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Gene: PDE3A |
Gene summary for PDE3A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PDE3A | Gene ID | 5139 |
| Gene name | phosphodiesterase 3A | |
| Gene Alias | CGI-PDE | |
| Cytomap | 12p12.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q14432 |
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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 |
| 5139 | PDE3A | HTA11_3410_2000001011 | Human | Colorectum | AD | 4.39e-86 | -1.47e+00 | 0.0155 |
| 5139 | PDE3A | HTA11_2487_2000001011 | Human | Colorectum | SER | 3.19e-07 | -5.10e-01 | -0.1808 |
| 5139 | PDE3A | HTA11_2951_2000001011 | Human | Colorectum | AD | 9.76e-17 | -1.35e+00 | 0.0216 |
| 5139 | PDE3A | HTA11_1938_2000001011 | Human | Colorectum | AD | 7.60e-43 | -1.22e+00 | -0.0811 |
| 5139 | PDE3A | HTA11_78_2000001011 | Human | Colorectum | AD | 6.25e-15 | -6.40e-01 | -0.1088 |
| 5139 | PDE3A | HTA11_347_2000001011 | Human | Colorectum | AD | 8.56e-09 | 5.52e-01 | -0.1954 |
| 5139 | PDE3A | HTA11_3361_2000001011 | Human | Colorectum | AD | 3.72e-36 | -1.00e+00 | -0.1207 |
| 5139 | PDE3A | HTA11_83_2000001011 | Human | Colorectum | SER | 1.71e-07 | -6.22e-01 | -0.1526 |
| 5139 | PDE3A | HTA11_696_2000001011 | Human | Colorectum | AD | 7.61e-12 | -5.03e-01 | -0.1464 |
| 5139 | PDE3A | HTA11_866_2000001011 | Human | Colorectum | AD | 2.10e-15 | -6.47e-01 | -0.1001 |
| 5139 | PDE3A | HTA11_1391_2000001011 | Human | Colorectum | AD | 6.55e-41 | -9.38e-01 | -0.059 |
| 5139 | PDE3A | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.37e-04 | -4.94e-01 | -0.2061 |
| 5139 | PDE3A | HTA11_5216_2000001011 | Human | Colorectum | SER | 1.15e-08 | -6.27e-01 | -0.1462 |
| 5139 | PDE3A | HTA11_546_2000001011 | Human | Colorectum | AD | 3.42e-09 | -6.81e-01 | -0.0842 |
| 5139 | PDE3A | HTA11_9341_2000001011 | Human | Colorectum | SER | 1.75e-14 | -1.14e+00 | -0.00410000000000005 |
| 5139 | PDE3A | HTA11_7862_2000001011 | Human | Colorectum | AD | 5.31e-12 | -5.91e-01 | -0.0179 |
| 5139 | PDE3A | HTA11_866_3004761011 | Human | Colorectum | AD | 1.40e-52 | -9.90e-01 | 0.096 |
| 5139 | PDE3A | HTA11_4255_2000001011 | Human | Colorectum | SER | 7.80e-14 | -8.86e-01 | 0.0446 |
| 5139 | PDE3A | HTA11_9408_2000001011 | Human | Colorectum | AD | 6.18e-15 | -1.13e+00 | 0.0451 |
| 5139 | PDE3A | HTA11_8622_2000001021 | Human | Colorectum | SER | 4.01e-21 | -1.12e+00 | 0.0528 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:0009410 | Colorectum | AD | response to xenobiotic stimulus | 128/3918 | 462/18723 | 2.69e-04 | 3.31e-03 | 128 |
| GO:0010720 | Colorectum | AD | positive regulation of cell development | 87/3918 | 298/18723 | 4.17e-04 | 4.71e-03 | 87 |
| GO:0071559 | Colorectum | AD | response to transforming growth factor beta | 74/3918 | 256/18723 | 1.45e-03 | 1.23e-02 | 74 |
| GO:0071560 | Colorectum | AD | cellular response to transforming growth factor beta stimulus | 72/3918 | 250/18723 | 1.85e-03 | 1.52e-02 | 72 |
| GO:00107201 | Colorectum | SER | positive regulation of cell development | 66/2897 | 298/18723 | 1.36e-03 | 1.50e-02 | 66 |
| GO:00107202 | Colorectum | MSS | positive regulation of cell development | 81/3467 | 298/18723 | 1.38e-04 | 2.06e-03 | 81 |
