Gene Page: ZIC1
Summary ?
| GeneID | 7545 |
| Symbol | ZIC1 |
| Synonyms | CRS6|ZIC|ZNF201 |
| Description | Zic family member 1 |
| Reference | MIM:600470|HGNC:HGNC:12872|Ensembl:ENSG00000152977|HPRD:02718|Vega:OTTHUMG00000159456 |
| Gene type | protein-coding |
| Map location | 3q24 |
| Pascal p-value | 0.001 |
| Sherlock p-value | 0.69 |
| Fetal beta | 0.596 |
| DMG | 1 (# studies) |
| eGene | Myers' cis & trans |
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). | 2 |
| PMID:cooccur | High-throughput literature-search | Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included. | |
| Literature | High-throughput literature-search | Co-occurance with Schizophrenia keywords: schizophrenia,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
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg16181396 | 3 | 147126206 | ZIC1 | 3.082E-4 | 0.589 | 0.04 | DMG:Wockner_2014 |
| cg05371578 | 3 | 147128157 | ZIC1 | 4.928E-4 | 0.515 | 0.047 | DMG:Wockner_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs16829545 | chr2 | 151977407 | ZIC1 | 7545 | 0 | trans | ||
| rs3845734 | chr2 | 171125572 | ZIC1 | 7545 | 0.01 | trans | ||
| rs7584986 | chr2 | 184111432 | ZIC1 | 7545 | 2.006E-5 | trans | ||
| rs1255634 | chr14 | 63972654 | ZIC1 | 7545 | 0.01 | trans | ||
| rs16955618 | chr15 | 29937543 | ZIC1 | 7545 | 1.208E-9 | 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.
No co-expressed genes in brain regions
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0003700 | transcription factor activity | TAS | 8542595 | |
| GO:0005515 | protein binding | IEA | - | |
| GO:0008270 | zinc ion binding | IEA | - | |
| GO:0046872 | metal ion binding | IEA | - | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0007420 | brain development | IDA | Brain (GO term level: 7) | 8542595 |
| GO:0008589 | regulation of smoothened signaling pathway | ISS | - | |
| GO:0007610 | behavior | ISS | - | |
| GO:0007389 | pattern specification process | ISS | - | |
| GO:0030154 | cell differentiation | IEA | - | |
| GO:0042472 | inner ear morphogenesis | ISS | - | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0005622 | intracellular | IEA | - | |
| GO:0005634 | nucleus | IDA | 8542595 | |
| GO:0005737 | cytoplasm | IDA | 18029348 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| DAVICIONI MOLECULAR ARMS VS ERMS DN | 182 | 111 | All SZGR 2.0 genes in this pathway |
| DOANE BREAST CANCER ESR1 DN | 48 | 28 | All SZGR 2.0 genes in this pathway |
| LEE NEURAL CREST STEM CELL DN | 118 | 79 | All SZGR 2.0 genes in this pathway |
| RODRIGUES THYROID CARCINOMA ANAPLASTIC UP | 722 | 443 | All SZGR 2.0 genes in this pathway |
| WONG ENDMETRIUM CANCER UP | 25 | 17 | All SZGR 2.0 genes in this pathway |
| RICKMAN HEAD AND NECK CANCER B | 48 | 22 | All SZGR 2.0 genes in this pathway |
| BENPORATH NANOG TARGETS | 988 | 594 | All SZGR 2.0 genes in this pathway |
| BENPORATH OCT4 TARGETS | 290 | 172 | All SZGR 2.0 genes in this pathway |
| BENPORATH SOX2 TARGETS | 734 | 436 | All SZGR 2.0 genes in this pathway |
| BENPORATH NOS TARGETS | 179 | 105 | All SZGR 2.0 genes in this pathway |
| BENPORATH SUZ12 TARGETS | 1038 | 678 | All SZGR 2.0 genes in this pathway |
| BENPORATH EED TARGETS | 1062 | 725 | All SZGR 2.0 genes in this pathway |
| BENPORATH ES WITH H3K27ME3 | 1118 | 744 | All SZGR 2.0 genes in this pathway |
| BENPORATH PRC2 TARGETS | 652 | 441 | All SZGR 2.0 genes in this pathway |
| BENPORATH ES CORE NINE CORRELATED | 100 | 68 | All SZGR 2.0 genes in this pathway |
| TESAR ALK TARGETS HUMAN ES 5D UP | 5 | 5 | All SZGR 2.0 genes in this pathway |
| BLALOCK ALZHEIMERS DISEASE UP | 1691 | 1088 | All SZGR 2.0 genes in this pathway |
| BROWNE HCMV INFECTION 8HR DN | 47 | 31 | All SZGR 2.0 genes in this pathway |
