Gene Page: PCM1
Summary ?
| GeneID | 5108 |
| Symbol | PCM1 |
| Synonyms | PTC4|RET/PCM-1 |
| Description | pericentriolar material 1 |
| Reference | MIM:600299|HGNC:HGNC:8727|Ensembl:ENSG00000078674|HPRD:02624|Vega:OTTHUMG00000163699 |
| Gene type | protein-coding |
| Map location | 8p22-p21.3 |
| Pascal p-value | 0.196 |
| Sherlock p-value | 0.53 |
| Fetal beta | 1.254 |
| eGene | Anterior cingulate cortex BA24 Caudate basal ganglia Cerebellar Hemisphere Cerebellum Cortex Frontal Cortex BA9 Hippocampus Hypothalamus Nucleus accumbens basal ganglia Putamen basal ganglia Myers' cis & trans Meta |
| Support | Ascano FMRP targets |
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. | |
| Association | A combined odds ratio method (Sun et al. 2008), association studies | 2 | Link to SZGene |
| GSMA_I | Genome scan meta-analysis | Psr: 0.031 | |
| GSMA_IIA | Genome scan meta-analysis (All samples) | Psr: 0.03086 | |
| GSMA_IIE | Genome scan meta-analysis (European-ancestry samples) | Psr: 0.00057 | |
| Literature | High-throughput literature-search | Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenias | Click to show details |
Section I. Genetics and epigenetics annotation
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs6986061 | chr8 | 17637673 | PCM1 | 5108 | 0.05 | cis | ||
| rs11779988 | 8 | 17784414 | PCM1 | ENSG00000078674.13 | 1.302E-8 | 0 | 4065 | gtex_brain_ba24 |
| rs4124899 | 8 | 17785258 | PCM1 | ENSG00000078674.13 | 1.484E-8 | 0 | 4909 | gtex_brain_ba24 |
| rs13261745 | 8 | 17787005 | PCM1 | ENSG00000078674.13 | 1.879E-8 | 0 | 6656 | gtex_brain_ba24 |
| rs12335048 | 8 | 17788261 | PCM1 | ENSG00000078674.13 | 1.172E-7 | 0 | 7912 | gtex_brain_ba24 |
| rs478420 | 8 | 17792853 | PCM1 | ENSG00000078674.13 | 3.329E-8 | 0 | 12504 | gtex_brain_ba24 |
| rs916550 | 8 | 17793084 | PCM1 | ENSG00000078674.13 | 1.496E-6 | 0 | 12735 | gtex_brain_ba24 |
| rs850835 | 8 | 17793638 | PCM1 | ENSG00000078674.13 | 3.317E-8 | 0 | 13289 | gtex_brain_ba24 |
| rs28655174 | 8 | 17804665 | PCM1 | ENSG00000078674.13 | 4.753E-7 | 0 | 24316 | gtex_brain_ba24 |
| rs13258901 | 8 | 17857028 | PCM1 | ENSG00000078674.13 | 7.498E-8 | 0 | 76679 | gtex_brain_ba24 |
| rs6586676 | 8 | 17857445 | PCM1 | ENSG00000078674.13 | 7.501E-8 | 0 | 77096 | gtex_brain_ba24 |
| rs7825899 | 8 | 17857880 | PCM1 | ENSG00000078674.13 | 4.872E-7 | 0 | 77531 | gtex_brain_ba24 |
| rs34027006 | 8 | 17871902 | PCM1 | ENSG00000078674.13 | 2.57E-8 | 0 | 91553 | gtex_brain_ba24 |
| rs433342 | 8 | 17747876 | PCM1 | ENSG00000078674.13 | 1.445E-6 | 0 | -32473 | gtex_brain_putamen_basal |
| rs6983087 | 8 | 17751776 | PCM1 | ENSG00000078674.13 | 1.635E-6 | 0 | -28573 | gtex_brain_putamen_basal |
| rs11779988 | 8 | 17784414 | PCM1 | ENSG00000078674.13 | 8.456E-8 | 0 | 4065 | gtex_brain_putamen_basal |
| rs4124899 | 8 | 17785258 | PCM1 | ENSG00000078674.13 | 8.183E-8 | 0 | 4909 | gtex_brain_putamen_basal |
| rs13261745 | 8 | 17787005 | PCM1 | ENSG00000078674.13 | 2.386E-8 | 0 | 6656 | gtex_brain_putamen_basal |
| rs12335048 | 8 | 17788261 | PCM1 | ENSG00000078674.13 | 5.586E-8 | 0 | 7912 | gtex_brain_putamen_basal |
| rs417088 | 8 | 17791218 | PCM1 | ENSG00000078674.13 | 3.332E-7 | 0 | 10869 | gtex_brain_putamen_basal |
| rs478420 | 8 | 17792853 | PCM1 | ENSG00000078674.13 | 5.336E-10 | 0 | 12504 | gtex_brain_putamen_basal |
| rs916550 | 8 | 17793084 | PCM1 | ENSG00000078674.13 | 1.117E-6 | 0 | 12735 | gtex_brain_putamen_basal |
| rs850835 | 8 | 17793638 | PCM1 | ENSG00000078674.13 | 5.075E-10 | 0 | 13289 | gtex_brain_putamen_basal |
