Gene Page: IQSEC1
Summary ?
| GeneID | 9922 |
| Symbol | IQSEC1 |
| Synonyms | ARF-GEP100|ARFGEP100|BRAG2|GEP100 |
| Description | IQ motif and Sec7 domain 1 |
| Reference | MIM:610166|HGNC:HGNC:29112|Ensembl:ENSG00000144711|HPRD:11052|Vega:OTTHUMG00000155398 |
| Gene type | protein-coding |
| Map location | 3p25.2 |
| Pascal p-value | 0.003 |
| Sherlock p-value | 0.571 |
| Fetal beta | -1.274 |
| DMG | 1 (# studies) |
| eGene | Cerebellar Hemisphere Cerebellum Myers' cis & trans |
| Support | INTRACELLULAR SIGNAL TRANSDUCTION G2Cdb.humanPSD G2Cdb.humanPSP CompositeSet Ascano FMRP targets |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:GWASdb | Genome-wide Association Studies | GWASdb records for schizophrenia | |
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| 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 |
| GSMA_I | Genome scan meta-analysis | Psr: 0.006 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg11145772 | 3 | 12966188 | IQSEC1 | 2.113E-4 | 0.391 | 0.035 | DMG:Wockner_2014 |
| cg12292584 | 3 | 12949457 | IQSEC1 | 4.167E-4 | 0.425 | 0.044 | DMG:Wockner_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs4079151 | chr3 | 12004652 | IQSEC1 | 9922 | 0.05 | cis | ||
| rs17035527 | chr3 | 12004824 | IQSEC1 | 9922 | 0.05 | cis | ||
| rs11926749 | chr3 | 12006745 | IQSEC1 | 9922 | 0.05 | cis | ||
| rs11926752 | chr3 | 12006771 | IQSEC1 | 9922 | 0.09 | cis | ||
| rs17035542 | chr3 | 12006854 | IQSEC1 | 9922 | 0.05 | cis | ||
| rs17035544 | chr3 | 12006891 | IQSEC1 | 9922 | 0.05 | cis | ||
| rs6751666 | chr2 | 103098570 | IQSEC1 | 9922 | 0.08 | trans | ||
| rs17027295 | chr2 | 103098870 | IQSEC1 | 9922 | 0.08 | trans | ||
| rs6543148 | chr2 | 103100218 | IQSEC1 | 9922 | 0.1 | trans | ||
| rs7566613 | chr2 | 103100494 | IQSEC1 | 9922 | 0.08 | trans | ||
| snp_a-2029385 | 0 | IQSEC1 | 9922 | 0.1 | 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 |
| MRPS2 | 0.92 | 0.93 |
| EMD | 0.91 | 0.90 |
| C7orf43 | 0.91 | 0.91 |
| LRRC41 | 0.90 | 0.89 |
| ERAL1 | 0.90 | 0.89 |
| PPP2R1A | 0.90 | 0.88 |
| LYPLA2 | 0.90 | 0.90 |
| TMEM115 | 0.89 | 0.89 |
| KDELR1 | 0.89 | 0.89 |
| ADPRHL2 | 0.89 | 0.90 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| MT-CO2 | -0.77 | -0.79 |
| AF347015.31 | -0.77 | -0.78 |
| AF347015.8 | -0.76 | -0.80 |
| AF347015.27 | -0.75 | -0.79 |
| AF347015.33 | -0.74 | -0.77 |
| MT-CYB | -0.74 | -0.78 |
| AF347015.21 | -0.73 | -0.81 |
| AF347015.2 | -0.72 | -0.78 |
| AF347015.15 | -0.70 | -0.77 |
| AF347015.26 | -0.69 | -0.76 |
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0005086 | ARF guanyl-nucleotide exchange factor activity | IEA | - | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0032012 | regulation of ARF protein signal transduction | IEA | - | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0005622 | intracellular | IEA | - | |
| GO:0005634 | nucleus | IEA | - | |
| GO:0005737 | cytoplasm | IEA | - |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| KEGG ENDOCYTOSIS | 183 | 132 | All SZGR 2.0 genes in this pathway |
| PID ARF6 PATHWAY | 35 | 27 | All SZGR 2.0 genes in this pathway |
| DEURIG T CELL PROLYMPHOCYTIC LEUKEMIA DN | 320 | 184 | All SZGR 2.0 genes in this pathway |
| CHARAFE BREAST CANCER LUMINAL VS BASAL UP | 380 | 215 | All SZGR 2.0 genes in this pathway |
| HOEBEKE LYMPHOID STEM CELL UP | 95 | 64 | All SZGR 2.0 genes in this pathway |
| RHEIN ALL GLUCOCORTICOID THERAPY UP | 78 | 41 | All SZGR 2.0 genes in this pathway |
| MULLIGHAN MLL SIGNATURE 1 UP | 380 | 236 | All SZGR 2.0 genes in this pathway |
| DODD NASOPHARYNGEAL CARCINOMA UP | 1821 | 933 | All SZGR 2.0 genes in this pathway |
| LASTOWSKA NEUROBLASTOMA COPY NUMBER DN | 800 | 473 | All SZGR 2.0 genes in this pathway |
| PEREZ TP53 TARGETS | 1174 | 695 | All SZGR 2.0 genes in this pathway |
| NUYTTEN NIPP1 TARGETS DN | 848 | 527 | All SZGR 2.0 genes in this pathway |
| CUI TCF21 TARGETS 2 DN | 830 | 547 | All SZGR 2.0 genes in this pathway |
| DOUGLAS BMI1 TARGETS UP | 566 | 371 | All SZGR 2.0 genes in this pathway |
| CREIGHTON ENDOCRINE THERAPY RESISTANCE 5 | 482 | 296 | All SZGR 2.0 genes in this pathway |
| STEIN ESRRA TARGETS UP | 388 | 234 | All SZGR 2.0 genes in this pathway |
| ZHANG TLX TARGETS 60HR UP | 293 | 203 | All SZGR 2.0 genes in this pathway |
| CROONQUIST NRAS VS STROMAL STIMULATION UP | 41 | 26 | All SZGR 2.0 genes in this pathway |
| STEIN ESRRA TARGETS | 535 | 325 | All SZGR 2.0 genes in this pathway |
| GUTIERREZ CHRONIC LYMPHOCYTIC LEUKEMIA UP | 12 | 5 | All SZGR 2.0 genes in this pathway |
| MARTENS BOUND BY PML RARA FUSION | 456 | 287 | All SZGR 2.0 genes in this pathway |