Gene Page: LSAMP
Summary ?
| GeneID | 4045 |
| Symbol | LSAMP |
| Synonyms | IGLON3|LAMP |
| Description | limbic system-associated membrane protein |
| Reference | MIM:603241|HGNC:HGNC:6705|Ensembl:ENSG00000185565|HPRD:09128|Vega:OTTHUMG00000159308 |
| Gene type | protein-coding |
| Map location | 3q13.31 |
| Pascal p-value | 0.209 |
| Sherlock p-value | 2.212E-6 |
| Fetal beta | -1.051 |
| eGene | Myers' cis & trans |
| Support | CELL ADHESION AND TRANSSYNAPTIC SIGNALING G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS G2Cdb.humanPSD G2Cdb.humanPSP CompositeSet |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| PMID:cooccur | High-throughput literature-search | Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included. | |
| GSMA_IIE | Genome scan meta-analysis (European-ancestry samples) | Psr: 0.04359 | |
| GSMA_IIA | Genome scan meta-analysis (All samples) | Psr: 0.04047 | |
| Literature | High-throughput literature-search | Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenias | Click to show details |
| GO_Annotation | Mapping neuro-related keywords to Gene Ontology annotations | Hits with neuro-related keywords: 1 |
Section I. Genetics and epigenetics annotation
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs6733654 | chr2 | 1963270 | LSAMP | 4045 | 0.09 | trans | ||
| rs1155107 | chr3 | 26843376 | LSAMP | 4045 | 0.18 | trans | ||
| rs17029291 | chr3 | 32402138 | LSAMP | 4045 | 0.11 | trans | ||
| rs6813178 | chr4 | 71575238 | LSAMP | 4045 | 0.17 | trans | ||
| rs6834662 | chr4 | 71605100 | LSAMP | 4045 | 0.05 | trans | ||
| rs16870339 | chr5 | 2705169 | LSAMP | 4045 | 0.19 | trans | ||
| rs235427 | chr8 | 133815575 | LSAMP | 4045 | 0.11 | trans | ||
| rs235428 | chr8 | 133815725 | LSAMP | 4045 | 0.17 | trans | ||
| rs16904746 | chr8 | 133844507 | LSAMP | 4045 | 0.1 | trans | ||
| rs4607971 | chr10 | 19407890 | LSAMP | 4045 | 0.09 | trans | ||
| rs1700369 | chr12 | 127842232 | LSAMP | 4045 | 0.18 | trans | ||
| rs2239335 | chr16 | 22897794 | LSAMP | 4045 | 0.18 | trans | ||
| rs6098023 | chr20 | 53113740 | LSAMP | 4045 | 0.02 | 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 |
| CA14 | 0.64 | 0.58 |
| DUSP10 | 0.62 | 0.56 |
| GLTP | 0.60 | 0.60 |
| C18orf56 | 0.60 | 0.48 |
| WIPF1 | 0.60 | 0.57 |
| JAM3 | 0.59 | 0.38 |
| CDC42EP1 | 0.59 | 0.57 |
| LASS2 | 0.59 | 0.54 |
| HSPA2 | 0.59 | 0.60 |
| CREB5 | 0.58 | 0.43 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| FBLIM1 | -0.31 | -0.31 |
| MYC | -0.31 | -0.27 |
| TMC2 | -0.30 | -0.32 |
| LEMD1 | -0.29 | -0.37 |
| ZNF599 | -0.29 | -0.30 |
| KRT19 | -0.29 | -0.35 |
| AKR1C2 | -0.28 | -0.26 |
| DACT1 | -0.28 | -0.26 |
| TRIM67 | -0.28 | -0.25 |
| DAB1 | -0.28 | -0.25 |
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0005515 | protein binding | IEA | - | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0007399 | nervous system development | TAS | neurite (GO term level: 5) | 8666243 |
| GO:0007155 | cell adhesion | IEA | - | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0005886 | plasma membrane | IEA | - | |
| GO:0031225 | anchored to membrane | IEA | - |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| LIU PROSTATE CANCER DN | 481 | 290 | All SZGR 2.0 genes in this pathway |
| THUM SYSTOLIC HEART FAILURE DN | 244 | 147 | All SZGR 2.0 genes in this pathway |
| RICKMAN HEAD AND NECK CANCER A | 100 | 63 | All SZGR 2.0 genes in this pathway |
| HELLER SILENCED BY METHYLATION DN | 105 | 67 | All SZGR 2.0 genes in this pathway |
| HELLER HDAC TARGETS DN | 292 | 189 | All SZGR 2.0 genes in this pathway |
| HELLER HDAC TARGETS SILENCED BY METHYLATION DN | 281 | 179 | All SZGR 2.0 genes in this pathway |
| ZHENG GLIOBLASTOMA PLASTICITY DN | 58 | 39 | All SZGR 2.0 genes in this pathway |
| YOSHIMURA MAPK8 TARGETS UP | 1305 | 895 | All SZGR 2.0 genes in this pathway |
| CHANDRAN METASTASIS DN | 306 | 191 | All SZGR 2.0 genes in this pathway |
| CHICAS RB1 TARGETS GROWING | 243 | 155 | All SZGR 2.0 genes in this pathway |
| GOBERT OLIGODENDROCYTE DIFFERENTIATION DN | 1080 | 713 | All SZGR 2.0 genes in this pathway |