| rs7839778 | 8 | 17798992 | PCM1 | ENSG00000078674.13 | 1.519E-6 | 0 | 18643 | gtex_brain_putamen_basal |
| rs10108545 | 8 | 17799241 | PCM1 | ENSG00000078674.13 | 1.732E-6 | 0 | 18892 | gtex_brain_putamen_basal |
| rs11203928 | 8 | 17800450 | PCM1 | ENSG00000078674.13 | 1.732E-6 | 0 | 20101 | gtex_brain_putamen_basal |
| rs208771 | 8 | 17800472 | PCM1 | ENSG00000078674.13 | 9.042E-7 | 0 | 20123 | gtex_brain_putamen_basal |
| rs208770 | 8 | 17800896 | PCM1 | ENSG00000078674.13 | 9.042E-7 | 0 | 20547 | gtex_brain_putamen_basal |
| rs2299593 | 8 | 17802370 | PCM1 | ENSG00000078674.13 | 1.532E-6 | 0 | 22021 | gtex_brain_putamen_basal |
| rs28655174 | 8 | 17804665 | PCM1 | ENSG00000078674.13 | 2.043E-7 | 0 | 24316 | gtex_brain_putamen_basal |
| rs2299597 | 8 | 17809011 | PCM1 | ENSG00000078674.13 | 1.734E-6 | 0 | 28662 | gtex_brain_putamen_basal |
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 |
| ZC3H11A | 0.85 | 0.85 |
| TAF1 | 0.85 | 0.85 |
| LRCH3 | 0.85 | 0.87 |
| ZSCAN29 | 0.85 | 0.85 |
| ZNF318 | 0.85 | 0.85 |
| UBR5 | 0.85 | 0.86 |
| CDC2L5 | 0.84 | 0.84 |
| PTPN21 | 0.84 | 0.86 |
| SETD5 | 0.84 | 0.84 |
| ZFYVE26 | 0.83 | 0.86 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| IFI27 | -0.65 | -0.71 |
| AF347015.31 | -0.63 | -0.70 |
| MT-CO2 | -0.62 | -0.69 |
| HIGD1B | -0.61 | -0.70 |
| MYL3 | -0.60 | -0.68 |
| AF347015.27 | -0.60 | -0.66 |
| AF347015.21 | -0.60 | -0.74 |
| FXYD1 | -0.60 | -0.66 |
| VAMP5 | -0.59 | -0.68 |
| C5orf53 | -0.58 | -0.59 |
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0005515 | protein binding | IPI | 15107855 | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0042384 | cilium biogenesis | IMP | 17574030 | |
| GO:0042384 | cilium biogenesis | TAS | 14520415 | |
| GO:0051297 | centrosome organization | IMP | 17574030 | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0000242 | pericentriolar material | TAS | 8120099 | |
| GO:0005856 | cytoskeleton | IEA | - | |
| GO:0005737 | cytoplasm | TAS | 8120099 | |
| GO:0034451 | centriolar satellite | IDA | 17574030 | |
| GO:0031513 | nonmotile primary cilium | IDA | 17574030 |
Section IV. Protein-protein interaction annotation
| Interactors | Aliases B | Official full name B | Experimental | Source | PubMed ID |
|---|---|---|---|---|---|
| ABI2 | ABI-2 | ABI2B | AIP-1 | AblBP3 | SSH3BP2 | argBPIA | argBPIB | abl interactor 2 | Two-hybrid | BioGRID | 16189514 |
| BBS4 | - | Bardet-Biedl syndrome 4 | - | HPRD,BioGRID | 15107855 |
| CCDC53 | CGI-116 | coiled-coil domain containing 53 | Two-hybrid | BioGRID | 16189514 |
| CEP72 | FLJ10565 | KIAA1519 | MGC5307 | centrosomal protein 72kDa | Two-hybrid | BioGRID | 16189514 |
| EPS8 | - | epidermal growth factor receptor pathway substrate 8 | Two-hybrid | BioGRID | 16189514 |
| EXOC8 | EXO84 | Exo84p | SEC84 | exocyst complex component 8 | Two-hybrid | BioGRID | 16189514 |
| HAP1 | HAP2 | HIP5 | HLP | hHLP1 | huntingtin-associated protein 1 | - | HPRD,BioGRID | 9361024 |
| ING5 | FLJ23842 | p28ING5 | inhibitor of growth family, member 5 | Two-hybrid | BioGRID | 16189514 |
| KIAA0368 | ECM29 | FLJ22036 | KIAA1962 | RP11-386D8.2 | KIAA0368 | Two-hybrid | BioGRID | 16189514 |
| KRT15 | CK15 | K15 | K1CO | keratin 15 | Two-hybrid | BioGRID | 16189514 |
| KRT19 | CK19 | K19 | K1CS | MGC15366 | keratin 19 | Two-hybrid | BioGRID | 16189514 |
| PCNT | KEN | MOPD2 | PCN | PCNT2 | PCNTB | PCTN2 | SCKL4 | pericentrin | - | HPRD,BioGRID | 11171385 |
