Gene Page: LRRC40
Summary ?
| GeneID | 55631 |
| Symbol | LRRC40 |
| Synonyms | dJ677H15.1 |
| Description | leucine rich repeat containing 40 |
| Reference | HGNC:HGNC:26004|Ensembl:ENSG00000066557|HPRD:08622|Vega:OTTHUMG00000009348 |
| Gene type | protein-coding |
| Map location | 1p31.1 |
| Pascal p-value | 0.583 |
| Fetal beta | 0.777 |
| DMG | 1 (# studies) |
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 |
| GSMA_IIA | Genome scan meta-analysis (All samples) | Psr: 0.02692 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg02809263 | 1 | 70671218 | LRRC40 | 3.8E-11 | -0.01 | 3.69E-7 | 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 |
| ZNF252 | 0.80 | 0.83 |
| YME1L1 | 0.79 | 0.82 |
| EIF2AK4 | 0.78 | 0.80 |
| IFNAR1 | 0.78 | 0.81 |
| DHX36 | 0.78 | 0.80 |
| UTP14C | 0.78 | 0.81 |
| TMEM184C | 0.78 | 0.78 |
| C5orf51 | 0.77 | 0.82 |
| XIAP | 0.77 | 0.82 |
| ZNF41 | 0.77 | 0.79 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| AF347015.31 | -0.65 | -0.67 |
| AF347015.21 | -0.64 | -0.65 |
| MT-CO2 | -0.63 | -0.66 |
| IFI27 | -0.62 | -0.65 |
| AF347015.8 | -0.61 | -0.65 |
| HIGD1B | -0.61 | -0.63 |
| MT-CYB | -0.61 | -0.64 |
| AF347015.2 | -0.60 | -0.63 |
| AF347015.27 | -0.60 | -0.63 |
| AF347015.33 | -0.59 | -0.62 |
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0003993 | acid phosphatase activity | IEA | - | |
| GO:0005515 | protein binding | IEA | - |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS DN | 463 | 290 | All SZGR 2.0 genes in this pathway |
| DODD NASOPHARYNGEAL CARCINOMA DN | 1375 | 806 | All SZGR 2.0 genes in this pathway |
| HAMAI APOPTOSIS VIA TRAIL UP | 584 | 356 | All SZGR 2.0 genes in this pathway |
| LASTOWSKA NEUROBLASTOMA COPY NUMBER DN | 800 | 473 | All SZGR 2.0 genes in this pathway |
| NUYTTEN NIPP1 TARGETS UP | 769 | 437 | All SZGR 2.0 genes in this pathway |
| WEI MIR34A TARGETS | 148 | 97 | All SZGR 2.0 genes in this pathway |
| MOREAUX MULTIPLE MYELOMA BY TACI DN | 172 | 107 | All SZGR 2.0 genes in this pathway |
| MARSON BOUND BY E2F4 UNSTIMULATED | 728 | 415 | All SZGR 2.0 genes in this pathway |
| ZHANG BREAST CANCER PROGENITORS UP | 425 | 253 | All SZGR 2.0 genes in this pathway |
| CHANG CORE SERUM RESPONSE UP | 212 | 128 | All SZGR 2.0 genes in this pathway |
| COLINA TARGETS OF 4EBP1 AND 4EBP2 | 356 | 214 | All SZGR 2.0 genes in this pathway |
| PILON KLF1 TARGETS DN | 1972 | 1213 | All SZGR 2.0 genes in this pathway |
| FOSTER KDM1A TARGETS DN | 211 | 119 | All SZGR 2.0 genes in this pathway |