Gene Page:NR1D1

Summary?
GeneID 9572
Symbol NR1D1
Synonyms EAR1|THRA1|THRAL|ear-1|hRev
Description nuclear receptor subfamily 1 group D member 1
Reference MIM:602408|HGNC:HGNC:7962|Ensembl:ENSG00000126368|HPRD:03873|Vega:OTTHUMG00000133327
Gene type protein-coding
Map location 17q11.2
Pascal p-value 0.06
Sherlock p-value 0.535
DMG 2 (# studies)
eGene 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. 2
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.
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
cg07889337 17 38257022 NR1D1 3.62E-5 -0.332 0.02 DMG:Wockner_2014
cg13476336 17 38255694 NR1D1 2.9E-8 -0.008 8.96E-6 DMG:Jaffe_2016

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs2068673 chr12 60333402 NR1D1 9572 0.19 trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

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
C1orf9 0.95 0.96
SP3 0.93 0.95
WAPAL 0.93 0.94
NUP133 0.93 0.95
CNOT1 0.93 0.96
KIAA1429 0.92 0.95
GSTCD 0.92 0.93
ZMYM4 0.92 0.94
AP001011.3 0.92 0.95
PRKDC 0.92 0.95
Top 10 negatively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
FXYD1 -0.70 -0.84
MT-CO2 -0.70 -0.84
AF347015.31 -0.69 -0.83
IFI27 -0.68 -0.83
AF347015.33 -0.67 -0.80
AF347015.27 -0.66 -0.79
HIGD1B -0.66 -0.82
HLA-F -0.66 -0.72
MT-CYB -0.65 -0.79
C5orf53 -0.65 -0.70

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
KEGG CIRCADIAN RHYTHM MAMMAL 13 13 All SZGR 2.0 genes in this pathway
PID CIRCADIAN PATHWAY 16 15 All SZGR 2.0 genes in this pathway
REACTOME BMAL1时钟NPAS2激活生理实验RESSION 36 27 All SZGR 2.0 genes in this pathway
REACTOME PPARA ACTIVATES GENE EXPRESSION 104 72 All SZGR 2.0 genes in this pathway
REACTOME RORA ACTIVATES CIRCADIAN EXPRESSION 24 17 All SZGR 2.0 genes in this pathway
REACTOME CIRCADIAN REPRESSION OF EXPRESSION BY REV ERBA 23 16 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
REACTOME METABOLISM OF LIPIDS AND LIPOPROTEINS 478 302 All SZGR 2.0 genes in this pathway
REACTOME FATTY ACID TRIACYLGLYCEROL AND KETONE BODY METABOLISM 168 115 All SZGR 2.0 genes in this pathway
REACTOME CIRCADIAN CLOCK 53 40 All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER UP 443 294 All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 4 5WK DN 196 131 All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 6 7WK DN 79 54 All SZGR 2.0 genes in this pathway
KONG E2F3 TARGETS 97 58 All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER UP 358 245 All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP 1037 673 All SZGR 2.0 genes in this pathway
BENPORATH MYC TARGETS WITH EBOX 230 156 All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS 775 494 All SZGR 2.0 genes in this pathway
NIKOLSKY BREAST CANCER 17Q11 Q21 AMPLICON 133 78 All SZGR 2.0 genes in this pathway
UEDA PERIFERAL CLOCK 169 111 All SZGR 2.0 genes in this pathway
FERNANDEZ BOUND BY MYC 182 116 All SZGR 2.0 genes in this pathway
GERY CEBP TARGETS 126 90 All SZGR 2.0 genes in this pathway
DAZARD UV RESPONSE CLUSTER G3 15 10 All SZGR 2.0 genes in this pathway
LEE AGING CEREBELLUM DN 86 66 All SZGR 2.0 genes in this pathway
DAZARD RESPONSE TO UV NHEK UP 244 151 All SZGR 2.0 genes in this pathway
VARELA ZMPSTE24 TARGETS UP 40 30 All SZGR 2.0 genes in this pathway
LEE CALORIE RESTRICTION MUSCLE DN 51 28 All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 STIMULATED 1022 619 All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 UNSTIMULATED 1229 713 All SZGR 2.0 genes in this pathway
ICHIBA GRAFT VERSUS HOST DISEASE 35D DN 49 34 All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103 714 All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 0 76 54 All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D 882 506 All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND WITH H4K20ME1 MARK 145 82 All SZGR 2.0 genes in this pathway
YANG BCL3 TARGETS UP 364 236 All SZGR 2.0 genes in this pathway
DELACROIX RARG BOUND MEF 367 231 All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725 838 All SZGR 2.0 genes in this pathway