Gene Page: RAB5C
Summary ?
| GeneID | 5878 |
| Symbol | RAB5C |
| Synonyms | L1880|RAB5CL|RAB5L|RABL |
| Description | RAB5C, member RAS oncogene family |
| Reference | MIM:604037|HGNC:HGNC:9785|Ensembl:ENSG00000108774|HPRD:04947|Vega:OTTHUMG00000169703 |
| Gene type | protein-coding |
| Map location | 17q21.2 |
| Pascal p-value | 0.595 |
| Sherlock p-value | 0.178 |
| Fetal beta | -0.253 |
| DMG | 1 (# studies) |
| eGene | Meta |
| Support | INTRACELLULAR TRAFFICKING G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS CompositeSet |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DMG:vanEijk_2014 | Genome-wide DNA methylation analysis | This dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250). | 4 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg13053608 | 17 | 40345673 | RAB5C | 4.97E-7 | -2.928 | DMG:vanEijk_2014 | |
| cg25687894 | 17 | 40075716 | RAB5C | 1.37E-5 | -4.369 | DMG:vanEijk_2014 | |
| cg14070162 | 17 | 40575582 | RAB5C | 4.1E-5 | -4.594 | DMG:vanEijk_2014 | |
| cg03001305 | 17 | 40439492 | RAB5C | 3.09E-6 | -6.226 | DMG:vanEijk_2014 |
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 |
| C10orf97 | 0.86 | 0.87 |
| RAB6A | 0.86 | 0.87 |
| CARS | 0.84 | 0.82 |
| YWHAZ | 0.84 | 0.85 |
| NDFIP1 | 0.83 | 0.85 |
| SEC61A2 | 0.83 | 0.82 |
| GARS | 0.83 | 0.79 |
| DSTN | 0.83 | 0.87 |
| ATP2C1 | 0.82 | 0.81 |
| YWHAB | 0.82 | 0.85 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| AF347015.2 | -0.64 | -0.56 |
| AF347015.8 | -0.61 | -0.53 |
| EIF4EBP3 | -0.61 | -0.67 |
| AF347015.21 | -0.60 | -0.48 |
| MT-CO2 | -0.60 | -0.52 |
| AF347015.31 | -0.59 | -0.52 |
| AF347015.33 | -0.59 | -0.52 |
| MT-CYB | -0.59 | -0.51 |
| AF347015.26 | -0.58 | -0.52 |
| AF347015.15 | -0.58 | -0.50 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| KEGG ENDOCYTOSIS | 183 | 132 | All SZGR 2.0 genes in this pathway |
| KEGG VASOPRESSIN REGULATED WATER REABSORPTION | 44 | 30 | All SZGR 2.0 genes in this pathway |
| REACTOME MEMBRANE TRAFFICKING | 129 | 74 | All SZGR 2.0 genes in this pathway |
| REACTOME TRANS GOLGI NETWORK VESICLE BUDDING | 60 | 31 | All SZGR 2.0 genes in this pathway |
| REACTOME GOLGI ASSOCIATED VESICLE BIOGENESIS | 53 | 27 | All SZGR 2.0 genes in this pathway |
| OSWALD HEMATOPOIETIC STEM CELL IN COLLAGEN GEL UP | 233 | 161 | All SZGR 2.0 genes in this pathway |
| SENESE HDAC2 TARGETS UP | 114 | 66 | All SZGR 2.0 genes in this pathway |
| MCBRYAN PUBERTAL BREAST 5 6WK DN | 137 | 97 | All SZGR 2.0 genes in this pathway |
| MCBRYAN PUBERTAL BREAST 6 7WK UP | 197 | 135 | All SZGR 2.0 genes in this pathway |
| MCBRYAN PUBERTAL TGFB1 TARGETS UP | 169 | 127 | All SZGR 2.0 genes in this pathway |
| SCHLOSSER SERUM RESPONSE UP | 134 | 93 | All SZGR 2.0 genes in this pathway |
| MARTORIATI MDM4 TARGETS FETAL LIVER UP | 227 | 137 | All SZGR 2.0 genes in this pathway |
| LOPEZ MBD TARGETS | 957 | 597 | All SZGR 2.0 genes in this pathway |
| SCHAEFFER PROSTATE DEVELOPMENT 48HR UP | 487 | 286 | All SZGR 2.0 genes in this pathway |
| GOLDRATH HOMEOSTATIC PROLIFERATION | 171 | 102 | All SZGR 2.0 genes in this pathway |
| REN ALVEOLAR RHABDOMYOSARCOMA DN | 408 | 274 | All SZGR 2.0 genes in this pathway |
| WU HBX TARGETS 1 DN | 23 | 14 | All SZGR 2.0 genes in this pathway |
| BROWNE HCMV INFECTION 12HR UP | 111 | 68 | All SZGR 2.0 genes in this pathway |
| RAMASWAMY METASTASIS UP | 66 | 43 | All SZGR 2.0 genes in this pathway |
| WU HBX TARGETS 2 UP | 23 | 13 | All SZGR 2.0 genes in this pathway |
| BROWNE HCMV INFECTION 24HR UP | 148 | 96 | All SZGR 2.0 genes in this pathway |
| MONNIER POSTRADIATION TUMOR ESCAPE UP | 393 | 244 | All SZGR 2.0 genes in this pathway |
| AGUIRRE PANCREATIC CANCER COPY NUMBER UP | 298 | 174 | All SZGR 2.0 genes in this pathway |
| SASSON RESPONSE TO GONADOTROPHINS DN | 87 | 66 | All SZGR 2.0 genes in this pathway |
| SASSON RESPONSE TO FORSKOLIN DN | 88 | 68 | All SZGR 2.0 genes in this pathway |
| CARD MIR302A TARGETS | 77 | 62 | All SZGR 2.0 genes in this pathway |
| HOLLEMAN ASPARAGINASE RESISTANCE B ALL DN | 15 | 10 | All SZGR 2.0 genes in this pathway |
| HOLLEMAN ASPARAGINASE RESISTANCE ALL DN | 25 | 14 | All SZGR 2.0 genes in this pathway |