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Gene: PPP6C |
Gene summary for PPP6C |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PPP6C | Gene ID | 5537 |
| Gene name | protein phosphatase 6 catalytic subunit | |
| Gene Alias | PP6 | |
| Cytomap | 9q33.3 | |
| Gene Type | protein-coding | GO ID | GO:0000082 | UniProtAcc | O00743 |
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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 |
| 5537 | PPP6C | LZE2T | Human | Esophagus | ESCC | 1.52e-03 | 3.70e-01 | 0.082 |
| 5537 | PPP6C | LZE4T | Human | Esophagus | ESCC | 1.87e-17 | 6.12e-01 | 0.0811 |
| 5537 | PPP6C | LZE7T | Human | Esophagus | ESCC | 6.37e-11 | 5.07e-01 | 0.0667 |
| 5537 | PPP6C | LZE8T | Human | Esophagus | ESCC | 5.69e-06 | 3.76e-01 | 0.067 |
| 5537 | PPP6C | LZE20T | Human | Esophagus | ESCC | 3.52e-06 | 4.66e-01 | 0.0662 |
| 5537 | PPP6C | LZE22D1 | Human | Esophagus | HGIN | 3.31e-03 | -1.02e-02 | 0.0595 |
| 5537 | PPP6C | LZE24T | Human | Esophagus | ESCC | 5.45e-22 | 6.54e-01 | 0.0596 |
| 5537 | PPP6C | LZE21T | Human | Esophagus | ESCC | 8.27e-08 | 2.16e-01 | 0.0655 |
| 5537 | PPP6C | LZE6T | Human | Esophagus | ESCC | 9.84e-12 | 5.81e-01 | 0.0845 |
| 5537 | PPP6C | P1T-E | Human | Esophagus | ESCC | 6.41e-08 | 4.64e-01 | 0.0875 |
| 5537 | PPP6C | P2T-E | Human | Esophagus | ESCC | 1.22e-45 | 8.17e-01 | 0.1177 |
| 5537 | PPP6C | P4T-E | Human | Esophagus | ESCC | 1.36e-34 | 8.81e-01 | 0.1323 |
| 5537 | PPP6C | P5T-E | Human | Esophagus | ESCC | 3.20e-16 | 2.49e-01 | 0.1327 |
| 5537 | PPP6C | P8T-E | Human | Esophagus | ESCC | 1.41e-53 | 9.41e-01 | 0.0889 |
| 5537 | PPP6C | P9T-E | Human | Esophagus | ESCC | 3.20e-22 | 5.69e-01 | 0.1131 |
| 5537 | PPP6C | P10T-E | Human | Esophagus | ESCC | 4.36e-39 | 5.59e-01 | 0.116 |
| 5537 | PPP6C | P11T-E | Human | Esophagus | ESCC | 1.75e-19 | 8.59e-01 | 0.1426 |
| 5537 | PPP6C | P12T-E | Human | Esophagus | ESCC | 9.86e-37 | 5.67e-01 | 0.1122 |
| 5537 | PPP6C | P15T-E | Human | Esophagus | ESCC | 4.13e-30 | 7.95e-01 | 0.1149 |
| 5537 | PPP6C | P16T-E | Human | Esophagus | ESCC | 1.38e-22 | 3.86e-01 | 0.1153 |
| Page: 1 2 3 4 5 |
| 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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:004819317 | Esophagus | HGIN | Golgi vesicle transport | 83/2587 | 296/18723 | 8.59e-11 | 8.89e-09 | 83 |
| GO:005165616 | Esophagus | HGIN | establishment of organelle localization | 90/2587 | 390/18723 | 4.27e-07 | 1.94e-05 | 90 |
| GO:00068889 | Esophagus | HGIN | endoplasmic reticulum to Golgi vesicle-mediated transport | 40/2587 | 130/18723 | 4.67e-07 | 2.07e-05 | 40 |
| GO:000690020 | Esophagus | HGIN | vesicle budding from membrane | 23/2587 | 61/18723 | 2.85e-06 | 9.93e-05 | 23 |
| GO:00447729 | Esophagus | HGIN | mitotic cell cycle phase transition | 89/2587 | 424/18723 | 2.80e-05 | 7.21e-04 | 89 |
| GO:00160509 | Esophagus | HGIN | vesicle organization | 65/2587 | 300/18723 | 1.24e-04 | 2.54e-03 | 65 |
| GO:000647017 | Esophagus | HGIN | protein dephosphorylation | 61/2587 | 281/18723 | 1.86e-04 | 3.51e-03 | 61 |
| GO:00000827 | Esophagus | HGIN | G1/S transition of mitotic cell cycle | 48/2587 | 214/18723 | 3.97e-04 | 6.07e-03 | 48 |
| GO:00448437 | Esophagus | HGIN | cell cycle G1/S phase transition | 52/2587 | 241/18723 | 6.19e-04 | 8.58e-03 | 52 |
