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Gene: PIK3C3 |
Gene summary for PIK3C3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PIK3C3 | Gene ID | 5289 |
| Gene name | phosphatidylinositol 3-kinase catalytic subunit type 3 | |
| Gene Alias | VPS34 | |
| Cytomap | 18q12.3 | |
| Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | A8MYT4 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 5289 | PIK3C3 | LZE4T | Human | Esophagus | ESCC | 8.77e-11 | 2.10e-01 | 0.0811 |
| 5289 | PIK3C3 | LZE7T | Human | Esophagus | ESCC | 6.20e-09 | 5.40e-01 | 0.0667 |
| 5289 | PIK3C3 | LZE20T | Human | Esophagus | ESCC | 4.83e-07 | 1.28e-01 | 0.0662 |
| 5289 | PIK3C3 | LZE24T | Human | Esophagus | ESCC | 4.94e-14 | 2.12e-01 | 0.0596 |
| 5289 | PIK3C3 | LZE21T | Human | Esophagus | ESCC | 3.05e-02 | 1.02e-01 | 0.0655 |
| 5289 | PIK3C3 | P1T-E | Human | Esophagus | ESCC | 1.38e-05 | 1.43e-01 | 0.0875 |
| 5289 | PIK3C3 | P2T-E | Human | Esophagus | ESCC | 5.28e-13 | 2.24e-01 | 0.1177 |
| 5289 | PIK3C3 | P4T-E | Human | Esophagus | ESCC | 1.29e-14 | 2.36e-01 | 0.1323 |
| 5289 | PIK3C3 | P5T-E | Human | Esophagus | ESCC | 1.08e-05 | 7.29e-02 | 0.1327 |
| 5289 | PIK3C3 | P8T-E | Human | Esophagus | ESCC | 2.63e-19 | 2.95e-01 | 0.0889 |
| 5289 | PIK3C3 | P9T-E | Human | Esophagus | ESCC | 1.95e-14 | 2.35e-01 | 0.1131 |
| 5289 | PIK3C3 | P10T-E | Human | Esophagus | ESCC | 7.81e-13 | 1.80e-01 | 0.116 |
| 5289 | PIK3C3 | P11T-E | Human | Esophagus | ESCC | 2.40e-05 | 2.14e-01 | 0.1426 |
| 5289 | PIK3C3 | P12T-E | Human | Esophagus | ESCC | 3.53e-10 | 2.09e-01 | 0.1122 |
| 5289 | PIK3C3 | P15T-E | Human | Esophagus | ESCC | 3.23e-05 | 8.94e-02 | 0.1149 |
| 5289 | PIK3C3 | P16T-E | Human | Esophagus | ESCC | 1.71e-10 | 1.57e-01 | 0.1153 |
| 5289 | PIK3C3 | P19T-E | Human | Esophagus | ESCC | 2.32e-04 | 2.03e-01 | 0.1662 |
| 5289 | PIK3C3 | P20T-E | Human | Esophagus | ESCC | 1.12e-13 | 2.39e-01 | 0.1124 |
| 5289 | PIK3C3 | P21T-E | Human | Esophagus | ESCC | 3.79e-12 | 1.72e-01 | 0.1617 |
| 5289 | PIK3C3 | P22T-E | Human | Esophagus | ESCC | 3.79e-14 | 2.11e-01 | 0.1236 |
| Page: 1 2 3 4 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:001623617 | Esophagus | ESCC | macroautophagy | 216/8552 | 291/18723 | 1.94e-23 | 4.57e-21 | 216 |
| GO:001605014 | Esophagus | ESCC | vesicle organization | 211/8552 | 300/18723 | 2.85e-18 | 2.87e-16 | 211 |
| GO:0071496111 | Esophagus | ESCC | cellular response to external stimulus | 215/8552 | 320/18723 | 4.29e-15 | 2.43e-13 | 215 |
| GO:001648210 | Esophagus | ESCC | cytosolic transport | 124/8552 | 168/18723 | 9.69e-14 | 4.69e-12 | 124 |
| GO:0031668111 | Esophagus | ESCC | cellular response to extracellular stimulus | 168/8552 | 246/18723 | 4.93e-13 | 2.23e-11 | 168 |
| GO:0031669110 | Esophagus | ESCC | cellular response to nutrient levels | 148/8552 | 215/18723 | 4.58e-12 | 1.76e-10 | 148 |
| GO:0031667111 | Esophagus | ESCC | response to nutrient levels | 289/8552 | 474/18723 | 9.25e-12 | 3.47e-10 | 289 |
| GO:000703314 | Esophagus | ESCC | vacuole organization | 127/8552 | 180/18723 | 1.04e-11 | 3.85e-10 | 127 |
| GO:005160418 | Esophagus | ESCC | protein maturation | 189/8552 | 294/18723 | 7.64e-11 | 2.39e-09 | 189 |
| GO:0009267110 | Esophagus | ESCC | cellular response to starvation | 110/8552 | 156/18723 | 2.63e-10 | 7.37e-09 | 110 |
| GO:004259419 | Esophagus | ESCC | response to starvation | 133/8552 | 197/18723 | 4.31e-10 | 1.14e-08 | 133 |
