basal ganglia Putamen basal ganglia Myers' cis & trans
Support	NEUROTROPHIN SIGNALING Potential synaptic genes

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	2	Link to SZGene
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenics,schizotypy,schizophrenias,schizotypal	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 10

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg10558494	11	27721280	BDNF	1.68E-8	-0.011	6.13E-6	DMG:Jaffe_2016

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs6474972		0	BDNF	627		0.19		trans
rs12452652	chr17	72235560	BDNF	627		0.09		trans
rs11030023	11	27505351	BDNF	ENSG00000176697.14	4.073E-6	0.03	238254	gtex_brain_putamen_basal
rs10835187	11	27505677	BDNF	ENSG00000176697.14	1.53E-6	0.03	237928	gtex_brain_putamen_basal
rs112806008	11	27506369	BDNF	ENSG00000176697.14	3.968E-6	0.03	237236	gtex_brain_putamen_basal
rs10767644	11	27520671	BDNF	ENSG00000176697.14	2.664E-6	0.03	222934	gtex_brain_putamen_basal
rs11030036	11	27525124	BDNF	ENSG00000176697.14	2.798E-6	0.03	218481	gtex_brain_putamen_basal
rs12362567	11	27526645	BDNF	ENSG00000176697.14	3.622E-6	0.03	216960	gtex_brain_putamen_basal
rs3763965	11	27528987	BDNF	ENSG00000176697.14	2.647E-6	0.03	214618	gtex_brain_putamen_basal
rs67924215	11	27533660	BDNF	ENSG00000176697.14	2.63E-6	0.03	209945	gtex_brain_putamen_basal
rs10835189	11	27541995	BDNF	ENSG00000176697.14	3.628E-6	0.03	201610	gtex_brain_putamen_basal
rs11030042	11	27542328	BDNF	ENSG00000176697.14	3.628E-6	0.03	201277	gtex_brain_putamen_basal
rs4528277	11	27565446	BDNF	ENSG00000176697.14	3.62E-6	0.03	178159	gtex_brain_putamen_basal
rs11603350	11	27567246	BDNF	ENSG00000176697.14	3.628E-6	0.03	176359	gtex_brain_putamen_basal
rs901926	11	27570553	BDNF	ENSG00000176697.14	3.628E-6	0.03	173052	gtex_brain_putamen_basal
rs1304101	11	27571594	BDNF	ENSG00000176697.14	3.628E-6	0.03	172011	gtex_brain_putamen_basal
rs10835193	11	27572337	BDNF	ENSG00000176697.14	3.974E-6	0.03	171268	gtex_brain_putamen_basal
rs11030048	11	27582949	BDNF	ENSG00000176697.14	3.628E-6	0.03	160656	gtex_brain_putamen_basal
rs11030052	11	27591812	BDNF	ENSG00000176697.14	3.63E-6	0.03	151793	gtex_brain_putamen_basal
rs1387145	11	27600158	BDNF	ENSG00000176697.14	3.635E-6	0.03	143447	gtex_brain_putamen_basal
rs10835196	11	27601335	BDNF	ENSG00000176697.14	3.637E-6	0.03	142270	gtex_brain_putamen_basal
rs12786828	11	27602642	BDNF	ENSG00000176697.14	3.638E-6	0.03	140963	gtex_brain_putamen_basal
rs2029364	11	27605728	BDNF	ENSG00000176697.14	3.637E-6	0.03	137877	gtex_brain_putamen_basal
rs2029363	11	27606044	BDNF	ENSG00000176697.14	3.642E-6	0.03	137561	gtex_brain_putamen_basal
rs2029362	11	27606133	BDNF	ENSG00000176697.14	3.642E-6	0.03	137472	gtex_brain_putamen_basal
rs1948186	11	27610574	BDNF	ENSG00000176697.14	3.66E-6	0.03	133031	gtex_brain_putamen_basal
rs11030058	11	27616499	BDNF	ENSG00000176697.14	4.021E-6	0.03	127106	gtex_brain_putamen_basal
rs11030059	11	27616617	BDNF	ENSG00000176697.14	3.974E-6	0.03	126988	gtex_brain_putamen_basal
rs10835199	11	27617034	BDNF	ENSG00000176697.14	4.112E-6	0.03	126571	gtex_brain_putamen_basal
rs10835200	11	27617074	BDNF	ENSG00000176697.14	4.114E-6	0.03	126531	gtex_brain_putamen_basal
rs11030060	11	27617566	BDNF	ENSG00000176697.14	3.968E-6	0.03	126039	gtex_brain_putamen_basal
rs11030062	11	27617626	BDNF	ENSG00000176697.14	3.998E-6	0.03	125979	gtex_brain_putamen_basal
rs11030064	11	27618016	BDNF	ENSG00000176697.14	4.227E-6	0.03	125589	gtex_brain_putamen_basal
rs11030065	11	27618108	BDNF	ENSG00000176697.14	4.232E-6	0.03	125497	gtex_brain_putamen_basal
rs10835202	11	27618555	BDNF	ENSG00000176697.14	4.243E-6	0.03	125050	gtex_brain_putamen_basal
rs7937150	11	27620360	BDNF	ENSG00000176697.14	4.236E-6	0.03	123245	gtex_brain_putamen_basal
rs7937485	11	27620473	BDNF	ENSG00000176697.14	4.236E-6	0.03	123132	gtex_brain_putamen_basal
rs12798439	11	27621960	BDNF	ENSG00000176697.14	4.236E-6	0.03	121645	gtex_brain_putamen_basal