| GO:00901146 | Esophagus | HGIN | COPII-coated vesicle budding | 11/2587 | 29/18723 | 1.08e-03 | 1.32e-02 | 11 |
| GO:005165010 | Esophagus | HGIN | establishment of vesicle localization | 35/2587 | 161/18723 | 3.89e-03 | 3.54e-02 | 35 |
| GO:00482075 | Esophagus | HGIN | vesicle targeting, rough ER to cis-Golgi | 6/2587 | 13/18723 | 4.97e-03 | 4.18e-02 | 6 |
| GO:00482085 | Esophagus | HGIN | COPII vesicle coating | 6/2587 | 13/18723 | 4.97e-03 | 4.18e-02 | 6 |
| GO:00481996 | Esophagus | HGIN | vesicle targeting, to, from or within Golgi | 8/2587 | 21/18723 | 5.00e-03 | 4.19e-02 | 8 |
| GO:00069017 | Esophagus | HGIN | vesicle coating | 7/2587 | 17/18723 | 5.21e-03 | 4.30e-02 | 7 |
| GO:005164810 | Esophagus | HGIN | vesicle localization | 37/2587 | 177/18723 | 6.03e-03 | 4.87e-02 | 37 |
| GO:004819318 | Esophagus | ESCC | Golgi vesicle transport | 231/8552 | 296/18723 | 1.82e-30 | 9.63e-28 | 231 |
| GO:005165617 | Esophagus | ESCC | establishment of organelle localization | 273/8552 | 390/18723 | 9.13e-23 | 1.81e-20 | 273 |
| GO:001605014 | Esophagus | ESCC | vesicle organization | 211/8552 | 300/18723 | 2.85e-18 | 2.87e-16 | 211 |
| GO:004477216 | Esophagus | ESCC | mitotic cell cycle phase transition | 281/8552 | 424/18723 | 4.63e-18 | 4.45e-16 | 281 |
| Page: 1 2 3 4 5 6 7 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| ∗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 |
| PPP6C | SNV | Missense_Mutation | rs781486938 | c.649N>A | p.Glu217Lys | p.E217K | O00743 | protein_coding | tolerated(0.05) | benign(0.031) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PPP6C | SNV | Missense_Mutation | rs768855518 | c.1013N>T | p.Thr338Met | p.T338M | O00743 | protein_coding | tolerated(0.22) | probably_damaging(0.945) | TCGA-AR-A256-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD |
| PPP6C | SNV | Missense_Mutation | novel | c.745N>T | p.Ala249Ser | p.A249S | O00743 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PPP6C | SNV | Missense_Mutation | novel | c.543N>C | p.Lys181Asn | p.K181N | O00743 | protein_coding | tolerated(0.14) | benign(0.062) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PPP6C | SNV | Missense_Mutation | c.663A>C | p.Glu221Asp | p.E221D | O00743 | protein_coding | deleterious(0.01) | possibly_damaging(0.907) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| PPP6C | SNV | Missense_Mutation | novel | c.704A>C | p.Asp235Ala | p.D235A | O00743 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| PPP6C | SNV | Missense_Mutation | c.56N>G | p.Leu19Arg | p.L19R | O00743 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-CK-5916-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| PPP6C | SNV | Missense_Mutation | c.811N>G | p.Cys271Gly | p.C271G | O00743 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CM-6166-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PPP6C | SNV | Missense_Mutation | novel | c.75N>C | p.Lys25Asn | p.K25N | O00743 | protein_coding | deleterious(0) | possibly_damaging(0.603) | TCGA-SS-A7HO-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | oxaliplatin | PD |
| PPP6C | SNV | Missense_Mutation | c.835N>A | p.Glu279Lys | p.E279K | O00743 | protein_coding | deleterious(0) | benign(0.113) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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 |
| Page: 1 |
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