| GO:00086544 | Esophagus | ESCC | phospholipid biosynthetic process | 162/8552 | 253/18723 | 2.59e-09 | 5.73e-08 | 162 |
| GO:000091016 | Esophagus | ESCC | cytokinesis | 115/8552 | 173/18723 | 2.48e-08 | 4.68e-07 | 115 |
| GO:00464744 | Esophagus | ESCC | glycerophospholipid biosynthetic process | 135/8552 | 211/18723 | 5.75e-08 | 1.02e-06 | 135 |
| GO:000703214 | Esophagus | ESCC | endosome organization | 61/8552 | 82/18723 | 1.13e-07 | 1.85e-06 | 61 |
| GO:190503712 | Esophagus | ESCC | autophagosome organization | 73/8552 | 103/18723 | 1.88e-07 | 2.93e-06 | 73 |
| GO:00989278 | Esophagus | ESCC | vesicle-mediated transport between endosomal compartments | 36/8552 | 43/18723 | 2.90e-07 | 4.20e-06 | 36 |
| GO:00450175 | Esophagus | ESCC | glycerolipid biosynthetic process | 154/8552 | 252/18723 | 5.20e-07 | 6.96e-06 | 154 |
| GO:000004513 | Esophagus | ESCC | autophagosome assembly | 69/8552 | 99/18723 | 1.10e-06 | 1.38e-05 | 69 |
| GO:00450226 | Esophagus | ESCC | early endosome to late endosome transport | 33/8552 | 40/18723 | 1.80e-06 | 2.11e-05 | 33 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05014210 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa05132211 | Esophagus | ESCC | Salmonella infection | 191/4205 | 249/8465 | 6.51e-19 | 5.45e-17 | 2.79e-17 | 191 |
| hsa05016210 | Esophagus | ESCC | Huntington disease | 226/4205 | 306/8465 | 1.38e-18 | 8.72e-17 | 4.46e-17 | 226 |
| hsa05022210 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
| hsa05010210 | Esophagus | ESCC | Alzheimer disease | 263/4205 | 384/8465 | 1.80e-14 | 5.47e-13 | 2.80e-13 | 263 |
| hsa05131211 | Esophagus | ESCC | Shigellosis | 176/4205 | 247/8465 | 2.27e-12 | 4.01e-11 | 2.05e-11 | 176 |
| hsa05167211 | Esophagus | ESCC | Kaposi sarcoma-associated herpesvirus infection | 136/4205 | 194/8465 | 4.28e-09 | 4.22e-08 | 2.16e-08 | 136 |
| hsa0414010 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
| hsa0414530 | Esophagus | ESCC | Phagosome | 100/4205 | 152/8465 | 3.81e-05 | 1.72e-04 | 8.82e-05 | 100 |
| hsa0501728 | Esophagus | ESCC | Spinocerebellar ataxia | 94/4205 | 143/8465 | 6.77e-05 | 2.90e-04 | 1.48e-04 | 94 |
| hsa051527 | Esophagus | ESCC | Tuberculosis | 111/4205 | 180/8465 | 7.14e-04 | 2.32e-03 | 1.19e-03 | 111 |
| hsa041362 | Esophagus | ESCC | Autophagy - other | 23/4205 | 32/8465 | 8.99e-03 | 2.14e-02 | 1.09e-02 | 23 |
| hsa0501438 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa05132310 | Esophagus | ESCC | Salmonella infection | 191/4205 | 249/8465 | 6.51e-19 | 5.45e-17 | 2.79e-17 | 191 |
| hsa0501638 | Esophagus | ESCC | Huntington disease | 226/4205 | 306/8465 | 1.38e-18 | 8.72e-17 | 4.46e-17 | 226 |
| hsa0502238 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
| hsa0501038 | Esophagus | ESCC | Alzheimer disease | 263/4205 | 384/8465 | 1.80e-14 | 5.47e-13 | 2.80e-13 | 263 |
| hsa05131310 | Esophagus | ESCC | Shigellosis | 176/4205 | 247/8465 | 2.27e-12 | 4.01e-11 | 2.05e-11 | 176 |
| hsa0516738 | Esophagus | ESCC | Kaposi sarcoma-associated herpesvirus infection | 136/4205 | 194/8465 | 4.28e-09 | 4.22e-08 | 2.16e-08 | 136 |
| hsa0414015 | Esophagus | ESCC | Autophagy - animal | 101/4205 | 141/8465 | 7.60e-08 | 6.21e-07 | 3.18e-07 | 101 |
| Page: 1 2 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| PIK3C3 | SMC | Skin | ADJ | MLKL,TNFSF9,VPS11, etc. | 7.03e-03 |  |
| PIK3C3 | FIB | Skin | ADJ | MLKL,TNFSF9,VPS11, etc. | 1.40e-02 | |
