Gene Page: LZTR1
Summary ?
| GeneID | 8216 |
| Symbol | LZTR1 |
| Synonyms | BTBD29|LZTR-1|NS10|SWNTS2 |
| Description | leucine-zipper-like transcription regulator 1 |
| Reference | MIM:600574|HGNC:HGNC:6742|Ensembl:ENSG00000099949|HPRD:08992|Vega:OTTHUMG00000150878 |
| Gene type | protein-coding |
| Map location | 22q11.21|22q11.1-q11.2 |
| Pascal p-value | 0.388 |
| Sherlock p-value | 0.722 |
| Fetal beta | 0.551 |
| DMG | 2 (# studies) |
| eGene | Cerebellum Hippocampus |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CNV:YES | Copy number variation studies | Manual curation | |
| 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. | 2 |
| DMG:Nishioka_2013 | Genome-wide DNA methylation analysis | The authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls. | 2 |
| GSMA_I | Genome scan meta-analysis | Psr: 0.031 |
Section I. Genetics and epigenetics annotation
DNM table
| Gene | Chromosome | Position | Ref | Alt | Transcript | AA change | Mutation type | Sift | CG46 | Trait | Study |
|---|---|---|---|---|---|---|---|---|---|---|---|
| LZTR1 | chr22 | 21351589 | C | T | NM_006767 | . | silent | Schizophrenia | DNM:Fromer_2014 |
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg03697316 | 22 | 21336741 | LZTR1 | -0.028 | 0.66 | DMG:Nishioka_2013 | |
| cg03352409 | 22 | 21336370 | LZTR1 | 8.66E-10 | -0.013 | 1.09E-6 | 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 |
| TMEM101 | 0.78 | 0.77 |
| ALG3 | 0.76 | 0.76 |
| SLC25A39 | 0.76 | 0.76 |
| GPAA1 | 0.74 | 0.76 |
| TMEM161A | 0.73 | 0.68 |
| VKORC1 | 0.72 | 0.73 |
| ILVBL | 0.72 | 0.75 |
| FAM69B | 0.72 | 0.68 |
| YIPF2 | 0.71 | 0.72 |
| CYHR1 | 0.71 | 0.69 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| MT-ATP8 | -0.44 | -0.43 |
| AF347015.21 | -0.41 | -0.40 |
| AF347015.8 | -0.41 | -0.36 |
| AF347015.27 | -0.40 | -0.38 |
| AF347015.18 | -0.40 | -0.47 |
| AF347015.26 | -0.39 | -0.38 |
| AF347015.15 | -0.38 | -0.33 |
| MT-CYB | -0.38 | -0.34 |
| AF347015.33 | -0.38 | -0.35 |
| SEC62 | -0.37 | -0.43 |
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0003700 | transcription factor activity | TAS | 7633402 | |
| GO:0005515 | protein binding | IEA | - | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0009653 | anatomical structure morphogenesis | TAS | 7633402 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| CHARAFE BREAST CANCER LUMINAL VS BASAL UP | 380 | 215 | All SZGR 2.0 genes in this pathway |
| WIKMAN ASBESTOS LUNG CANCER DN | 28 | 13 | All SZGR 2.0 genes in this pathway |
| GRAESSMANN APOPTOSIS BY DOXORUBICIN UP | 1142 | 669 | All SZGR 2.0 genes in this pathway |
| GRAESSMANN RESPONSE TO MC AND DOXORUBICIN UP | 612 | 367 | All SZGR 2.0 genes in this pathway |
| TSAI RESPONSE TO IONIZING RADIATION | 149 | 101 | All SZGR 2.0 genes in this pathway |
| GROSS HYPOXIA VIA HIF1A UP | 77 | 49 | All SZGR 2.0 genes in this pathway |
| GROSS HYPOXIA VIA ELK3 AND HIF1A DN | 103 | 71 | All SZGR 2.0 genes in this pathway |
| BENPORATH MYC MAX TARGETS | 775 | 494 | All SZGR 2.0 genes in this pathway |
| WONG IFNA2 RESISTANCE DN | 34 | 20 | All SZGR 2.0 genes in this pathway |
| BLALOCK ALZHEIMERS DISEASE UP | 1691 | 1088 | All SZGR 2.0 genes in this pathway |
| LEE METASTASIS AND ALTERNATIVE SPLICING UP | 74 | 51 | All SZGR 2.0 genes in this pathway |
| QI PLASMACYTOMA DN | 100 | 63 | All SZGR 2.0 genes in this pathway |
| DANG BOUND BY MYC | 1103 | 714 | All SZGR 2.0 genes in this pathway |
| KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP | 682 | 440 | All SZGR 2.0 genes in this pathway |
| FOSTER KDM1A TARGETS DN | 211 | 119 | All SZGR 2.0 genes in this pathway |