SZGR2

Summary ?

GeneID	23187
Symbol	PHLDB1
Synonyms	LL5A
Description	pleckstrin homology like domain family B member 1
Reference	MIM:612834\|HGNC:HGNC:23697\|Ensembl:ENSG00000019144\|HPRD:15128\|Vega:OTTHUMG00000166341
Gene type	protein-coding
Map location	11q23.3
Pascal p-value	0.22
Fetal beta	0.554
DMG	1 (# studies)
eGene	Cerebellum Myers' cis & trans
Support	G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS CompositeSet Darnell FMRP targets

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
CV:PheWAS	Phenome-wide association studies (PheWAS)	157 SNPs associated with schizophrenia	1
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).	1
DNM:Fromer_2014	Whole Exome Sequencing analysis	This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
GSMA_I	Genome scan meta-analysis	Psr: 0.006

Section I. Genetics and epigenetics annotation

CV:PheWAS

SNP ID	Chromosome	Position	Allele	P	Function	Gene	Up/Down Distance
rs498872	11	118477367	null	1.581	PHLDB1	null

DNM table

Gene	Chromosome	Position	Ref	Alt	Transcript	AA change	Mutation type	Sift	CG46	Trait	Study
PHLDB1	chr11	118499232	G	A	NM_001144758 NM_001144759 NM_015157	p.565G>R p.565G>R p.565G>R	missense missense missense			Schizophrenia	DNM:Fromer_2014

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg20110707	11	118481992	PHLDB1	3.073E-4	-0.37	0.04	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs1003316	chr8	134515933	PHLDB1	23187		0.18		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
AL033532.1	0.99	0.94
ZBED4	0.96	0.92
BRD1	0.96	0.90
BRD3	0.96	0.90
KDM4B	0.96	0.94
KLF7	0.95	0.92
EHMT1	0.95	0.87
PHF2	0.95	0.87
KDM2B	0.95	0.92
EIF2C4	0.95	0.88

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
HLA-F	-0.72	-0.79
C5orf53	-0.72	-0.77
AIFM3	-0.71	-0.75
FBXO2	-0.70	-0.67
HEPN1	-0.70	-0.77
ALDOC	-0.70	-0.70
TSC22D4	-0.70	-0.79
CLU	-0.70	-0.71
S100B	-0.69	-0.84
AF347015.27	-0.69	-0.90

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
WATANABE RECTAL CANCER RADIOTHERAPY RESPONSIVE UP	108	67	All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION DN	329	219	All SZGR 2.0 genes in this pathway
LANDIS ERBB2 BREAST TUMORS 65 DN	37	22	All SZGR 2.0 genes in this pathway
LANDIS ERBB2 BREAST TUMORS 324 DN	149	93	All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS	1038	678	All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS	882	572	All SZGR 2.0 genes in this pathway
GALINDO IMMUNE RESPONSE TO ENTEROTOXIN	85	67	All SZGR 2.0 genes in this pathway
HENDRICKS SMARCA4 TARGETS UP	56	35	All SZGR 2.0 genes in this pathway
FOSTER TOLERANT MACROPHAGE DN	409	268	All SZGR 2.0 genes in this pathway
GRADE COLON VS RECTAL CANCER DN	56	36	All SZGR 2.0 genes in this pathway
CHEN METABOLIC SYNDROM NETWORK	1210	725	All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC DN	253	192	All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 24HR DN	505	328	All SZGR 2.0 genes in this pathway
FIGUEROA AML METHYLATION CLUSTER 3 DN	42	24	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP	745	475	All SZGR 2.0 genes in this pathway
KOINUMA TARGETS OF SMAD2 OR SMAD3	824	528	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP	489	314	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
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-124.1	1076	1082	1A	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-124/506	784	790	m8	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	784	790	m8	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-149	796	803	1A,m8	hsa-miR-149^brain	UCUGGCUCCGUGUCUUCACUCC
miR-182	307	313	1A	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-185	649	656	1A,m8	hsa-miR-185^brain	UGGAGAGAAAGGCAGUUC
miR-200bc/429	1156	1162	m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-326	477	483	1A	hsa-miR-326	CCUCUGGGCCCUUCCUCCAG
miR-9	309	315	1A	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-96	307	313	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: PHLDB1