| PIK3C3 | LYMEND | Skin | SCCIS | MLKL,TNFSF9,VPS11, etc. | 1.27e-02 |  |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| PIK3C3 | SNV | Missense_Mutation | novel | c.1108N>T | p.His370Tyr | p.H370Y | Q8NEB9 | protein_coding | deleterious(0.04) | benign(0.025) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| PIK3C3 | SNV | Missense_Mutation | c.1826N>A | p.Ala609Asp | p.A609D | Q8NEB9 | protein_coding | deleterious(0) | possibly_damaging(0.66) | TCGA-A2-A04N-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cytoxan | SD | |
| PIK3C3 | SNV | Missense_Mutation | c.609G>T | p.Met203Ile | p.M203I | Q8NEB9 | protein_coding | tolerated(0.17) | benign(0.067) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| PIK3C3 | SNV | Missense_Mutation | c.2114G>C | p.Arg705Thr | p.R705T | Q8NEB9 | protein_coding | deleterious(0) | possibly_damaging(0.65) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| PIK3C3 | SNV | Missense_Mutation | novel | c.140N>T | p.Ser47Leu | p.S47L | Q8NEB9 | protein_coding | tolerated(0.07) | benign(0.051) | TCGA-AC-A5XS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | femara | SD |
| PIK3C3 | SNV | Missense_Mutation | c.292C>T | p.Pro98Ser | p.P98S | Q8NEB9 | protein_coding | tolerated(1) | benign(0) | TCGA-AN-A0XU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PIK3C3 | SNV | Missense_Mutation | c.907N>T | p.Pro303Ser | p.P303S | Q8NEB9 | protein_coding | tolerated(0.14) | probably_damaging(0.942) | TCGA-GM-A2DO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | CR | |
| PIK3C3 | SNV | Missense_Mutation | c.1652N>A | p.Arg551Gln | p.R551Q | Q8NEB9 | protein_coding | tolerated(0.4) | benign(0.018) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| PIK3C3 | SNV | Missense_Mutation | rs376188539 | c.521N>A | p.Arg174His | p.R174H | Q8NEB9 | protein_coding | deleterious(0) | probably_damaging(0.969) | TCGA-BI-A0VS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PIK3C3 | SNV | Missense_Mutation | c.1212N>C | p.Lys404Asn | p.K404N | Q8NEB9 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-EA-A1QT-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| 5289 | PIK3C3 | KINASE, PHOSPHATIDYLINOSITOL 3 KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | inhibitor | PKI-587 | GEDATOLISIB | |
| 5289 | PIK3C3 | KINASE, PHOSPHATIDYLINOSITOL 3 KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | inhibitor | PWT33597 | ||
| 5289 | PIK3C3 | KINASE, PHOSPHATIDYLINOSITOL 3 KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | inhibitor | XL-765 | VOXTALISIB | |
| 5289 | PIK3C3 | KINASE, PHOSPHATIDYLINOSITOL 3 KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | inhibitor | 252827496 | ||
| 5289 | PIK3C3 | KINASE, PHOSPHATIDYLINOSITOL 3 KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | inhibitor | 381118852 | ||
| 5289 | PIK3C3 | KINASE, PHOSPHATIDYLINOSITOL 3 KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | inhibitor | 385612248 | ||
| 5289 | PIK3C3 | KINASE, PHOSPHATIDYLINOSITOL 3 KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | SF1126 | |||
| 5289 | PIK3C3 | KINASE, PHOSPHATIDYLINOSITOL 3 KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | inhibitor | GDC-0980 | APITOLISIB | |
| 5289 | PIK3C3 | KINASE, PHOSPHATIDYLINOSITOL 3 KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | inhibitor | PX-866 | SONOLISIB | |
| 5289 | PIK3C3 | KINASE, PHOSPHATIDYLINOSITOL 3 KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | inhibitor | GDC-0941 | PICTILISIB |
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