Gene Page: LLGL2
Summary ?
| GeneID | 3993 |
| Symbol | LLGL2 |
| Synonyms | HGL|Hugl-2|LGL2 |
| Description | lethal giant larvae homolog 2, scribble cell polarity complex component |
| Reference | HGNC:HGNC:6629|Ensembl:ENSG00000073350|HPRD:10041|Vega:OTTHUMG00000179685 |
| Gene type | protein-coding |
| Map location | 17q25.1 |
| Pascal p-value | 0.565 |
| Sherlock p-value | 0.352 |
| Fetal beta | -0.413 |
| eGene | Myers' cis & trans Meta |
| 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
| Gene | Chromosome | Position | Ref | Alt | Transcript | AA change | Mutation type | Sift | CG46 | Trait | Study |
|---|---|---|---|---|---|---|---|---|---|---|---|
| LLGL2 | chr17 | 73559230 | C | T | NM_001015002 NM_001031803 NM_004524 | p.222R>C p.222R>C p.222R>C | missense missense missense | Schizophrenia | DNM:Fromer_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs2502827 | chr1 | 176044216 | LLGL2 | 3993 | 0.15 | trans | ||
| rs6753473 | chr2 | 26526418 | LLGL2 | 3993 | 0.2 | trans | ||
| rs16829545 | chr2 | 151977407 | LLGL2 | 3993 | 3.836E-7 | trans | ||
| rs7584986 | chr2 | 184111432 | LLGL2 | 3993 | 0.03 | trans | ||
| rs17158735 | chr10 | 2681063 | LLGL2 | 3993 | 0.12 | trans | ||
| rs2393316 | chr10 | 59333070 | LLGL2 | 3993 | 0.19 | trans | ||
| rs16955618 | chr15 | 29937543 | LLGL2 | 3993 | 3.63E-13 | trans | ||
| rs1041786 | chr21 | 22617710 | LLGL2 | 3993 | 0.07 | 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 |
| CHD5 | 0.64 | 0.70 |
| BRUNOL4 | 0.64 | 0.66 |
| PITPNM3 | 0.62 | 0.70 |
| ANKRD6 | 0.62 | 0.70 |
| STYK1 | 0.61 | 0.67 |
| AP006285.4 | 0.61 | 0.67 |
| NPTXR | 0.61 | 0.67 |
| KRTAP5-2 | 0.61 | 0.65 |
| KIAA0284 | 0.61 | 0.67 |
| PNMA5 | 0.60 | 0.69 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| IMPA2 | -0.33 | -0.40 |
| ACAA2 | -0.29 | -0.29 |
| PECI | -0.29 | -0.31 |
| GNG11 | -0.29 | -0.29 |
| ANP32B | -0.28 | -0.36 |
| UXT | -0.28 | -0.27 |
| TEAD4 | -0.27 | -0.29 |
| TAX1BP3 | -0.27 | -0.22 |
| AF347015.21 | -0.27 | -0.15 |
| C14orf23 | -0.27 | -0.10 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| KEGG TIGHT JUNCTION | 134 | 86 | All SZGR 2.0 genes in this pathway |
| CHARAFE BREAST CANCER LUMINAL VS BASAL UP | 380 | 215 | All SZGR 2.0 genes in this pathway |
| CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL UP | 450 | 256 | All SZGR 2.0 genes in this pathway |
| ODONNELL TFRC TARGETS UP | 456 | 228 | All SZGR 2.0 genes in this pathway |
| ODONNELL TARGETS OF MYC AND TFRC UP | 83 | 50 | All SZGR 2.0 genes in this pathway |
| WAMUNYOKOLI OVARIAN CANCER LMP UP | 265 | 158 | All SZGR 2.0 genes in this pathway |
| WAMUNYOKOLI OVARIAN CANCER GRADES 1 2 UP | 137 | 84 | All SZGR 2.0 genes in this pathway |
| DODD NASOPHARYNGEAL CARCINOMA UP | 1821 | 933 | All SZGR 2.0 genes in this pathway |
| RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED DN | 805 | 505 | All SZGR 2.0 genes in this pathway |
| CHIARADONNA NEOPLASTIC TRANSFORMATION KRAS DN | 142 | 95 | 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 |
| RASHI RESPONSE TO IONIZING RADIATION 5 | 147 | 89 | All SZGR 2.0 genes in this pathway |
| SCHAEFFER PROSTATE DEVELOPMENT 48HR UP | 487 | 286 | All SZGR 2.0 genes in this pathway |
| NIKOLSKY BREAST CANCER 17Q21 Q25 AMPLICON | 335 | 181 | All SZGR 2.0 genes in this pathway |
| LI WILMS TUMOR VS FETAL KIDNEY 1 UP | 182 | 119 | All SZGR 2.0 genes in this pathway |
| BLALOCK ALZHEIMERS DISEASE UP | 1691 | 1088 | All SZGR 2.0 genes in this pathway |
| MCDOWELL ACUTE LUNG INJURY DN | 48 | 33 | All SZGR 2.0 genes in this pathway |
| KRIGE RESPONSE TO TOSEDOSTAT 6HR UP | 953 | 554 | All SZGR 2.0 genes in this pathway |
| KRIGE RESPONSE TO TOSEDOSTAT 24HR UP | 783 | 442 | All SZGR 2.0 genes in this pathway |
| HELLER HDAC TARGETS UP | 317 | 208 | All SZGR 2.0 genes in this pathway |
| RIZKI TUMOR INVASIVENESS 3D UP | 210 | 124 | All SZGR 2.0 genes in this pathway |
| AMBROSINI FLAVOPIRIDOL TREATMENT TP53 | 109 | 63 | All SZGR 2.0 genes in this pathway |
| MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 | 1069 | 729 | All SZGR 2.0 genes in this pathway |
| BOYAULT LIVER CANCER SUBCLASS G1 UP | 113 | 70 | All SZGR 2.0 genes in this pathway |
| MEISSNER NPC HCP WITH H3K4ME2 | 491 | 319 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN NPC HCP WITH H3K27ME3 | 341 | 243 | All SZGR 2.0 genes in this pathway |
| ZEMBUTSU SENSITIVITY TO CISPLATIN | 20 | 14 | All SZGR 2.0 genes in this pathway |
| DURAND STROMA NS UP | 162 | 103 | All SZGR 2.0 genes in this pathway |
| ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY | 1839 | 928 | All SZGR 2.0 genes in this pathway |
| ZWANG EGF INTERVAL DN | 214 | 124 | All SZGR 2.0 genes in this pathway |