Gene Page:COPB2
Summary?
| GeneID | 9276 |
| Symbol | COPB2 |
| Synonyms | beta'-COP |
| Description | coatomer protein complex subunit beta 2 (beta prime) |
| Reference | MIM:606990|HGNC:HGNC:2232|Ensembl:ENSG00000184432|HPRD:06103|Vega:OTTHUMG00000159959 |
| Gene type | protein-coding |
| Map location | 3q23 |
| Pascal p-value | 0.303 |
| Sherlock p-value | 0.004 |
| Fetal beta | -0.157 |
| DMG | 1 (# studies) |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:GWASdb | Genome-wide Association Studies | GWASdb records for schizophrenia | |
| 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. | 1 |
| Network | Shortest path distance of core genes in the Human protein-protein interaction network | Contribution to shortest path in PPI network: 1.6555 |
Section I. Genetics and epigenetics annotation
Differentially methylated gene
Differentially methylated gene| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg09650667 | 3 | 139108740 | COPB2 | 4.04E-8 | -0.01 | 1.14E-5 | 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 |
| MRPL45 | 0.90 | 0.92 |
| CCT4 | 0.90 | 0.90 |
| DYM | 0.89 | 0.90 |
| MRPL3 | 0.88 | 0.89 |
| CCT5 | 0.88 | 0.88 |
| RFWD2 | 0.88 | 0.90 |
| VTA1 | 0.88 | 0.89 |
| ARF4 | 0.88 | 0.91 |
| ZNF410 | 0.88 | 0.90 |
| PWP1 | 0.88 | 0.90 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| MT-CO2 | -0.71 | -0.78 |
| AF347015.8 | -0.71 | -0.80 |
| AF347015.33 | -0.70 | -0.78 |
| AF347015.27 | -0.70 | -0.78 |
| MT-CYB | -0.69 | -0.78 |
| AF347015.15 | -0.69 | -0.78 |
| AF347015.26 | -0.69 | -0.80 |
| AF347015.31 | -0.69 | -0.76 |
| AF347015.2 | -0.68 | -0.79 |
| AIFM3 | -0.66 | -0.73 |
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0005515 | protein binding | IPI | 17220478|17353931 | |
| GO:0005198 | structural molecule activity | IEA | - | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0016044 | membrane organization | EXP | 11031247 | |
| GO:0006886 | intracellular protein transport | IEA | - | |
| GO:0006890 | retrograde vesicle-mediated transport, Golgi to ER | EXP | 11031247 | |
| GO:0006890 | retrograde vesicle-mediated transport, Golgi to ER | TAS | 11030615 | |
| GO:0006891 | intra-Golgi vesicle-mediated transport | IDA | 8335000 | |
| GO:0016192 | vesicle-mediated transport | IEA | - | |
| GO:0048205 | COPI coating of Golgi vesicle | EXP | 16956762 | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0000139 | Golgi membrane | IEA | - | |
| GO:0005794 | Golgi apparatus | IEA | - | |
| GO:0005829 | cytosol | EXP | 8533093|8599108 | |
| GO:0005737 | cytoplasm | IEA | - | |
| GO:0030117 | membrane coat | IEA | - | |
| GO:0016020 | membrane | IEA | - | |
| GO:0031410 | cytoplasmic vesicle | IEA | - | |
| GO:0030126 | COPI vesicle coat | IDA | 8335000 |
第四部分,注释蛋白质间交互作用
| Interactors | Aliases B | Official full name B | Experimental | Source | PubMed ID |
|---|---|---|---|---|---|
| COPA | FLJ26320 | HEP-COP | coatomer protein complex, subunit alpha | Two-hybrid | BioGRID | 10921873 |
| COPA | FLJ26320 | HEP-COP | coatomer protein complex, subunit alpha | - | HPRD | 8537409|8940050 |
| COPB1 | COPB | DKFZp761K102 | FLJ10341 | coatomer protein complex, subunit beta 1 | Affinity Capture-Western Two-hybrid |
BioGRID | 8940050|10921873 |
| COPE | FLJ13241 | epsilon-COP | coatomer protein complex, subunit epsilon | Two-hybrid | BioGRID | 10921873 |
| COPG | COPG1 | FLJ21068 | coatomer protein complex, subunit gamma | Two-hybrid | BioGRID | 10921873 |
