SZGR2

Summary ?

GeneID	5332
Symbol	PLCB4
Synonyms	ARCND2\|PI-PLC
Description	phospholipase C beta 4
Reference	MIM:600810\|HGNC:HGNC:9059\|Ensembl:ENSG00000101333\|HPRD:02885\|Vega:OTTHUMG00000031853
Gene type	protein-coding
Map location	20p12
Pascal p-value	0.794
Sherlock p-value	0.292
Fetal beta	-0.224
eGene	Cerebellum Myers' cis & trans Meta
Support	CANABINOID INTRACELLULAR SIGNAL TRANSDUCTION METABOTROPIC GLUTAMATE RECEPTOR SEROTONIN

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: 0.046
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 2

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs6055624	chr20	8171571	PLCB4	5332	0.15	cis
rs16994533	chr20	8218964	PLCB4	5332	0.11	cis
rs16829545	chr2	151977407	PLCB4	5332	2.81E-8	trans
rs3845734	chr2	171125572	PLCB4	5332	0.02	trans
rs7584986	chr2	184111432	PLCB4	5332	1.961E-4	trans
rs2183142	chr4	159232695	PLCB4	5332	0.07	trans
rs3111196	chr5	54402889	PLCB4	5332	0.15	trans
rs17762315	chr5	76807576	PLCB4	5332	0.1	trans
rs9461864	chr6	33481468	PLCB4	5332	0.17	trans
rs2393316	chr10	59333070	PLCB4	5332	0.09	trans
rs16955618	chr15	29937543	PLCB4	5332	3.598E-13	trans
rs1940436	chr18	415400	PLCB4	5332	0.16	trans
rs1041786	chr21	22617710	PLCB4	5332	0	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
AL161668.2	0.82	0.84
KIAA0195	0.81	0.80
ARAP1	0.81	0.81
LTBP3	0.80	0.80
SLC27A1	0.80	0.84
ASAP3	0.78	0.78
GPR56	0.78	0.82
CASKIN2	0.77	0.77
GPT2	0.77	0.75
DNM2	0.77	0.76

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
PPEF1	-0.49	-0.49
THOC7	-0.48	-0.52
CALM2	-0.48	-0.50
BRP44	-0.48	-0.55
GLMN	-0.47	-0.54
GPR160	-0.47	-0.55
TCEAL7	-0.47	-0.51
TMEM70	-0.46	-0.53
USMG5	-0.45	-0.59
BEX5	-0.45	-0.47

