Gene Page: LCN1
Summary ?
| GeneID | 3933 |
| Symbol | LCN1 |
| Synonyms | PMFA|TLC|TP|VEGP |
| Description | lipocalin 1 |
| Reference | MIM:151675|HGNC:HGNC:6525|Ensembl:ENSG00000160349|HPRD:01059|Vega:OTTHUMG00000020908 |
| Gene type | protein-coding |
| Map location | 9q34 |
| Pascal p-value | 0.013 |
| eGene | Anterior cingulate cortex BA24 Cortex Frontal Cortex BA9 Meta |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS |
Section I. Genetics and epigenetics annotation
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs56024916 | 9 | 138414956 | LCN1 | ENSG00000160349.5 | 4.79214E-8 | 0.01 | 1672 | gtex_brain_ba24 |
| rs56239374 | 9 | 138415201 | LCN1 | ENSG00000160349.5 | 4.63254E-8 | 0.01 | 1917 | gtex_brain_ba24 |
| rs56120410 | 9 | 138415238 | LCN1 | ENSG00000160349.5 | 9.46796E-7 | 0.01 | 1954 | gtex_brain_ba24 |
Section II. Transcriptome annotation
General gene expression (GTEx)
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 |
| SAT1 | 0.87 | 0.85 |
| MT1G | 0.85 | 0.78 |
| SLC25A33 | 0.83 | 0.72 |
| SCRG1 | 0.83 | 0.82 |
| MT3 | 0.82 | 0.82 |
| PSMB8 | 0.82 | 0.85 |
| CBR3 | 0.82 | 0.86 |
| RLBP1 | 0.81 | 0.83 |
| TLCD1 | 0.81 | 0.84 |
| MT1F | 0.81 | 0.77 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| USP7 | -0.66 | -0.73 |
| MYO18A | -0.66 | -0.71 |
| ANKRD17 | -0.66 | -0.74 |
| EIF4ENIF1 | -0.65 | -0.74 |
| MCM3AP | -0.65 | -0.74 |
| HNRNPUL2 | -0.65 | -0.68 |
| PDXDC1 | -0.65 | -0.74 |
| ARIH1 | -0.65 | -0.77 |
| NOLC1 | -0.65 | -0.73 |
| HERC1 | -0.65 | -0.75 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| NADLER HYPERGLYCEMIA AT OBESITY | 58 | 35 | All SZGR 2.0 genes in this pathway |
| ACEVEDO METHYLATED IN LIVER CANCER DN | 940 | 425 | All SZGR 2.0 genes in this pathway |