Gene Page:LIMD1
Summary?
| GeneID | 8994 |
| Symbol | LIMD1 |
| Synonyms | - |
| Description | LIM domains containing 1 |
| Reference | MIM:604543|HGNC:HGNC:6612|HPRD:05177| |
| Gene type | protein-coding |
| Map location | 3p21.3 |
| Pascal p-value | 0.953 |
| Fetal beta | 1.583 |
| eGene | Cortex Frontal Cortex BA9 Nucleus accumbens basal ganglia Myers' cis & trans 元 |
| Support | CompositeSet |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DNM:Fromer_2014 | Whole Exome Sequencing analysis | This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA. |
Section I. Genetics and epigenetics annotation
DNM table
DNM table| Gene | Chromosome | Position | Ref | Alt | Transcript | AA change | Mutation type | Sift | CG46 | Trait | Study |
|---|---|---|---|---|---|---|---|---|---|---|---|
| LIMD1 | chr3 | 45637495 | C | G | NM_014240 | p.375T>R | missense | Schizophrenia | DNM:Fromer_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs2494067 | chr1 | 108245614 | LIMD1 | 8994 | 0.17 | 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
死神:胎儿(13 - 26 postconception周),圣2: 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 |
| WDR45L | 0.80 | 0.74 |
| IKZF5 | 0.80 | 0.80 |
| KIAA1737 | 0.79 | 0.78 |
| KIAA0196 | 0.79 | 0.75 |
| BCL2L13 | 0.79 | 0.75 |
| HIATL1 | 0.79 | 0.74 |
| RFT1 | 0.78 | 0.73 |
| ADIPOR1 | 0.78 | 0.69 |
| KIAA0652 | 0.78 | 0.76 |
| SLC35A5 | 0.78 | 0.75 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| AF347015.21 | -0.65 | -0.50 |
| AF347015.18 | -0.64 | -0.52 |
| IL32 | -0.60 | -0.48 |
| AC098691.2 | -0.60 | -0.50 |
| AF347015.8 | -0.58 | -0.46 |
| MT-CO2 | -0.57 | -0.46 |
| MT-ATP8 | -0.54 | -0.46 |
| AC100783.1 | -0.53 | -0.43 |
| AC010300.1 | -0.53 | -0.49 |
| AF347015.26 | -0.52 | -0.40 |
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 |
| SENESE HDAC3 TARGETS DN | 536 | 332 | All SZGR 2.0 genes in this pathway |
| RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED DN | 805 | 505 | 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 |
| LIU COMMON CANCER GENES | 79 | 47 | All SZGR 2.0 genes in this pathway |
| BLALOCK ALZHEIMERS DISEASE UP | 1691 | 1088 | All SZGR 2.0 genes in this pathway |
| CREIGHTON ENDOCRINE THERAPY RESISTANCE 3 | 720 | 440 | All SZGR 2.0 genes in this pathway |
| CHANDRAN METASTASIS UP | 221 | 135 | All SZGR 2.0 genes in this pathway |
| SENGUPTA EBNA1 ANTICORRELATED | 173 | 85 | All SZGR 2.0 genes in this pathway |
| KYNG RESPONSE TO H2O2 VIA ERCC6 UP | 40 | 30 | All SZGR 2.0 genes in this pathway |
| CHICAS RB1 TARGETS CONFLUENT | 567 | 365 | All SZGR 2.0 genes in this pathway |
| PILON KLF1 TARGETS DN | 1972 | 1213 | All SZGR 2.0 genes in this pathway |
| PASINI SUZ12 TARGETS DN | 315 | 215 | All SZGR 2.0 genes in this pathway |
| FEVR CTNNB1 TARGETS DN | 553 | 343 | All SZGR 2.0 genes in this pathway |