| GO:00094101 | Colorectum | MSS | response to xenobiotic stimulus | 110/3467 | 462/18723 | 2.36e-03 | 1.92e-02 | 110 |
| GO:00107203 | Colorectum | FAP | positive regulation of cell development | 72/2622 | 298/18723 | 1.67e-06 | 6.99e-05 | 72 |
| GO:00715591 | Colorectum | FAP | response to transforming growth factor beta | 63/2622 | 256/18723 | 3.82e-06 | 1.32e-04 | 63 |
| GO:00715601 | Colorectum | FAP | cellular response to transforming growth factor beta stimulus | 61/2622 | 250/18723 | 7.22e-06 | 2.19e-04 | 61 |
| GO:0046683 | Colorectum | FAP | response to organophosphorus | 33/2622 | 131/18723 | 4.61e-04 | 5.39e-03 | 33 |
| GO:0003018 | Colorectum | FAP | vascular process in circulatory system | 56/2622 | 263/18723 | 7.67e-04 | 8.12e-03 | 56 |
| GO:0014074 | Colorectum | FAP | response to purine-containing compound | 35/2622 | 148/18723 | 1.09e-03 | 1.05e-02 | 35 |
| GO:0021700 | Colorectum | FAP | developmental maturation | 57/2622 | 280/18723 | 2.08e-03 | 1.72e-02 | 57 |
| GO:00094102 | Colorectum | FAP | response to xenobiotic stimulus | 87/2622 | 462/18723 | 2.15e-03 | 1.77e-02 | 87 |
| GO:00107204 | Colorectum | CRC | positive regulation of cell development | 60/2078 | 298/18723 | 3.27e-06 | 1.47e-04 | 60 |
| GO:00715592 | Colorectum | CRC | response to transforming growth factor beta | 51/2078 | 256/18723 | 2.33e-05 | 6.65e-04 | 51 |
| GO:00715602 | Colorectum | CRC | cellular response to transforming growth factor beta stimulus | 49/2078 | 250/18723 | 5.17e-05 | 1.19e-03 | 49 |
| GO:00030181 | Colorectum | CRC | vascular process in circulatory system | 45/2078 | 263/18723 | 2.10e-03 | 2.08e-02 | 45 |
| GO:00217001 | Colorectum | CRC | developmental maturation | 47/2078 | 280/18723 | 2.52e-03 | 2.38e-02 | 47 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04022 | Colorectum | MSS | cGMP-PKG signaling pathway | 51/1875 | 167/8465 | 6.83e-03 | 2.73e-02 | 1.67e-02 | 51 |
| hsa040221 | Colorectum | MSS | cGMP-PKG signaling pathway | 51/1875 | 167/8465 | 6.83e-03 | 2.73e-02 | 1.67e-02 | 51 |
| hsa040222 | Colorectum | FAP | cGMP-PKG signaling pathway | 42/1404 | 167/8465 | 2.84e-03 | 1.27e-02 | 7.70e-03 | 42 |
| hsa04024 | Colorectum | FAP | cAMP signaling pathway | 51/1404 | 225/8465 | 1.02e-02 | 3.68e-02 | 2.24e-02 | 51 |
| hsa040223 | Colorectum | FAP | cGMP-PKG signaling pathway | 42/1404 | 167/8465 | 2.84e-03 | 1.27e-02 | 7.70e-03 | 42 |
| hsa040241 | Colorectum | FAP | cAMP signaling pathway | 51/1404 | 225/8465 | 1.02e-02 | 3.68e-02 | 2.24e-02 | 51 |
| hsa040242 | Colorectum | CRC | cAMP signaling pathway | 47/1091 | 225/8465 | 4.57e-04 | 4.77e-03 | 3.23e-03 | 47 |
| hsa040243 | Colorectum | CRC | cAMP signaling pathway | 47/1091 | 225/8465 | 4.57e-04 | 4.77e-03 | 3.23e-03 | 47 |
| hsa040224 | Oral cavity | EOLP | cGMP-PKG signaling pathway | 36/1218 | 167/8465 | 7.34e-03 | 2.12e-02 | 1.25e-02 | 36 |
| hsa0402211 | Oral cavity | EOLP | cGMP-PKG signaling pathway | 36/1218 | 167/8465 | 7.34e-03 | 2.12e-02 | 1.25e-02 | 36 |
| hsa0402221 | Oral cavity | NEOLP | cGMP-PKG signaling pathway | 35/1112 | 167/8465 | 3.02e-03 | 1.25e-02 | 7.85e-03 | 35 |
