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Gene: PDE12 |
Gene summary for PDE12 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PDE12 | Gene ID | 201626 |
| Gene name | phosphodiesterase 12 | |
| Gene Alias | 2'-PDE | |
| Cytomap | 3p14.3 | |
| Gene Type | protein-coding | GO ID | GO:0000288 | UniProtAcc | F6T1Q0 |
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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 |
| 201626 | PDE12 | HCC1_Meng | Human | Liver | HCC | 1.24e-41 | 3.37e-02 | 0.0246 |
| 201626 | PDE12 | HCC2_Meng | Human | Liver | HCC | 1.35e-06 | -1.40e-02 | 0.0107 |
| 201626 | PDE12 | HCC1 | Human | Liver | HCC | 1.47e-04 | 3.09e+00 | 0.5336 |
| 201626 | PDE12 | HCC2 | Human | Liver | HCC | 8.15e-05 | 1.92e+00 | 0.5341 |
| 201626 | PDE12 | S014 | Human | Liver | HCC | 1.59e-02 | 2.13e-01 | 0.2254 |
| 201626 | PDE12 | S016 | Human | Liver | HCC | 1.22e-05 | 3.12e-01 | 0.2243 |
| 201626 | PDE12 | S027 | Human | Liver | HCC | 1.64e-03 | 5.28e-01 | 0.2446 |
| 201626 | PDE12 | S028 | Human | Liver | HCC | 7.97e-14 | 6.99e-01 | 0.2503 |
| 201626 | PDE12 | S029 | Human | Liver | HCC | 1.21e-12 | 6.41e-01 | 0.2581 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:000609122 | Liver | HCC | generation of precursor metabolites and energy | 340/7958 | 490/18723 | 4.04e-34 | 2.85e-31 | 340 |
| GO:000989622 | Liver | HCC | positive regulation of catabolic process | 335/7958 | 492/18723 | 3.83e-31 | 1.87e-28 | 335 |
| GO:003133122 | Liver | HCC | positive regulation of cellular catabolic process | 295/7958 | 427/18723 | 3.20e-29 | 1.45e-26 | 295 |
| GO:001603222 | Liver | HCC | viral process | 286/7958 | 415/18723 | 4.41e-28 | 1.86e-25 | 286 |
| GO:004427021 | Liver | HCC | cellular nitrogen compound catabolic process | 303/7958 | 451/18723 | 9.76e-27 | 3.64e-24 | 303 |
| GO:004670021 | Liver | HCC | heterocycle catabolic process | 299/7958 | 445/18723 | 2.07e-26 | 7.29e-24 | 299 |
| GO:190136121 | Liver | HCC | organic cyclic compound catabolic process | 325/7958 | 495/18723 | 6.52e-26 | 2.18e-23 | 325 |
| GO:001943921 | Liver | HCC | aromatic compound catabolic process | 309/7958 | 467/18723 | 1.56e-25 | 4.94e-23 | 309 |
| GO:000640121 | Liver | HCC | RNA catabolic process | 201/7958 | 278/18723 | 3.88e-24 | 1.02e-21 | 201 |
| GO:003465521 | Liver | HCC | nucleobase-containing compound catabolic process | 273/7958 | 407/18723 | 4.84e-24 | 1.23e-21 | 273 |
| GO:000906012 | Liver | HCC | aerobic respiration | 147/7958 | 189/18723 | 3.13e-23 | 6.61e-21 | 147 |
| GO:190331121 | Liver | HCC | regulation of mRNA metabolic process | 205/7958 | 288/18723 | 3.38e-23 | 6.90e-21 | 205 |
| GO:004533312 | Liver | HCC | cellular respiration | 171/7958 | 230/18723 | 6.35e-23 | 1.26e-20 | 171 |
| GO:004603422 | Liver | HCC | ATP metabolic process | 198/7958 | 277/18723 | 8.30e-23 | 1.55e-20 | 198 |
| GO:001598022 | Liver | HCC | energy derivation by oxidation of organic compounds | 221/7958 | 318/18723 | 1.02e-22 | 1.86e-20 | 221 |
| GO:000640221 | Liver | HCC | mRNA catabolic process | 169/7958 | 232/18723 | 4.50e-21 | 6.96e-19 | 169 |
| GO:000611912 | Liver | HCC | oxidative phosphorylation | 110/7958 | 141/18723 | 6.58e-18 | 7.45e-16 | 110 |
| GO:001905822 | Liver | HCC | viral life cycle | 209/7958 | 317/18723 | 2.05e-17 | 2.09e-15 | 209 |
| GO:000641722 | Liver | HCC | regulation of translation | 287/7958 | 468/18723 | 8.79e-17 | 8.08e-15 | 287 |
| GO:004348721 | Liver | HCC | regulation of RNA stability | 119/7958 | 170/18723 | 3.20e-13 | 1.71e-11 | 119 |
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| 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 |
| PDE12 | SNV | Missense_Mutation | novel | c.326N>T | p.Ser109Leu | p.S109L | Q6L8Q7 | protein_coding | tolerated(0.3) | benign(0.003) | TCGA-D8-A4Z1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
| PDE12 | insertion | Nonsense_Mutation | novel | c.417_418insCCTGTTTGTACTTGAGAGGGTTAGGC | p.Asp140ProfsTer5 | p.D140Pfs*5 | Q6L8Q7 | protein_coding | TCGA-A8-A07U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | SD | ||
| PDE12 | insertion | Frame_Shift_Ins | novel | c.1825_1826insGACCATCCTGGCT | p.Lys609ArgfsTer28 | p.K609Rfs*28 | Q6L8Q7 | protein_coding | TCGA-A8-A0AB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| PDE12 | insertion | Frame_Shift_Ins | novel | c.1827_1828insCACGATGAAACCCCGTC | p.Ter610HisfsTer16 | p.*610Hfs*16 | Q6L8Q7 | protein_coding | TCGA-A8-A0AB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| PDE12 | insertion | Nonsense_Mutation | novel | c.779_780insTGAAAATTAAAGCTTTTCCATAATTG | p.Ser261GlufsTer3 | p.S261Efs*3 | Q6L8Q7 | protein_coding | TCGA-BH-A0HX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adrimycin | SD | ||
| PDE12 | deletion | Frame_Shift_Del | c.533delC | p.Pro178LeufsTer67 | p.P178Lfs*67 | Q6L8Q7 | protein_coding | TCGA-E9-A1RE-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD | |||
| PDE12 | deletion | Frame_Shift_Del | novel | c.1081delN | p.Leu361TrpfsTer5 | p.L361Wfs*5 | Q6L8Q7 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| PDE12 | SNV | Missense_Mutation | c.1160N>A | p.Arg387Gln | p.R387Q | Q6L8Q7 | protein_coding | tolerated(0.07) | probably_damaging(0.981) | TCGA-EK-A2RC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PDE12 | SNV | Missense_Mutation | c.1291N>G | p.Arg431Gly | p.R431G | Q6L8Q7 | protein_coding | deleterious(0) | probably_damaging(0.986) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| PDE12 | SNV | Missense_Mutation | novel | c.470T>C | p.Val157Ala | p.V157A | Q6L8Q7 | protein_coding | deleterious(0) | possibly_damaging(0.829) | TCGA-AA-A01C-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
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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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