Gene Page: LRIT1
Summary ?
| GeneID | 26103 |
| Symbol | LRIT1 |
| Synonyms | FIGLER9|LRRC21|PAL |
| Description | leucine-rich repeat, Ig-like and transmembrane domains 1 |
| Reference | MIM:616103|HGNC:HGNC:23404|Ensembl:ENSG00000148602|HPRD:14315|Vega:OTTHUMG00000018632 |
| Gene type | protein-coding |
| Map location | 10q23 |
| Pascal p-value | 0.032 |
| Fetal beta | -0.117 |
| DMG | 1 (# studies) |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| 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). | 1 |
Section I. Genetics and epigenetics annotation
DNM table
| Gene | Chromosome | Position | Ref | Alt | Transcript | AA change | Mutation type | Sift | CG46 | Trait | Study |
|---|---|---|---|---|---|---|---|---|---|---|---|
| LRIT1 | chr10 | 85991878 | G | A | NM_015613 | . | silent | Schizophrenia | DNM:Xu_2012 |
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg05375443 | 10 | 85997426 | LRIT1 | 9.12E-5 | 0.348 | 0.027 | DMG:Wockner_2014 |
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 |
| ACYP2 | 0.85 | 0.86 |
| DDIT3 | 0.84 | 0.85 |
| ACOT13 | 0.83 | 0.87 |
| CREM | 0.82 | 0.83 |
| HIGD1A | 0.82 | 0.80 |
| CISD3 | 0.81 | 0.82 |
| NDUFA4 | 0.81 | 0.82 |
| C12orf62 | 0.81 | 0.82 |
| C5orf32 | 0.79 | 0.83 |
| AGPHD1 | 0.79 | 0.81 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| VAV2 | -0.68 | -0.70 |
| KIAA1949 | -0.68 | -0.71 |
| GMIP | -0.66 | -0.62 |
| C19orf57 | -0.66 | -0.59 |
| VASH1 | -0.66 | -0.70 |
| KIAA1211 | -0.66 | -0.67 |
| ZCCHC8 | -0.65 | -0.61 |
| JUP | -0.65 | -0.66 |
| ZNF551 | -0.65 | -0.61 |
| CRMP1 | -0.65 | -0.59 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| PUJANA ATM PCC NETWORK | 1442 | 892 | All SZGR 2.0 genes in this pathway |
| ZWANG DOWN BY 2ND EGF PULSE | 293 | 119 | All SZGR 2.0 genes in this pathway |