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:0008083	growth factor activity	IEA		-
GO:0008083	growth factor activity	TAS		2236018
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007412	axon target recognition	IEA	axon (GO term level: 13)	-
GO:0007411	axon guidance	IEA	axon (GO term level: 13)	-
GO:0007406	negative regulation of neuroblast proliferation	IEA	neurogenesis (GO term level: 10)	-
GO:0008038	neuron recognition	IEA	neuron (GO term level: 4)	-
GO:0014047	glutamate secretion	IEA	glutamate, Neurotransmitter (GO term level: 7)	-
GO:0048167	regulation of synaptic plasticity	IEA	Synap (GO term level: 8)	-
GO:0042490	mechanoreceptor differentiation	IEA	neuron (GO term level: 9)	-
GO:0045666	positive regulation of neuron differentiation	IEA	neuron (GO term level: 10)	-
GO:0043524	negative regulation of neuron apoptosis	IEA	neuron (GO term level: 9)	-
GO:0016358	dendrite development	IEA	neurite, dendrite (GO term level: 11)	-
GO:0001657	ureteric bud development	IEA		-
GO:0007631	feeding behavior	IEA		-
GO:0007611	learning or memory	IEA		-
GO:0006916	anti-apoptosis	IEA		-
GO:0042493	response to drug	IEA		-
GO:0042596	fear response	IEA		-
GO:0021675	nerve development	IEA		-
GO:0019222	regulation of metabolic process	IEA		-
GO:0046668	regulation of retinal cell programmed cell death	IEA		-
GO:0048839	inner ear development	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005576	extracellular region	IEA		-
GO:0016023	cytoplasmic membrane-bounded vesicle	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG MAPK SIGNALING PATHWAY	267	205	All SZGR 2.0 genes in this pathway
KEGG NEUROTROPHIN SIGNALING PATHWAY	126	103	All SZGR 2.0 genes in this pathway
KEGG HUNTINGTONS DISEASE	185	109	All SZGR 2.0 genes in this pathway
PID SHP2 PATHWAY	58	46	All SZGR 2.0 genes in this pathway
PID AJDISS 2PATHWAY	48	38	All SZGR 2.0 genes in this pathway
PID P75 NTR PATHWAY	69	51	All SZGR 2.0 genes in this pathway
PID TRKR PATHWAY	62	48	All SZGR 2.0 genes in this pathway
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL UP	285	181	All SZGR 2.0 genes in this pathway
WILCOX RESPONSE TO PROGESTERONE DN	66	44	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
CHARAFE BREAST CANCER BASAL VS MESENCHYMAL DN	50	36	All SZGR 2.0 genes in this pathway
BASAKI YBX1 TARGETS UP	290	177	All SZGR 2.0 genes in this pathway
RODRIGUES NTN1 TARGETS UP	17	11	All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 8D UP	157	91	All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS DN	459	276	All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 12HR DN	209	122	All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA UP	536	340	All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS	1174	695	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 XPCS DN	88	71	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN	855	609	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 COMMON DN	483	336	All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS FETAL LIVER DN	514	319	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP	1037	673	All SZGR 2.0 genes in this pathway
INGRAM SHH TARGETS UP	127	79	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN	637	377	All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 120 HELA	69	47	All SZGR 2.0 genes in this pathway
ZHANG RESPONSE TO IKK INHIBITOR AND TNF DN	103	64	All SZGR 2.0 genes in this pathway
KANG IMMORTALIZED BY TERT UP	89	61	All SZGR 2.0 genes in this pathway
AFFAR YY1 TARGETS UP	214	133	All SZGR 2.0 genes in this pathway
REN ALVEOLAR RHABDOMYOSARCOMA DN	408	274	All SZGR 2.0 genes in this pathway
MODY HIPPOCAMPUS POSTNATAL	63	50	All SZGR 2.0 genes in this pathway
WESTON VEGFA TARGETS 6HR	59	38	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 10HR DN	56	37	All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS DN	371	218	All SZGR 2.0 genes in this pathway
MCCLUNG DELTA FOSB TARGETS 2WK	48	36	All SZGR 2.0 genes in this pathway
WESTON VEGFA TARGETS 12HR	35	23	All SZGR 2.0 genes in this pathway