| RAMPON ENRICHED LEARNING ENVIRONMENT LATE UP | 22 | 16 | All SZGR 2.0 genes in this pathway |
| BROWNE HCMV INFECTION 12HR DN | 101 | 64 | All SZGR 2.0 genes in this pathway |
| LEIN CEREBELLUM MARKERS | 85 | 47 | All SZGR 2.0 genes in this pathway |
| TESAR ALK TARGETS EPISC 3D UP | 7 | 7 | All SZGR 2.0 genes in this pathway |
| TESAR ALK TARGETS EPISC 4D UP | 7 | 6 | All SZGR 2.0 genes in this pathway |
| TESAR ALK AND JAK TARGETS MOUSE ES D4 UP | 5 | 5 | All SZGR 2.0 genes in this pathway |
| KONDO PROSTATE CANCER WITH H3K27ME3 | 196 | 93 | All SZGR 2.0 genes in this pathway |
| SMID BREAST CANCER RELAPSE IN BONE DN | 315 | 197 | All SZGR 2.0 genes in this pathway |
| SMID BREAST CANCER LUMINAL B DN | 564 | 326 | All SZGR 2.0 genes in this pathway |
| SMID BREAST CANCER BASAL UP | 648 | 398 | All SZGR 2.0 genes in this pathway |
| YAUCH HEDGEHOG SIGNALING PARACRINE DN | 264 | 159 | All SZGR 2.0 genes in this pathway |
| MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 | 1069 | 729 | All SZGR 2.0 genes in this pathway |
| YAGI AML WITH INV 16 TRANSLOCATION | 422 | 277 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN MCV6 HCP WITH H3K27ME3 | 435 | 318 | All SZGR 2.0 genes in this pathway |
| PLASARI TGFB1 TARGETS 10HR DN | 244 | 157 | 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-103/107 | 1893 | 1899 | m8 | hsa-miR-103brain | AGCAGCAUUGUACAGGGCUAUGA |
| hsa-miR-107brain | AGCAGCAUUGUACAGGGCUAUCA | ||||
| miR-140 | 841 | 847 | 1A | hsa-miR-140brain | AGUGGUUUUACCCUAUGGUAG |
| miR-15/16/195/424/497 | 1894 | 1900 | m8 | hsa-miR-15abrain | UAGCAGCACAUAAUGGUUUGUG |
| hsa-miR-16brain | UAGCAGCACGUAAAUAUUGGCG | ||||
| hsa-miR-15bbrain | UAGCAGCACAUCAUGGUUUACA | ||||
| hsa-miR-195SZ | UAGCAGCACAGAAAUAUUGGC | ||||
| hsa-miR-424 | CAGCAGCAAUUCAUGUUUUGAA | ||||
| hsa-miR-497 | CAGCAGCACACUGUGGUUUGU | ||||
| miR-17-5p/20/93.mr/106/519.d | 950 | 956 | 1A | hsa-miR-17-5p | CAAAGUGCUUACAGUGCAGGUAGU |
| hsa-miR-20abrain | UAAAGUGCUUAUAGUGCAGGUAG | ||||
| hsa-miR-106a | AAAAGUGCUUACAGUGCAGGUAGC | ||||
| hsa-miR-106bSZ | UAAAGUGCUGACAGUGCAGAU | ||||
| hsa-miR-20bSZ | CAAAGUGCUCAUAGUGCAGGUAG | ||||
| hsa-miR-519d | CAAAGUGCCUCCCUUUAGAGUGU | ||||
| miR-19 | 1289 | 1295 | 1A | hsa-miR-19a | UGUGCAAAUCUAUGCAAAACUGA |
| hsa-miR-19b | UGUGCAAAUCCAUGCAAAACUGA | ||||
| miR-194 | 906 | 912 | 1A | hsa-miR-194 | UGUAACAGCAACUCCAUGUGGA |
| miR-203.1 | 666 | 672 | m8 | hsa-miR-203 | UGAAAUGUUUAGGACCACUAG |
| miR-214 | 1160 | 1166 | m8 | hsa-miR-214brain | ACAGCAGGCACAGACAGGCAG |
| miR-23 | 577 | 584 | 1A,m8 | hsa-miR-23abrain | AUCACAUUGCCAGGGAUUUCC |
| hsa-miR-23bbrain | AUCACAUUGCCAGGGAUUACC | ||||
| miR-299-5p | 1464 | 1470 | 1A | hsa-miR-299-5p | UGGUUUACCGUCCCACAUACAU |
| miR-323 | 577 | 583 | 1A | hsa-miR-323brain | GCACAUUACACGGUCGACCUCU |
| hsa-miR-323brain | GCACAUUACACGGUCGACCUCU | ||||
| miR-346 | 1976 | 1983 | 1A,m8 | hsa-miR-346brain | UGUCUGCCCGCAUGCCUGCCUCU |
| miR-363 | 660 | 666 | 1A | hsa-miR-363 | AUUGCACGGUAUCCAUCUGUAA |
| miR-381 | 651 | 657 | 1A | hsa-miR-381 | UAUACAAGGGCAAGCUCUCUGU |
| miR-409-5p | 973 | 979 | m8 | hsa-miR-409-5p | AGGUUACCCGAGCAACUUUGCA |
| miR-452 | 661 | 668 | 1A,m8 | hsa-miR-452 | UGUUUGCAGAGGAAACUGAGAC |
| miR-487b | 592 | 598 | m8 | hsa-miR-487b | AAUCGUACAGGGUCAUCCACUU |
| miR-493-5p | 1530 | 1536 | 1A | hsa-miR-493-5p | UUGUACAUGGUAGGCUUUCAUU |
| hsa-miR-493-5p | UUGUACAUGGUAGGCUUUCAUU | ||||
| miR-494 | 709 | 715 | 1A | hsa-miR-494brain | UGAAACAUACACGGGAAACCUCUU |
| miR-496 | 883 | 890 | 1A,m8 | hsa-miR-496 | AUUACAUGGCCAAUCUC |
| hsa-miR-496 | AUUACAUGGCCAAUCUC | ||||
| miR-539 | 1719 | 1726 | 1A,m8 | hsa-miR-539 | GGAGAAAUUAUCCUUGGUGUGU |
| miR-543 | 552 | 558 | m8 | hsa-miR-543 | AAACAUUCGCGGUGCACUUCU |
- 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.