SZGR2

Summary ?

GeneID	654
Symbol	BMP6
Synonyms	VGR\|VGR1
Description	bone morphogenetic protein 6
Reference	MIM:112266\|HGNC:HGNC:1073\|Ensembl:ENSG00000153162\|HPRD:00211\|Vega:OTTHUMG00000014217
Gene type	protein-coding
Map location	6p24-p23
Pascal p-value	0.11
Sherlock p-value	0.66
Fetal beta	-0.136
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
GSMA_I	Genome scan meta-analysis	Psr: 0.0159
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenias	Click to show details

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs546975	chr1	91963738	BMP6	654	0.03	trans
rs4236095	chr6	47368686	BMP6	654	0.02	trans
snp_a-2266657		0	BMP6	654	0.15	trans
rs2430483	chr7	104548631	BMP6	654	0.07	trans
rs2061799	chr9	97795003	BMP6	654	0.01	trans
rs10149864	chr14	86719683	BMP6	654	0	trans
rs5029382	chr18	45981525	BMP6	654	0.11	trans
rs1877412	chr18	45987674	BMP6	654	0.09	trans
rs11873703	chr18	61448702	BMP6	654	0.19	trans
rs16999569	chr19	22902709	BMP6	654	0.09	trans
rs12973782	chr19	22905126	BMP6	654	0.09	trans
snp_a-2090370		0	BMP6	654	0.09	trans
rs12980129	chr19	22908910	BMP6	654	0.02	trans
rs2194111	chr19	22922548	BMP6	654	0.09	trans
rs6095741	chr20	48666589	BMP6	654	0.02	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
SLC4A4	0.86	0.79
PPAP2B	0.86	0.85
ATP13A4	0.85	0.77
ACSS3	0.84	0.81
AQP4	0.83	0.77
SSPN	0.83	0.75
SLC1A3	0.83	0.84
PDLIM5	0.82	0.80
ITPR2	0.82	0.73
ADD3	0.82	0.78

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
MED19	-0.36	-0.39
AC011491.1	-0.35	-0.37
RAB33A	-0.34	-0.37
DCTPP1	-0.33	-0.36
DPF1	-0.33	-0.30
BZW2	-0.32	-0.33
GPR21	-0.32	-0.29
POLB	-0.32	-0.34
ACTL6B	-0.31	-0.31
ARL4D	-0.31	-0.29

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005125	cytokine activity	IEA		-
GO:0005515	protein binding	IEA		-
GO:0008083	growth factor activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006955	immune response	IMP		16886151
GO:0006954	inflammatory response	IEA		-
GO:0007275	multicellular organismal development	IEA		-
GO:0030501	positive regulation of bone mineralization	IDA		18436533
GO:0030509	BMP signaling pathway	IEA		-
GO:0051216	cartilage development	IEA		-
GO:0032349	positive regulation of aldosterone biosynthetic process	IDA		16527843
GO:0040007	growth	IEA		-
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	IDA		16527843
GO:0045669	positive regulation of osteoblast differentiation	IDA		18436533
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005576	extracellular region	IEA		-
GO:0005615	extracellular space	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG HEDGEHOG SIGNALING PATHWAY	56	42	All SZGR 2.0 genes in this pathway
KEGG TGF BETA SIGNALING PATHWAY	86	64	All SZGR 2.0 genes in this pathway
PID BMP PATHWAY	42	31	All SZGR 2.0 genes in this pathway
UDAYAKUMAR MED1 TARGETS DN	240	171	All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS	1062	725	All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS DN	357	212	All SZGR 2.0 genes in this pathway
STOSSI RESPONSE TO ESTRADIOL	50	35	All SZGR 2.0 genes in this pathway
PETROVA ENDOTHELIUM LYMPHATIC VS BLOOD DN	162	102	All SZGR 2.0 genes in this pathway
AFFAR YY1 TARGETS UP	214	133	All SZGR 2.0 genes in this pathway
PETROVA PROX1 TARGETS DN	64	38	All SZGR 2.0 genes in this pathway
JAZAERI BREAST CANCER BRCA1 VS BRCA2 DN	43	31	All SZGR 2.0 genes in this pathway
KAYO CALORIE RESTRICTION MUSCLE DN	87	59	All SZGR 2.0 genes in this pathway
CHIBA RESPONSE TO TSA UP	52	33	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR UP	180	125	All SZGR 2.0 genes in this pathway
WESTON VEGFA TARGETS	108	71	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 14HR UP	156	101	All SZGR 2.0 genes in this pathway
TSENG IRS1 TARGETS UP	113	71	All SZGR 2.0 genes in this pathway
WESTON VEGFA TARGETS 3HR	74	47	All SZGR 2.0 genes in this pathway
TSENG ADIPOGENIC POTENTIAL UP	30	19	All SZGR 2.0 genes in this pathway
RIZKI TUMOR INVASIVENESS 3D UP	210	124	All SZGR 2.0 genes in this pathway
TOYOTA TARGETS OF MIR34B AND MIR34C	463	262	All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS DN	435	289	All SZGR 2.0 genes in this pathway
SHAFFER IRF4 TARGETS IN MYELOMA VS MATURE B LYMPHOCYTE	101	76	All SZGR 2.0 genes in this pathway
SHAFFER IRF4 TARGETS IN PLASMA CELL VS MATURE B LYMPHOCYTE	67	51	All SZGR 2.0 genes in this pathway
SHAFFER IRF4 TARGETS IN ACTIVATED B LYMPHOCYTE	81	66	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
ZHAN LATE DIFFERENTIATION GENES UP	33	24	All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 AND H3K27ME3	349	234	All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 HCP WITH H3K27ME3	435	318	All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K27ME3	341	243	All SZGR 2.0 genes in this pathway
LU EZH2 TARGETS DN	414	237	All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS UP	279	155	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-124.1	55	62	1A,m8	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-124/506	55	61	1A	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	55	61	1A	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-219	1015	1021	1A	hsa-miR-219^brain	UGAUUGUCCAAACGCAAUUCU

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: BMP6