| TTC8 | BBS8 | tetratricopeptide repeat domain 8 | - | HPRD | 14520415 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| REACTOME CELL CYCLE | 421 | 253 | All SZGR 2.0 genes in this pathway |
| REACTOME CELL CYCLE MITOTIC | 325 | 185 | All SZGR 2.0 genes in this pathway |
| REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES | 66 | 43 | All SZGR 2.0 genes in this pathway |
| REACTOME LOSS OF NLP FROM MITOTIC CENTROSOMES | 59 | 38 | All SZGR 2.0 genes in this pathway |
| REACTOME MITOTIC G2 G2 M PHASES | 81 | 50 | All SZGR 2.0 genes in this pathway |
| HOLLMANN APOPTOSIS VIA CD40 UP | 201 | 125 | All SZGR 2.0 genes in this pathway |
| FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS DN | 463 | 290 | All SZGR 2.0 genes in this pathway |
| DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP | 1382 | 904 | All SZGR 2.0 genes in this pathway |
| DEURIG T CELL PROLYMPHOCYTIC LEUKEMIA DN | 320 | 184 | All SZGR 2.0 genes in this pathway |
| OSWALD HEMATOPOIETIC STEM CELL IN COLLAGEN GEL DN | 275 | 168 | All SZGR 2.0 genes in this pathway |
| GRAESSMANN APOPTOSIS BY DOXORUBICIN DN | 1781 | 1082 | All SZGR 2.0 genes in this pathway |
| HAMAI APOPTOSIS VIA TRAIL UP | 584 | 356 | All SZGR 2.0 genes in this pathway |
| MYLLYKANGAS AMPLIFICATION HOT SPOT 9 | 8 | 6 | All SZGR 2.0 genes in this pathway |
| TOMLINS METASTASIS DN | 20 | 16 | All SZGR 2.0 genes in this pathway |
| BENPORATH MYC MAX TARGETS | 775 | 494 | All SZGR 2.0 genes in this pathway |
| STARK PREFRONTAL CORTEX 22Q11 DELETION DN | 517 | 309 | All SZGR 2.0 genes in this pathway |
| ASTON MAJOR DEPRESSIVE DISORDER UP | 49 | 36 | All SZGR 2.0 genes in this pathway |
| GUO HEX TARGETS UP | 81 | 54 | All SZGR 2.0 genes in this pathway |
| PARK HSC MARKERS | 44 | 31 | All SZGR 2.0 genes in this pathway |
| BLALOCK ALZHEIMERS DISEASE UP | 1691 | 1088 | All SZGR 2.0 genes in this pathway |
| CREIGHTON ENDOCRINE THERAPY RESISTANCE 2 | 473 | 224 | All SZGR 2.0 genes in this pathway |
| GAVIN FOXP3 TARGETS CLUSTER P2 | 79 | 55 | All SZGR 2.0 genes in this pathway |
| MARTINEZ RB1 TARGETS UP | 673 | 430 | All SZGR 2.0 genes in this pathway |
| MARTINEZ TP53 TARGETS UP | 602 | 364 | All SZGR 2.0 genes in this pathway |
| MARTINEZ RB1 AND TP53 TARGETS UP | 601 | 369 | All SZGR 2.0 genes in this pathway |
| BONOME OVARIAN CANCER SURVIVAL OPTIMAL DEBULKING | 246 | 152 | All SZGR 2.0 genes in this pathway |
| ZHANG BREAST CANCER PROGENITORS UP | 425 | 253 | All SZGR 2.0 genes in this pathway |
| WANG TUMOR INVASIVENESS UP | 374 | 247 | All SZGR 2.0 genes in this pathway |
| GRESHOCK CANCER COPY NUMBER UP | 323 | 240 | All SZGR 2.0 genes in this pathway |
| YOSHIMURA MAPK8 TARGETS DN | 366 | 257 | All SZGR 2.0 genes in this pathway |
| ZHANG TLX TARGETS 36HR DN | 185 | 116 | All SZGR 2.0 genes in this pathway |
| HAN SATB1 TARGETS UP | 395 | 249 | All SZGR 2.0 genes in this pathway |
| CAIRO HEPATOBLASTOMA CLASSES UP | 605 | 377 | All SZGR 2.0 genes in this pathway |
| DANG BOUND BY MYC | 1103 | 714 | All SZGR 2.0 genes in this pathway |
| PECE MAMMARY STEM CELL DN | 146 | 88 | All SZGR 2.0 genes in this pathway |
| ACEVEDO FGFR1 TARGETS IN PROSTATE CANCER MODEL UP | 289 | 184 | 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 |
Section VI. microRNA annotation
| miRNA family | Target position | miRNA ID | miRNA seq | ||
|---|---|---|---|---|---|
| UTR start | UTR end | Match method | |||
| miR-496 | 90 | 96 | 1A | hsa-miR-496 | AUUACAUGGCCAAUCUC |
- SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
- Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.