Gene Page: LIME1
Summary ?
| GeneID | 54923 |
| Symbol | LIME1 |
| Synonyms | LIME|dJ583P15.4 |
| Description | Lck interacting transmembrane adaptor 1 |
| Reference | MIM:609809|HGNC:HGNC:26016|Ensembl:ENSG00000203896|HPRD:07904|Vega:OTTHUMG00000032999 |
| Gene type | protein-coding |
| Map location | 20q13.3 |
| Pascal p-value | 0.003 |
| Sherlock p-value | 0.56 |
| Fetal beta | -0.153 |
| DMG | 1 (# studies) |
| eGene | Myers' cis & trans |
| Support | G2Cdb.humanPSD G2Cdb.humanPSP |
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). | 3 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg21201401 | 20 | 62367884 | LIME1 | 1.37E-5 | 0.802 | 0.014 | DMG:Wockner_2014 |
| cg20513976 | 20 | 62367893 | LIME1 | 5.52E-5 | 0.685 | 0.022 | DMG:Wockner_2014 |
| cg00446123 | 20 | 62367888 | LIME1 | 1.517E-4 | 0.754 | 0.032 | DMG:Wockner_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs3845734 | chr2 | 171125572 | LIME1 | 54923 | 0.05 | trans | ||
| rs1368303 | chr5 | 147672388 | LIME1 | 54923 | 0.11 | trans | ||
| rs17104720 | chr14 | 77127308 | LIME1 | 54923 | 0.09 | trans | ||
| rs16955618 | chr15 | 29937543 | LIME1 | 54923 | 1.519E-5 | 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 |
| THAP11 | 0.92 | 0.90 |
| MRPS16 | 0.91 | 0.89 |
| BYSL | 0.91 | 0.91 |
| COG4 | 0.91 | 0.89 |
| PSMD3 | 0.91 | 0.91 |
| RIC8A | 0.90 | 0.91 |
| ZFP64 | 0.90 | 0.90 |
| LRRC41 | 0.90 | 0.91 |
| CHMP7 | 0.90 | 0.91 |
| DCAKD | 0.90 | 0.88 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| AF347015.27 | -0.76 | -0.85 |
| AF347015.8 | -0.75 | -0.86 |
| AF347015.31 | -0.74 | -0.82 |
| MT-CO2 | -0.74 | -0.82 |
| AF347015.33 | -0.74 | -0.83 |
| MT-CYB | -0.72 | -0.82 |
| AF347015.15 | -0.71 | -0.82 |
| AF347015.21 | -0.71 | -0.85 |
| AF347015.2 | -0.69 | -0.81 |
| AF347015.26 | -0.69 | -0.82 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| CHEMNITZ RESPONSE TO PROSTAGLANDIN E2 DN | 391 | 222 | All SZGR 2.0 genes in this pathway |
| NIKOLSKY BREAST CANCER 20Q12 Q13 AMPLICON | 149 | 76 | All SZGR 2.0 genes in this pathway |
| GAVIN FOXP3 TARGETS CLUSTER P2 | 79 | 55 | All SZGR 2.0 genes in this pathway |
| SMID BREAST CANCER NORMAL LIKE UP | 476 | 285 | All SZGR 2.0 genes in this pathway |
| SHEDDEN LUNG CANCER GOOD SURVIVAL A12 | 317 | 177 | All SZGR 2.0 genes in this pathway |
| MILI PSEUDOPODIA CHEMOTAXIS DN | 457 | 302 | All SZGR 2.0 genes in this pathway |
| WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D | 882 | 506 | All SZGR 2.0 genes in this pathway |