Gene Page: PIK3C2B
Summary ?
| GeneID | 5287 |
| Symbol | PIK3C2B |
| Synonyms | C2-PI3K |
| Description | phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta |
| Reference | MIM:602838|HGNC:HGNC:8972|Ensembl:ENSG00000133056|HPRD:04160|Vega:OTTHUMG00000036101 |
| Gene type | protein-coding |
| Map location | 1q32 |
| TADA p-value | 0.005 |
| Fetal beta | 0.971 |
| eGene | Caudate basal ganglia Myers' cis & trans |
| Support | CompositeSet |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DNM:Fromer_2014 | Whole Exome Sequencing analysis | This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA. |
Section I. Genetics and epigenetics annotation
DNM table
| Gene | Chromosome | Position | Ref | Alt | Transcript | AA change | Mutation type | Sift | CG46 | Trait | Study |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PIK3C2B | chr1 | 204403561..204403568 | ACTTACCG | A | NM_002646 NM_002646 | . . | splice-deletion frameshift | Schizophrenia | DNM:Fromer_2014 | ||
| PIK3C2B | chr1 | 204438839 | T | C | NM_002646 | p.31Q>R | missense | Schizophrenia | DNM:Fromer_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs10994209 | chr10 | 61877705 | PIK3C2B | 5287 | 0.15 | 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.
Top co-expressed genes in brain regions
| Top 10 positively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| C18orf22 | 0.59 | 0.54 |
| C9orf7 | 0.59 | 0.54 |
| MICAL1 | 0.58 | 0.54 |
| ZNF3 | 0.58 | 0.53 |
| SH3BP2 | 0.58 | 0.54 |
| ZNF669 | 0.58 | 0.52 |
| CCDC101 | 0.58 | 0.56 |
| BAT1 | 0.57 | 0.53 |
| LRRC45 | 0.57 | 0.51 |
| ZNF435 | 0.57 | 0.52 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| CA4 | -0.45 | -0.52 |
| TINAGL1 | -0.45 | -0.52 |
| RGS5 | -0.44 | -0.52 |
| ABCG2 | -0.44 | -0.50 |
| FBXO2 | -0.44 | -0.49 |
| SLC39A8 | -0.44 | -0.50 |
| CA2 | -0.44 | -0.56 |
| ATP10A | -0.43 | -0.51 |
| ASPHD1 | -0.43 | -0.48 |
| HLA-F | -0.43 | -0.48 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| KEGG INOSITOL PHOSPHATE METABOLISM | 54 | 42 | All SZGR 2.0 genes in this pathway |
| KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM | 76 | 56 | All SZGR 2.0 genes in this pathway |
| PID KIT PATHWAY | 52 | 40 | All SZGR 2.0 genes in this pathway |
| REACTOME PHOSPHOLIPID METABOLISM | 198 | 112 | All SZGR 2.0 genes in this pathway |
| REACTOME SYNTHESIS OF PIPS AT THE PLASMA MEMBRANE | 31 | 23 | All SZGR 2.0 genes in this pathway |
| REACTOME PI METABOLISM | 48 | 34 | All SZGR 2.0 genes in this pathway |
| REACTOME METABOLISM OF LIPIDS AND LIPOPROTEINS | 478 | 302 | All SZGR 2.0 genes in this pathway |
| HORIUCHI WTAP TARGETS UP | 306 | 188 | 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 |
| GARGALOVIC RESPONSE TO OXIDIZED PHOSPHOLIPIDS BLACK DN | 11 | 5 | All SZGR 2.0 genes in this pathway |
| TONKS TARGETS OF RUNX1 RUNX1T1 FUSION ERYTHROCYTE UP | 157 | 104 | All SZGR 2.0 genes in this pathway |
| DODD NASOPHARYNGEAL CARCINOMA UP | 1821 | 933 | All SZGR 2.0 genes in this pathway |
| LINDGREN BLADDER CANCER CLUSTER 1 DN | 378 | 231 | All SZGR 2.0 genes in this pathway |
| SCHLOSSER SERUM RESPONSE DN | 712 | 443 | All SZGR 2.0 genes in this pathway |
| TCGA GLIOBLASTOMA COPY NUMBER UP | 75 | 36 | All SZGR 2.0 genes in this pathway |
| TENEDINI MEGAKARYOCYTE MARKERS | 66 | 48 | All SZGR 2.0 genes in this pathway |
| MARTINEZ RESPONSE TO TRABECTEDIN UP | 71 | 49 | All SZGR 2.0 genes in this pathway |
| BLALOCK ALZHEIMERS DISEASE UP | 1691 | 1088 | All SZGR 2.0 genes in this pathway |
| SARRIO EPITHELIAL MESENCHYMAL TRANSITION DN | 154 | 101 | All SZGR 2.0 genes in this pathway |
| ACEVEDO LIVER CANCER WITH H3K27ME3 DN | 228 | 114 | All SZGR 2.0 genes in this pathway |
| BOQUEST STEM CELL DN | 216 | 143 | All SZGR 2.0 genes in this pathway |
| VALK AML CLUSTER 10 | 33 | 22 | All SZGR 2.0 genes in this pathway |
| VALK AML WITH EVI1 | 25 | 15 | All SZGR 2.0 genes in this pathway |
| DUTERTRE ESTRADIOL RESPONSE 24HR DN | 505 | 328 | All SZGR 2.0 genes in this pathway |
| KOINUMA TARGETS OF SMAD2 OR SMAD3 | 824 | 528 | All SZGR 2.0 genes in this pathway |
| ZWANG DOWN BY 2ND EGF PULSE | 293 | 119 | All SZGR 2.0 genes in this pathway |