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004871	signal transducer activity	IEA		-
GO:0005509	calcium ion binding	IEA		-
GO:0005515	protein binding	IEA		-
GO:0005515	protein binding	IPI		16767099
GO:0004435	phosphoinositide phospholipase C activity	IEA		-
GO:0016787	hydrolase activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016042	lipid catabolic process	IEA		-
GO:0007242	intracellular signaling cascade	IEA		-
GO:0006629	lipid metabolic process	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0014069	postsynaptic density	IEA	Synap (GO term level: 10)	-
GO:0030425	dendrite	IEA	neuron, axon, dendrite (GO term level: 6)	-
GO:0005792	microsome	IEA		-
GO:0005790	smooth endoplasmic reticulum	IEA		-
GO:0005634	nucleus	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG INOSITOL PHOSPHATE METABOLISM	54	42	All SZGR 2.0 genes in this pathway
KEGG CALCIUM SIGNALING PATHWAY	178	134	All SZGR 2.0 genes in this pathway
KEGG CHEMOKINE SIGNALING PATHWAY	190	128	All SZGR 2.0 genes in this pathway
KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM	76	56	All SZGR 2.0 genes in this pathway
KEGG VASCULAR SMOOTH MUSCLE CONTRACTION	115	81	All SZGR 2.0 genes in this pathway
KEGG WNT SIGNALING PATHWAY	151	112	All SZGR 2.0 genes in this pathway
KEGG GAP JUNCTION	90	68	All SZGR 2.0 genes in this pathway
KEGG LONG TERM POTENTIATION	70	57	All SZGR 2.0 genes in this pathway
KEGG LONG TERM DEPRESSION	70	53	All SZGR 2.0 genes in this pathway
KEGG GNRH SIGNALING PATHWAY	101	77	All SZGR 2.0 genes in this pathway
KEGG MELANOGENESIS	102	80	All SZGR 2.0 genes in this pathway
KEGG ALZHEIMERS DISEASE	169	110	All SZGR 2.0 genes in this pathway
KEGG HUNTINGTONS DISEASE	185	109	All SZGR 2.0 genes in this pathway
ST G ALPHA I PATHWAY	35	29	All SZGR 2.0 genes in this pathway
REACTOME GASTRIN CREB SIGNALLING PATHWAY VIA PKC AND MAPK	205	136	All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY GPCR	920	449	All SZGR 2.0 genes in this pathway
REACTOME OPIOID SIGNALLING	78	56	All SZGR 2.0 genes in this pathway
REACTOME PLC BETA MEDIATED EVENTS	43	32	All SZGR 2.0 genes in this pathway
REACTOME G ALPHA Q SIGNALLING EVENTS	184	116	All SZGR 2.0 genes in this pathway
REACTOME GPCR DOWNSTREAM SIGNALING	805	368	All SZGR 2.0 genes in this pathway
DAVICIONI TARGETS OF PAX FOXO1 FUSIONS DN	68	49	All SZGR 2.0 genes in this pathway
BASAKI YBX1 TARGETS UP	290	177	All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 MUTATED SIGNATURE 1 DN	126	86	All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 SIGNATURE 3 DN	162	116	All SZGR 2.0 genes in this pathway
JAATINEN HEMATOPOIETIC STEM CELL UP	316	190	All SZGR 2.0 genes in this pathway
ODONNELL METASTASIS UP	82	58	All SZGR 2.0 genes in this pathway
STREICHER LSM1 TARGETS UP	44	34	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
LINDGREN BLADDER CANCER HIGH RECURRENCE	49	31	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN	855	609	All SZGR 2.0 genes in this pathway
DAWSON METHYLATED IN LYMPHOMA TCL1	59	45	All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK	1652	1023	All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK	1442	892	All SZGR 2.0 genes in this pathway
RICKMAN TUMOR DIFFERENTIATED WELL VS POORLY UP	236	139	All SZGR 2.0 genes in this pathway
RICKMAN TUMOR DIFFERENTIATED WELL VS MODERATELY UP	109	69	All SZGR 2.0 genes in this pathway
RICKMAN METASTASIS UP	344	180	All SZGR 2.0 genes in this pathway
RICKMAN HEAD AND NECK CANCER A	100	63	All SZGR 2.0 genes in this pathway
STARK PREFRONTAL CORTEX 22Q11 DELETION DN	517	309	All SZGR 2.0 genes in this pathway
ROZANOV MMP14 TARGETS UP	266	171	All SZGR 2.0 genes in this pathway
HADDAD T LYMPHOCYTE AND NK PROGENITOR UP	78	56	All SZGR 2.0 genes in this pathway
AFFAR YY1 TARGETS UP	214	133	All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS DN	371	218	All SZGR 2.0 genes in this pathway
ULE SPLICING VIA NOVA2	43	38	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 6HR DN	160	101	All SZGR 2.0 genes in this pathway
RIGGINS TAMOXIFEN RESISTANCE DN	220	147	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER WITH H3K27ME3 DN	228	114	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL UP	648	398	All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP	871	505	All SZGR 2.0 genes in this pathway
GRADE COLON AND RECTAL CANCER UP	285	167	All SZGR 2.0 genes in this pathway
HUANG DASATINIB RESISTANCE DN	69	44	All SZGR 2.0 genes in this pathway
FIRESTEIN PROLIFERATION	175	125	All SZGR 2.0 genes in this pathway
SASAI TARGETS OF CXCR6 AND PTCH1 UP	13	9	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA C D DN	252	155	All SZGR 2.0 genes in this pathway
GU PDEF TARGETS UP	71	49	All SZGR 2.0 genes in this pathway
MARIADASON RESPONSE TO BUTYRATE CURCUMIN SULINDAC TSA 1	10	7	All SZGR 2.0 genes in this pathway
NIELSEN GIST	98	66	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 1HR DN	222	147	All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA PRONEURAL	177	132	All SZGR 2.0 genes in this pathway
WIERENGA PML INTERACTOME	42	23	All SZGR 2.0 genes in this pathway
TORCHIA TARGETS OF EWSR1 FLI1 FUSION DN	321	200	All SZGR 2.0 genes in this pathway
IKEDA MIR30 TARGETS UP	116	87	All SZGR 2.0 genes in this pathway
SERVITJA ISLET HNF1A TARGETS UP	163	111	All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN	784	464	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE NOT VIA P38	337	236	All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM A	182	108	All SZGR 2.0 genes in this pathway
ACEVEDO FGFR1 TARGETS IN PROSTATE CANCER MODEL DN	308	187	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
let-7/98	493	499	1A	hsa-let-7a^brain	UGAGGUAGUAGGUUGUAUAGUU
				hsa-let-7b^brain	UGAGGUAGUAGGUUGUGUGGUU
				hsa-let-7c^brain	UGAGGUAGUAGGUUGUAUGGUU
				hsa-let-7d^brain	AGAGGUAGUAGGUUGCAUAGU
				hsa-let-7e^brain	UGAGGUAGGAGGUUGUAUAGU
				hsa-let-7f^brain	UGAGGUAGUAGAUUGUAUAGUU
				hsa-miR-98^brain	UGAGGUAGUAAGUUGUAUUGUU
				hsa-let-7g^SZ	UGAGGUAGUAGUUUGUACAGU
				hsa-let-7i^brain	UGAGGUAGUAGUUUGUGCUGU
miR-130/301	399	405	1A	hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
miR-183	507	513	m8	hsa-miR-183	UAUGGCACUGGUAGAAUUCACUG
miR-190	1122	1128	1A	hsa-miR-190	UGAUAUGUUUGAUAUAUUAGGU
miR-214	1200	1206	m8	hsa-miR-214^brain	ACAGCAGGCACAGACAGGCAG
miR-23	752	758	m8	hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
miR-23	752	758	m8	hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
miR-30-5p	651	657	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-323	752	758	1A	hsa-miR-323^brain	GCACAUUACACGGUCGACCUCU
miR-365	1031	1037	m8	hsa-miR-365	UAAUGCCCCUAAAAAUCCUUAU
miR-378	1126	1132	1A	hsa-miR-378	CUCCUGACUCCAGGUCCUGUGU
miR-381	1348	1354	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-96	597	604	1A,m8	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: PLCB4