Gene Page: SPG7
Summary ?
| GeneID | 6687 |
| Symbol | SPG7 |
| Synonyms | CAR|CMAR|PGN|SPG5C |
| Description | SPG7, paraplegin matrix AAA peptidase subunit |
| Reference | MIM:602783|HGNC:HGNC:11237|Ensembl:ENSG00000197912|HPRD:04149|Vega:OTTHUMG00000138046 |
| Gene type | protein-coding |
| Map location | 16q24.3 |
| Pascal p-value | 1.212E-4 |
| Sherlock p-value | 0.839 |
| Fetal beta | 0.258 |
| DMG | 1 (# studies) |
| eGene | Anterior cingulate cortex BA24 Cortex Frontal Cortex BA9 Hypothalamus Myers' cis & trans Meta |
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). | 1 |
| GO_Annotation | Mapping neuro-related keywords to Gene Ontology annotations | Hits with neuro-related keywords: 2 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg04186815 | 16 | 89613903 | SPG7 | 1.57E-4 | 0.386 | 0.032 | DMG:Wockner_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs12677942 | chr8 | 31539941 | SPG7 | 6687 | 0.2 | trans | ||
| rs4785684 | 16 | 89574576 | SPG7 | ENSG00000197912.9 | 6.76826E-7 | 0 | 17251 | gtex_brain_ba24 |
| rs56289056 | 16 | 89581650 | SPG7 | ENSG00000197912.9 | 4.31022E-8 | 0 | 24325 | gtex_brain_ba24 |
| rs62070325 | 16 | 89583189 | SPG7 | ENSG00000197912.9 | 2.16393E-6 | 0 | 25864 | gtex_brain_ba24 |
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 |
| MRPL9 | 0.88 | 0.85 |
| RPL26L1 | 0.88 | 0.87 |
| PSMA7 | 0.88 | 0.90 |
| ARL3 | 0.87 | 0.86 |
| DIABLO | 0.86 | 0.86 |
| PSMB7 | 0.86 | 0.87 |
| SARNP | 0.86 | 0.85 |
| EIF3G | 0.86 | 0.85 |
| ERH | 0.85 | 0.84 |
| PFDN2 | 0.85 | 0.80 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| AF347015.33 | -0.63 | -0.66 |
| MT-CO2 | -0.63 | -0.61 |
| MT-CYB | -0.62 | -0.65 |
| AF347015.8 | -0.62 | -0.63 |
| AF347015.2 | -0.62 | -0.65 |
| AF347015.27 | -0.61 | -0.64 |
| AF347015.15 | -0.61 | -0.65 |
| AF347015.26 | -0.61 | -0.66 |
| AF347015.31 | -0.60 | -0.61 |
| AF347015.9 | -0.58 | -0.65 |
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0000166 | nucleotide binding | IEA | - | |
| GO:0003674 | molecular_function | ND | - | |
| GO:0005524 | ATP binding | IEA | - | |
| GO:0004222 | metalloendopeptidase activity | IDA | 11549317 | |
| GO:0004222 | metalloendopeptidase activity | IEA | - | |
| GO:0008270 | zinc ion binding | IEA | - | |
| GO:0017111 | nucleoside-triphosphatase activity | IEA | - | |
| GO:0008233 | peptidase activity | TAS | 9635427 | |
| GO:0051082 | unfolded protein binding | TAS | 9635427 | |
| GO:0046872 | metal ion binding | IEA | - | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0008089 | anterograde axon cargo transport | IEA | axon (GO term level: 9) | - |
| GO:0007399 | nervous system development | TAS | neurite (GO term level: 5) | 9635427 |
| GO:0006508 | proteolysis | TAS | 9635427 | |
| GO:0007165 | signal transduction | NAS | 9405655 | |
| GO:0007005 | mitochondrion organization | IEA | - | |
| GO:0030155 | regulation of cell adhesion | NAS | 9405655 | |
| GO:0030163 | protein catabolic process | IEA | - | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0005575 | cellular_component | ND | - | |
| GO:0005739 | mitochondrion | TAS | 9635427 | |
| GO:0016020 | membrane | IEA | - | |
| GO:0016021 | integral to membrane | IEA | - | |
| GO:0031966 | mitochondrial membrane | IEA | - |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| LIU SOX4 TARGETS DN | 309 | 191 | All SZGR 2.0 genes in this pathway |
| LIU CMYB TARGETS UP | 165 | 106 | All SZGR 2.0 genes in this pathway |
| RODRIGUES NTN1 TARGETS DN | 158 | 102 | All SZGR 2.0 genes in this pathway |
| WANG CLIM2 TARGETS UP | 269 | 146 | All SZGR 2.0 genes in this pathway |
| MULLIGHAN NPM1 MUTATED SIGNATURE 1 UP | 276 | 165 | All SZGR 2.0 genes in this pathway |
| MULLIGHAN NPM1 MUTATED SIGNATURE 2 UP | 139 | 83 | All SZGR 2.0 genes in this pathway |
| MULLIGHAN NPM1 SIGNATURE 3 UP | 341 | 197 | All SZGR 2.0 genes in this pathway |
| TIEN INTESTINE PROBIOTICS 24HR UP | 557 | 331 | All SZGR 2.0 genes in this pathway |
| DODD NASOPHARYNGEAL CARCINOMA UP | 1821 | 933 | All SZGR 2.0 genes in this pathway |
| ENK UV RESPONSE EPIDERMIS UP | 293 | 179 | All SZGR 2.0 genes in this pathway |
| BARRIER CANCER RELAPSE NORMAL SAMPLE DN | 31 | 19 | All SZGR 2.0 genes in this pathway |
| SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP | 479 | 299 | All SZGR 2.0 genes in this pathway |
| NUYTTEN EZH2 TARGETS DN | 1024 | 594 | All SZGR 2.0 genes in this pathway |
| NIKOLSKY BREAST CANCER 16Q24 AMPLICON | 53 | 38 | All SZGR 2.0 genes in this pathway |
| BAELDE DIABETIC NEPHROPATHY UP | 86 | 48 | All SZGR 2.0 genes in this pathway |
| BROWNE HCMV INFECTION 48HR DN | 504 | 323 | All SZGR 2.0 genes in this pathway |
| ZHENG BOUND BY FOXP3 | 491 | 310 | All SZGR 2.0 genes in this pathway |
| GRATIAS RETINOBLASTOMA 16Q24 | 17 | 15 | All SZGR 2.0 genes in this pathway |
| MOOTHA HUMAN MITODB 6 2002 | 429 | 260 | All SZGR 2.0 genes in this pathway |
| MOOTHA MITOCHONDRIA | 447 | 277 | All SZGR 2.0 genes in this pathway |
| SENGUPTA EBNA1 ANTICORRELATED | 173 | 85 | All SZGR 2.0 genes in this pathway |
| MARTENS BOUND BY PML RARA FUSION | 456 | 287 | All SZGR 2.0 genes in this pathway |
| KRIEG HYPOXIA NOT VIA KDM3A | 770 | 480 | All SZGR 2.0 genes in this pathway |