Gene Page:PHLDB1

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)

Not available

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
死神:胎儿(13 - 26 postconception周), 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甲基化簇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
UTR start UTR end Match method
miR-124.1 1076 1082 1A hsa-miR-124a UUAAGGCACGCGGUGAAUGCCA
miR-124/506 784 790 m8 hsa-miR-506 UAAGGCACCCUUCUGAGUAGA
hsa-miR-124brain UAAGGCACGCGGUGAAUGCC
miR-149 796 803 1A,m8 hsa-miR-149brain UCUGGCUCCGUGUCUUCACUCC
miR-182 307 313 1A hsa-miR-182 UUUGGCAAUGGUAGAACUCACA
miR-185 649 656 1A,m8 hsa-miR-185brain 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-9SZ UCUUUGGUUAUCUAGCUGUAUGA
miR-96 307 313 1A hsa-miR-96brain UUUGGCACUAGCACAUUUUUGC