Gene Page: LYSMD4
Summary ?
| GeneID | 145748 |
| Symbol | LYSMD4 |
| Synonyms | - |
| Description | LysM domain containing 4 |
| Reference | HGNC:HGNC:26571|Ensembl:ENSG00000183060|HPRD:08153|Vega:OTTHUMG00000149853 |
| Gene type | protein-coding |
| Map location | 15q26.3 |
| Pascal p-value | 0.224 |
| Sherlock p-value | 0.099 |
| DEG p-value | DEG:Sanders_2014:DS1_p=0.151:DS1_beta=0.038200:DS2_p=1.37e-01:DS2_beta=0.076:DS2_FDR=3.60e-01 |
| Fetal beta | 0.155 |
| DMG | 1 (# studies) |
| eGene | Caudate basal ganglia Cerebellar Hemisphere Cerebellum Cortex Frontal Cortex BA9 Hippocampus Nucleus accumbens basal ganglia Putamen basal ganglia Myers' cis & trans Meta |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DEG:Sanders_2013 | Microarray | Whole-genome gene expression profiles using microarrays on lymphoblastoid cell lines (LCLs) from 413 cases and 446 controls. | |
| 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
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg18550509 | 15 | 100273145 | LYSMD4 | 1.38E-5 | -0.271 | 0.014 | DMG:Wockner_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs12898636 | chr15 | 100282240 | LYSMD4 | 145748 | 0.18 | cis | ||
| rs7923495 | chr10 | 83175767 | LYSMD4 | 145748 | 0.14 | trans | ||
| rs17097683 | chr10 | 83176233 | LYSMD4 | 145748 | 0.14 | trans | ||
| rs11203155 | chr21 | 43170140 | LYSMD4 | 145748 | 0.16 | trans | ||
| rs35747287 | 15 | 100273607 | LYSMD4 | ENSG00000183060.11 | 1.22468E-6 | 0.03 | 159 | gtex_brain_putamen_basal |
| rs11631604 | 15 | 100273617 | LYSMD4 | ENSG00000183060.11 | 1.97252E-6 | 0.03 | 149 | gtex_brain_putamen_basal |
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.
No co-expressed genes in brain regions
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| STARK PREFRONTAL CORTEX 22Q11 DELETION DN | 517 | 309 | All SZGR 2.0 genes in this pathway |
| NIKOLSKY BREAST CANCER 15Q26 AMPLICON | 22 | 19 | All SZGR 2.0 genes in this pathway |
| IVANOVA HEMATOPOIESIS EARLY PROGENITOR | 532 | 309 | All SZGR 2.0 genes in this pathway |
| CREIGHTON ENDOCRINE THERAPY RESISTANCE 3 | 720 | 440 | All SZGR 2.0 genes in this pathway |
| BRUECKNER TARGETS OF MIRLET7A3 DN | 78 | 49 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN ES ICP WITH H3K4ME3 | 718 | 401 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN NPC ICP WITH H3K4ME3 | 445 | 257 | All SZGR 2.0 genes in this pathway |
| JUBAN TARGETS OF SPI1 AND FLI1 UP | 115 | 73 | All SZGR 2.0 genes in this pathway |