SZGR2

Summary ?

GeneID	607
Symbol	BCL9
Synonyms	LGS
Description	B-cell CLL/lymphoma 9
Reference	MIM:602597\|HGNC:HGNC:1008\|Ensembl:ENSG00000116128\|HPRD:04000\|Vega:OTTHUMG00000014031
Gene type	protein-coding
Map location	1q21
Sherlock p-value	0.234
Fetal beta	1.862
DMG	1 (# studies)
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CNV:YES	Copy number variation studies	Manual curation
CV:GWAScat	Genome-wide Association Studies	This data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
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
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: 0.0235
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.00814
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg12608682	1	147071766	BCL9	4.097E-4	-0.226	0.044	DMG:Wockner_2014
cg21813591	1	147071537	BCL9	4.703E-4	-0.626	0.046	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs16829545	chr2	151977407	BCL9	607	0	trans
rs3106445	chr3	165326464	BCL9	607	0.19	trans
rs1199915		0	BCL9	607	0.1	trans
rs520325	chr3	165361016	BCL9	607	0.11	trans
rs16955618	chr15	29937543	BCL9	607	0.03	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
OGDHL	0.90	0.91
FADS6	0.85	0.86
EML2	0.85	0.89
SPOCK2	0.83	0.84
CEND1	0.82	0.88
TOM1	0.82	0.83
ABHD12	0.81	0.84
LPCAT4	0.81	0.84
MYH7B	0.81	0.79
DLGAP3	0.80	0.89

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
KIAA1949	-0.52	-0.49
TUBB2B	-0.51	-0.56
ZNF300	-0.51	-0.44
RBMX2	-0.50	-0.62
IGF2BP3	-0.50	-0.56
ZNF551	-0.49	-0.45
ZNF311	-0.49	-0.46
FNBP1L	-0.49	-0.41
CD24	-0.49	-0.37
CARHSP1	-0.49	-0.59

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005515	protein binding	IPI		11955446 \|17113272
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016055	Wnt receptor signaling pathway	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
WNT SIGNALING	89	71	All SZGR 2.0 genes in this pathway
PID BETA CATENIN NUC PATHWAY	80	60	All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER UP	443	294	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION UP	552	347	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
SUZUKI AMPLIFIED IN ORAL CANCER	16	12	All SZGR 2.0 genes in this pathway
MYLLYKANGAS AMPLIFICATION HOT SPOT 17	25	12	All SZGR 2.0 genes in this pathway
MYLLYKANGAS AMPLIFICATION HOT SPOT 24	14	7	All SZGR 2.0 genes in this pathway
DAIRKEE TERT TARGETS DN	124	79	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 6HR DN	514	330	All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS	988	594	All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS	734	436	All SZGR 2.0 genes in this pathway
PENG GLUTAMINE DEPRIVATION UP	38	25	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 6HR DN	160	101	All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP	566	371	All SZGR 2.0 genes in this pathway
FOSTER TOLERANT MACROPHAGE DN	409	268	All SZGR 2.0 genes in this pathway
GRESHOCK CANCER COPY NUMBER UP	323	240	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS DN	457	302	All SZGR 2.0 genes in this pathway
LU EZH2 TARGETS DN	414	237	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN	1972	1213	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP B	549	316	All SZGR 2.0 genes in this pathway
ZWANG EGF INTERVAL DN	214	124	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-101	409	416	1A,m8	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-129-5p	597	603	1A	hsa-miR-129^brain	CUUUUUGCGGUCUGGGCUUGC
miR-129-5p	597	603	1A	hsa-miR-129-5p	CUUUUUGCGGUCUGGGCUUGCU
miR-140	1201	1207	m8	hsa-miR-140^brain	AGUGGUUUUACCCUAUGGUAG
miR-144	410	416	1A	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-15/16/195/424/497	1	7	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-181	149	155	1A	hsa-miR-181a^brain	AACAUUCAACGCUGUCGGUGAGU
				hsa-miR-181b^SZ	AACAUUCAUUGCUGUCGGUGGG
				hsa-miR-181c^brain	AACAUUCAACCUGUCGGUGAGU
				hsa-miR-181d^brain	AACAUUCAUUGUUGUCGGUGGGUU
miR-186	361	367	m8	hsa-miR-186	CAAAGAAUUCUCCUUUUGGGCUU
miR-188	428	434	m8	hsa-miR-188	CAUCCCUUGCAUGGUGGAGGGU
miR-200bc/429	580	586	1A	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-204/211	427	433	m8	hsa-miR-204^brain	UUCCCUUUGUCAUCCUAUGCCU
miR-204/211	427	433	m8	hsa-miR-211	UUCCCUUUGUCAUCCUUCGCCU
miR-216	36	42	m8	hsa-miR-216	UAAUCUCAGCUGGCAACUGUG
miR-218	592	599	1A,m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-22	850	856	m8	hsa-miR-22^brain	AAGCUGCCAGUUGAAGAACUGU
miR-25/32/92/363/367	856	862	1A	hsa-miR-25^brain	CAUUGCACUUGUCUCGGUCUGA
				hsa-miR-32	UAUUGCACAUUACUAAGUUGC
				hsa-miR-92	UAUUGCACUUGUCCCGGCCUG
				hsa-miR-367	AAUUGCACUUUAGCAAUGGUGA
				hsa-miR-92b^SZ	UAUUGCACUCGUCCCGGCCUC
miR-30-5p	486	492	m8	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
				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-329	194	200	m8	hsa-miR-329^brain	AACACACCUGGUUAACCUCUUU
miR-330	124	130	m8	hsa-miR-330^brain	GCAAAGCACACGGCCUGCAGAGA
miR-330	124	130	m8	hsa-miR-330^brain	GCAAAGCACACGGCCUGCAGAGA
miR-338	477	483	m8	hsa-miR-338^brain	UCCAGCAUCAGUGAUUUUGUUGA
miR-503	1	7	1A	hsa-miR-503	UAGCAGCGGGAACAGUUCUGCAG

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: BCL9