| COPZ2 | MGC23008 | coatomer protein complex, subunit zeta 2 | - | HPRD | 8940050 |
| ILK | DKFZp686F1765 | P59 | integrin-linked kinase | Affinity Capture-MS | BioGRID | 17353931 |
| NFKB1 | DKFZp686C01211 | EBP-1 | KBF1 | MGC54151 | NF-kappa-B | NFKB-p105 | NFKB-p50 | p105 | nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 | Affinity Capture-MS | BioGRID | 14743216 |
| PRKCE | MGC125656 | MGC125657 | PKCE | nPKC-epsilon | protein kinase C, epsilon | Affinity Capture-MS Affinity Capture-Western |
BioGRID | 11897493 |
| PRKCE | MGC125656 | MGC125657 | PKCE | nPKC-epsilon | protein kinase C, epsilon | - | HPRD | 9360998 |
| RGS2 | G0S8 | regulator of G-protein signaling 2, 24kDa | - | HPRD,BioGRID | 10982407 |
| RGS4 | DKFZp761F1924 | MGC2124 | MGC60244 | RGP4 | SCZD9 | regulator of G-protein signaling 4 | - | HPRD,BioGRID | 10982407 |
| SACM1L | DKFZp686A0231 | KIAA0851 | SAC1 | SAC1 suppressor of actin mutations 1-like (yeast) | hSac1 interacts with beta-COP. | BIND | 14527956 |
| TH1L | HSPC130 | NELF -C | NELF-D | TH1 | TH1-like (Drosophila) | Affinity Capture-MS | BioGRID | 17353931 |
| TSC22D1 | DKFZp686O19206 | MGC17597 | RP11-269C23.2 | TGFB1I4 | TSC22 | TSC22 domain family, member 1 | Affinity Capture-MS | BioGRID | 17353931 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| REACTOME MEMBRANE TRAFFICKING | 129 | 74 | All SZGR 2.0 genes in this pathway |
| DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP | 1382 | 904 | All SZGR 2.0 genes in this pathway |
| LINDGREN BLADDER CANCER CLUSTER 3 UP | 329 | 196 | All SZGR 2.0 genes in this pathway |
| GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION DN | 234 | 147 | All SZGR 2.0 genes in this pathway |
| GRAESSMANN RESPONSE TO MC AND SERUM DEPRIVATION DN | 84 | 54 | All SZGR 2.0 genes in this pathway |
| OUELLET OVARIAN CANCER INVASIVE VS LMP UP | 117 | 85 | All SZGR 2.0 genes in this pathway |
| HEIDENBLAD AMPLICON 8Q24 DN | 46 | 28 | All SZGR 2.0 genes in this pathway |
| MOHANKUMAR TLX1 TARGETS UP | 414 | 287 | All SZGR 2.0 genes in this pathway |
| SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN DN | 584 | 395 | All SZGR 2.0 genes in this pathway |
| LOPEZ MBD TARGETS | 957 | 597 | All SZGR 2.0 genes in this pathway |
| CAFFAREL RESPONSE TO THC 24HR 5 DN | 59 | 35 | All SZGR 2.0 genes in this pathway |
| PENG LEUCINE DEPRIVATION DN | 187 | 122 | All SZGR 2.0 genes in this pathway |
| PENG RAPAMYCIN RESPONSE DN | 245 | 154 | All SZGR 2.0 genes in this pathway |
| REN ALVEOLAR RHABDOMYOSARCOMA DN | 408 | 274 | All SZGR 2.0 genes in this pathway |
| RHODES CANCER META SIGNATURE | 64 | 47 | All SZGR 2.0 genes in this pathway |
| 击倒卡路里限制肌肉DN | 87 | 59 | All SZGR 2.0 genes in this pathway |
| CREIGHTON ENDOCRINE THERAPY RESISTANCE 5 | 482 | 296 | All SZGR 2.0 genes in this pathway |
| PELLICCIOTTA HDAC IN ANTIGEN PRESENTATION UP | 64 | 40 | All SZGR 2.0 genes in this pathway |
| KYNG DNA DAMAGE BY GAMMA AND UV RADIATION | 88 | 65 | All SZGR 2.0 genes in this pathway |
| KYNG DNA DAMAGE DN | 195 | 135 | All SZGR 2.0 genes in this pathway |
| RIZKI TUMOR INVASIVENESS 2D UP | 69 | 46 | All SZGR 2.0 genes in this pathway |
| ACEVEDO LIVER CANCER UP | 973 | 570 | All SZGR 2.0 genes in this pathway |
| ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP | 863 | 514 | All SZGR 2.0 genes in this pathway |
| YAGI AML WITH INV 16 TRANSLOCATION | 422 | 277 | All SZGR 2.0 genes in this pathway |
| PILON KLF1 TARGETS DN | 1972 | 1213 | All SZGR 2.0 genes in this pathway |