Gene Page:NR1H3

Summary?
GeneID 10062
Symbol NR1H3
Synonyms LXR-a|LXRA|RLD-1
Description nuclear receptor subfamily 1 group H member 3
Reference MIM:602423|HGNC:HGNC:7966|Ensembl:ENSG00000025434|HPRD:07211|Vega:OTTHUMG00000150628
Gene type protein-coding
Map location 11p11.2
Pascal p-value 0.044
Sherlock p-value 0.282
Fetal beta -0.405
DMG 1 (# studies)
eGene Hypothalamus
Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
DMG:Jaffe_2016 Genome-wide DNA methylation analysis This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg24419099 11 47270565 NR1H3 3.17E-10 -0.017 7.03E-7 DMG:Jaffe_2016

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs2452512 chr10 60954418 NR1H3 10062 0.08 trans
rs12450116 chr17 53333924 NR1H3 10062 0.09 trans
rs4465127 chrX 75360522 NR1H3 10062 0.04 trans
rs6648110 chrX 75871494 NR1H3 10062 0.01 trans
rs6648142 chrX 75928565 NR1H3 10062 0.01 trans
rs192069 chrX 76053555 NR1H3 10062 0 trans
rs7881752 chrX 76197379 NR1H3 10062 0.03 trans
rs5982340 chrX 76230686 NR1H3 10062 0.01 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
ZNF280D 0.93 0.95
DHX29 0.92 0.95
LARS 0.92 0.95
USP15 0.92 0.94
C1orf103 0.92 0.94
ZNF354A 0.91 0.94
PLAA 0.91 0.94
TPP2 0.91 0.93
GPBP1 0.91 0.94
C10orf137 0.91 0.93
Top 10 negatively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
MT-CO2 -0.80 -0.86
AF347015.31 -0.80 -0.86
AF347015.33 -0.79 -0.86
FXYD1 -0.79 -0.87
AF347015.8 -0.78 -0.86
AF347015.27 -0.78 -0.84
HLA-F -0.77 -0.81
IFI27 -0.77 -0.86
HIGD1B -0.77 -0.86
MT-CYB -0.76 -0.83

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
KEGG PPAR SIGNALING PATHWAY 69 47 All SZGR 2.0 genes in this pathway
BIOCARTA PPARA PATHWAY 58 43 All SZGR 2.0 genes in this pathway
BIOCARTA NUCLEARRS PATHWAY 15 12 All SZGR 2.0 genes in this pathway
PID RXR VDR PATHWAY 26 24 All SZGR 2.0 genes in this pathway
REACTOME GENERIC TRANSCRIPTION PATHWAY 352 181 All SZGR 2.0 genes in this pathway
REACTOME NUCLEAR RECEPTOR TRANSCRIPTION PATHWAY 49 36 All SZGR 2.0 genes in this pathway
PICCALUGA ANGIOIMMUNOBLASTIC LYMPHOMA UP 205 140 All SZGR 2.0 genes in this pathway
BERTUCCI MEDULLARY VS DUCTAL BREAST CANCER UP 206 111 All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS UP 149 84 All SZGR 2.0 genes in this pathway
LANDIS BREAST CANCER PROGRESSION DN 70 43 All SZGR 2.0 genes in this pathway
LANDIS ERBB2 BREAST PRENEOPLASTIC DN 55 33 All SZGR 2.0 genes in this pathway
LANDIS ERBB2 BREAST TUMORS 324 DN 149 93 All SZGR 2.0 genes in this pathway
HAMAI APOPTOSIS VIA TRAIL DN 186 107 All SZGR 2.0 genes in this pathway
RIZ ERYTHROID DIFFERENTIATION 12HR 43 35 All SZGR 2.0 genes in this pathway
ROVERSI GLIOMA COPY NUMBER UP 100 75 All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN 1024 594 All SZGR 2.0 genes in this pathway
ROZANOV MMP14 TARGETS UP 266 171 All SZGR 2.0 genes in this pathway
LEE LIVER CANCER CIPROFIBRATE DN 66 43 All SZGR 2.0 genes in this pathway
LEE LIVER CANCER MYC TGFA DN 65 44 All SZGR 2.0 genes in this pathway
LEE LIVER CANCER ACOX1 DN 65 39 All SZGR 2.0 genes in this pathway
LEE LIVER CANCER MYC E2F1 DN 64 38 All SZGR 2.0 genes in this pathway
LEE LIVER CANCER DENA DN 74 45 All SZGR 2.0 genes in this pathway
LEE LIVER CANCER E2F1 DN 64 42 All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS DN 366 238 All SZGR 2.0 genes in this pathway
LENAOUR DENDRITIC CELL MATURATION UP 114 84 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 16HR DN 86 62 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 24HR DN 148 102 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 14HR DN 298 200 All SZGR 2.0 genes in this pathway
RUAN RESPONSE TO TNF DN 84 50 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR DN 504 323 All SZGR 2.0 genes in this pathway
LI ADIPOGENESIS BY ACTIVATED PPARG 17 12 All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 6 189 112 All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR UP 953 554 All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR DN 1011 592 All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 STIMULATED 1022 619 All SZGR 2.0 genes in this pathway
LEE METASTASIS AND ALTERNATIVE SPLICING DN 45 31 All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL CULTURED VS FRESH UP 425 298 All SZGR 2.0 genes in this pathway
QI PLASMACYTOMA UP 259 185 All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO CSF2RB AND IL4 DN 315 201 All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF UP 418 282 All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF VS CSF2RB AND IL4 UP 408 276 All SZGR 2.0 genes in this pathway
KYNG WERNER SYNDROM AND NORMAL AGING UP 93 62 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 30MIN DN 150 99 All SZGR 2.0 genes in this pathway
WANG CLASSIC ADIPOGENIC TARGETS OF PPARG 26 15 All SZGR 2.0 genes in this pathway
CHYLA CBFA2T3 TARGETS UP 387 225 All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS UP 504 321 All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 UP 430 288 All SZGR 2.0 genes in this pathway
STEGER ADIPOGENESIS UP 21 16 All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D 882 506 All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM B 517 302 All SZGR 2.0 genes in this pathway