| hsa0402231 | Oral cavity | NEOLP | cGMP-PKG signaling pathway | 35/1112 | 167/8465 | 3.02e-03 | 1.25e-02 | 7.85e-03 | 35 |
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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 |
| PDE3A | SNV | Missense_Mutation | c.1679N>A | p.Gly560Asp | p.G560D | Q14432 | protein_coding | tolerated(0.63) | benign(0.01) | TCGA-A2-A0EO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| PDE3A | SNV | Missense_Mutation | c.1921N>A | p.Asp641Asn | p.D641N | Q14432 | protein_coding | deleterious(0.04) | benign(0.109) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| PDE3A | SNV | Missense_Mutation | rs776833954 | c.2014N>A | p.Leu672Ile | p.L672I | Q14432 | protein_coding | tolerated(0.08) | possibly_damaging(0.833) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PDE3A | SNV | Missense_Mutation | c.2786G>A | p.Gly929Glu | p.G929E | Q14432 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AO-A03V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | fluorouracil | SD | |
| PDE3A | SNV | Missense_Mutation | rs150253039 | c.1045G>A | p.Val349Ile | p.V349I | Q14432 | protein_coding | deleterious(0.04) | probably_damaging(0.985) | TCGA-AQ-A04H-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxotere | SD |
| PDE3A | SNV | Missense_Mutation | c.1249N>C | p.Asp417His | p.D417H | Q14432 | protein_coding | tolerated(0.07) | benign(0.444) | TCGA-AR-A0TP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| PDE3A | SNV | Missense_Mutation | c.2653N>A | p.Phe885Ile | p.F885I | Q14432 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AR-A24Z-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| PDE3A | SNV | Missense_Mutation | c.2123N>A | p.Gly708Asp | p.G708D | Q14432 | protein_coding | deleterious(0.03) | possibly_damaging(0.795) | TCGA-B6-A0I6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| PDE3A | SNV | Missense_Mutation | c.2363C>T | p.Ser788Leu | p.S788L | Q14432 | protein_coding | deleterious(0.04) | benign(0.068) | TCGA-BH-A18V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PDE3A | SNV | Missense_Mutation | c.3003N>T | p.Gln1001His | p.Q1001H | Q14432 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-D8-A1JK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 |
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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 |
| 5139 | PDE3A | ENZYME, DRUGGABLE GENOME | VESNARINONE | VESNARINONE | ||
| 5139 | PDE3A | ENZYME, DRUGGABLE GENOME | K-134 | K-134 | 23110051 | |
| 5139 | PDE3A | ENZYME, DRUGGABLE GENOME | 349U85.HCL | |||
| 5139 | PDE3A | ENZYME, DRUGGABLE GENOME | inhibitor | CHEMBL628 | PENTOXIFYLLINE | |
| 5139 | PDE3A | ENZYME, DRUGGABLE GENOME | inhibitor | CHEMBL1200578 | THEOPHYLLINE SODIUM GLYCINATE | |
| 5139 | PDE3A | ENZYME, DRUGGABLE GENOME | inhibitor | CHEMBL190 | THEOPHYLLINE | |
| 5139 | PDE3A | ENZYME, DRUGGABLE GENOME | RPL-554 | |||
| 5139 | PDE3A | ENZYME, DRUGGABLE GENOME | inhibitor | 178103691 | ANAGRELIDE | |
| 5139 | PDE3A | ENZYME, DRUGGABLE GENOME | hydrochlorothiazide | HYDROCHLOROTHIAZIDE | 31327267 | |
| 5139 | PDE3A | ENZYME, DRUGGABLE GENOME | inhibitor | 178103971 | IBUDILAST |
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