Gene Page: NUPL2
Summary ?
GeneID | 11097 |
Symbol | NUPL2 |
Synonyms | CG1|NLP-1|NLP_1|hCG1 |
Description | nucleoporin like 2 |
Reference | HGNC:HGNC:17010|Ensembl:ENSG00000136243|HPRD:14855|Vega:OTTHUMG00000096955 |
Gene type | protein-coding |
Map location | 7p15 |
Pascal p-value | 0.113 |
Sherlock p-value | 0.877 |
Fetal beta | 0.207 |
DMG | 2 (# studies) |
eGene | Caudate basal ganglia Cerebellar Hemisphere Cerebellum Cortex Frontal Cortex BA9 Hippocampus Nucleus accumbens basal ganglia Meta |
Support | CompositeSet |
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 |
DNM:Fromer_2014 | Whole Exome Sequencing analysis | This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA. | |
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
DNM table
Gene | Chromosome | Position | Ref | Alt | Transcript | AA change | Mutation type | Sift | CG46 | Trait | Study |
---|---|---|---|---|---|---|---|---|---|---|---|
NUPL2 | chr7 | 23221811 | A | AGGCAGCAACCGC | NM_007342 | . | out-of-frame-codon-insertion | Schizophrenia | DNM:Fromer_2014 |
Differentially methylated gene
Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
---|---|---|---|---|---|---|---|
cg20723844 | 7 | 23220997 | NUPL2 | 3.056E-4 | 0.282 | 0.04 | DMG:Wockner_2014 |
cg19941686 | 7 | 23221979 | NUPL2 | 6.89E-8 | -0.01 | 1.68E-5 | DMG:Jaffe_2016 |
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 |
PSMB4 | 0.92 | 0.92 |
DCTPP1 | 0.92 | 0.94 |
CUEDC2 | 0.91 | 0.93 |
PSMA7 | 0.91 | 0.93 |
POP7 | 0.91 | 0.91 |
SF3B5 | 0.91 | 0.94 |
PSMB3 | 0.91 | 0.88 |
UFD1L | 0.90 | 0.91 |
C16orf91 | 0.90 | 0.90 |
C12orf10 | 0.90 | 0.89 |
Top 10 negatively co-expressed genes | ||
Gene | Pearson's Correlation | Spearman's Correlation |
AF347015.26 | -0.69 | -0.79 |
AF347015.15 | -0.67 | -0.74 |
AF347015.2 | -0.66 | -0.74 |
AF347015.8 | -0.66 | -0.72 |
MT-CYB | -0.65 | -0.73 |
AF347015.27 | -0.64 | -0.73 |
AF347015.33 | -0.64 | -0.72 |
MT-CO2 | -0.63 | -0.68 |
SLC6A12 | -0.61 | -0.66 |
MYH14 | -0.60 | -0.68 |
Section V. Pathway annotation
Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
---|---|---|---|
REACTOME METABOLISM OF NON CODING RNA | 49 | 29 | All SZGR 2.0 genes in this pathway |
REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES | 66 | 45 | All SZGR 2.0 genes in this pathway |
REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA | 140 | 77 | All SZGR 2.0 genes in this pathway |
REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM | 54 | 34 | All SZGR 2.0 genes in this pathway |
REACTOME TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES | 413 | 270 | All SZGR 2.0 genes in this pathway |
REACTOME MRNA PROCESSING | 161 | 86 | All SZGR 2.0 genes in this pathway |
REACTOME TRANSPORT OF MATURE MRNA DERIVED FROM AN INTRONLESS TRANSCRIPT | 33 | 21 | All SZGR 2.0 genes in this pathway |
REACTOME SLC MEDIATED TRANSMEMBRANE TRANSPORT | 241 | 157 | All SZGR 2.0 genes in this pathway |
REACTOME GLUCOSE TRANSPORT | 38 | 29 | All SZGR 2.0 genes in this pathway |
REACTOME METABOLISM OF RNA | 330 | 155 | All SZGR 2.0 genes in this pathway |
REACTOME INTERFERON SIGNALING | 159 | 116 | All SZGR 2.0 genes in this pathway |
REACTOME METABOLISM OF CARBOHYDRATES | 247 | 154 | All SZGR 2.0 genes in this pathway |
REACTOME INFLUENZA LIFE CYCLE | 203 | 72 | All SZGR 2.0 genes in this pathway |
REACTOME NEP NS2 INTERACTS WITH THE CELLULAR EXPORT MACHINERY | 27 | 19 | All SZGR 2.0 genes in this pathway |
REACTOME HIV INFECTION | 207 | 122 | All SZGR 2.0 genes in this pathway |
REACTOME TRANSPORT OF RIBONUCLEOPROTEINS INTO THE HOST NUCLEUS | 27 | 19 | All SZGR 2.0 genes in this pathway |
REACTOME HIV LIFE CYCLE | 125 | 69 | All SZGR 2.0 genes in this pathway |
REACTOME HOST INTERACTIONS OF HIV FACTORS | 132 | 81 | All SZGR 2.0 genes in this pathway |
REACTOME LATE PHASE OF HIV LIFE CYCLE | 104 | 61 | All SZGR 2.0 genes in this pathway |
REACTOME INTERACTIONS OF VPR WITH HOST CELLULAR PROTEINS | 33 | 21 | All SZGR 2.0 genes in this pathway |
REACTOME REGULATION OF GLUCOKINASE BY GLUCOKINASE REGULATORY PROTEIN | 27 | 19 | All SZGR 2.0 genes in this pathway |
REACTOME IMMUNE SYSTEM | 933 | 616 | All SZGR 2.0 genes in this pathway |
REACTOME CYTOKINE SIGNALING IN IMMUNE SYSTEM | 270 | 204 | All SZGR 2.0 genes in this pathway |
HOLLMANN APOPTOSIS VIA CD40 DN | 267 | 178 | All SZGR 2.0 genes in this pathway |
DODD NASOPHARYNGEAL CARCINOMA DN | 1375 | 806 | All SZGR 2.0 genes in this pathway |
PUJANA BRCA1 PCC NETWORK | 1652 | 1023 | All SZGR 2.0 genes in this pathway |
IVANOVA HEMATOPOIESIS EARLY PROGENITOR | 532 | 309 | All SZGR 2.0 genes in this pathway |
BROWNE HCMV INFECTION 10HR DN | 56 | 37 | All SZGR 2.0 genes in this pathway |
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP | 863 | 514 | All SZGR 2.0 genes in this pathway |
YAGI AML WITH INV 16 TRANSLOCATION | 422 | 277 | All SZGR 2.0 genes in this pathway |
BROWNE HCMV INFECTION 1HR DN | 222 | 147 | All SZGR 2.0 genes in this pathway |
KOINUMA TARGETS OF SMAD2 OR SMAD3 | 824 | 528 | All SZGR 2.0 genes in this pathway |