WESTON VEGFA TARGETS	108	71	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 8	86	57	All SZGR 2.0 genes in this pathway
GENTILE UV RESPONSE CLUSTER D2	41	30	All SZGR 2.0 genes in this pathway
KAAB HEART ATRIUM VS VENTRICLE DN	261	183	All SZGR 2.0 genes in this pathway
GENTILE UV HIGH DOSE DN	312	203	All SZGR 2.0 genes in this pathway
MCCLUNG CREB1 TARGETS UP	100	72	All SZGR 2.0 genes in this pathway
LEE AGING CEREBELLUM UP	84	58	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 3	720	440	All SZGR 2.0 genes in this pathway
LOPES METHYLATED IN COLON CANCER DN	28	26	All SZGR 2.0 genes in this pathway
SANSOM APC MYC TARGETS	217	138	All SZGR 2.0 genes in this pathway
MCCABE BOUND BY HOXC6	469	239	All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN UP	439	257	All SZGR 2.0 genes in this pathway
TOYOTA TARGETS OF MIR34B AND MIR34C	463	262	All SZGR 2.0 genes in this pathway
MISHRA CARCINOMA ASSOCIATED FIBROBLAST DN	24	13	All SZGR 2.0 genes in this pathway
LIN NPAS4 TARGETS DN	68	48	All SZGR 2.0 genes in this pathway
HELLEBREKERS SILENCED DURING TUMOR ANGIOGENESIS	80	56	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS DN	366	257	All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS DN	435	289	All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS UP	395	249	All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS DN	442	275	All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3	1069	729	All SZGR 2.0 genes in this pathway
KYNG WERNER SYNDROM AND NORMAL AGING DN	225	124	All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC DN	253	192	All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE	721	492	All SZGR 2.0 genes in this pathway
HOELZEL NF1 TARGETS DN	115	73	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 DN	918	550	All SZGR 2.0 genes in this pathway
PASINI SUZ12 TARGETS DN	315	215	All SZGR 2.0 genes in this pathway
WINZEN DEGRADED VIA KHSRP	100	70	All SZGR 2.0 genes in this pathway
IKEDA MIR1 TARGETS UP	53	39	All SZGR 2.0 genes in this pathway
IKEDA MIR30 TARGETS UP	116	87	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE VIA P38 PARTIAL	160	106	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
NABA SECRETED FACTORS	344	197	All SZGR 2.0 genes in this pathway
NABA MATRISOME ASSOCIATED	753	411	All SZGR 2.0 genes in this pathway
NABA MATRISOME	1028	559	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	220	226	m8	hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
				hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
				hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
miR-10	65	72	1A,m8	hsa-miR-10a	UACCCUGUAGAUCCGAAUUUGUG
miR-10	65	72	1A,m8	hsa-miR-10b	UACCCUGUAGAACCGAAUUUGU
miR-103/107	299	305	m8	hsa-miR-103^brain	AGCAGCAUUGUACAGGGCUAUGA
miR-103/107	299	305	m8	hsa-miR-107^brain	AGCAGCAUUGUACAGGGCUAUCA
miR-15/16/195/424/497	300	306	m8	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-155	2797	2803	1A	hsa-miR-155	UUAAUGCUAAUCGUGAUAGGGG
miR-182	252	258	m8	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-191	393	399	m8	hsa-miR-191^brain	CAACGGAAUCCCAAAAGCAGCU
miR-210	196	202	1A	hsa-miR-210	CUGUGCGUGUGACAGCGGCUGA
miR-30-5p	397	403	1A	hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
miR-365	2796	2802	1A	hsa-miR-365	UAAUGCCCCUAAAAAUCCUUAU
miR-381	11	17	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-381	11	17	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-382	199	206	1A,m8	hsa-miR-382^brain	GAAGUUGUUCGUGGUGGAUUCG
miR-409-3p	389	395	m8	hsa-miR-409-3p	CGAAUGUUGCUCGGUGAACCCCU
miR-410	2768	2774	1A	hsa-miR-410	AAUAUAACACAGAUGGCCUGU
miR-495	552	558	m8	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
				hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
				hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
				hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
				hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-496	2727	2734	1A,m8	hsa-miR-496	AUUACAUGGCCAAUCUC

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: BDNF