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Gene: PDE3B |
Gene summary for PDE3B |
Gene summary. |
Gene information | Species | Human | Gene symbol | PDE3B | Gene ID | 5140 |
Gene name | phosphodiesterase 3B | |
Gene Alias | HcGIP1 | |
Cytomap | 11p15.2 | |
Gene Type | protein-coding | GO ID | GO:0001525 | UniProtAcc | A7E2E5 |
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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 |
5140 | PDE3B | HTA11_3410_2000001011 | Human | Colorectum | AD | 7.43e-26 | -5.93e-01 | 0.0155 |
5140 | PDE3B | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.50e-04 | -4.80e-01 | -0.1808 |
5140 | PDE3B | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.85e-02 | -4.29e-01 | -0.1207 |
5140 | PDE3B | HTA11_696_2000001011 | Human | Colorectum | AD | 1.24e-02 | -3.86e-01 | -0.1464 |
5140 | PDE3B | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.85e-03 | -3.78e-01 | -0.059 |
5140 | PDE3B | HTA11_866_3004761011 | Human | Colorectum | AD | 5.40e-08 | -4.68e-01 | 0.096 |
5140 | PDE3B | HTA11_4255_2000001011 | Human | Colorectum | SER | 1.65e-02 | -6.90e-01 | 0.0446 |
5140 | PDE3B | HTA11_9408_2000001011 | Human | Colorectum | AD | 1.14e-02 | -7.90e-01 | 0.0451 |
5140 | PDE3B | HTA11_8622_2000001021 | Human | Colorectum | SER | 1.79e-03 | -4.73e-01 | 0.0528 |
5140 | PDE3B | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.98e-07 | -4.18e-01 | 0.0674 |
5140 | PDE3B | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.87e-23 | -6.64e-01 | 0.294 |
5140 | PDE3B | HTA11_99999965104_69814 | Human | Colorectum | MSS | 2.63e-06 | -3.57e-01 | 0.281 |
5140 | PDE3B | HTA11_99999971662_82457 | Human | Colorectum | MSS | 4.73e-15 | -5.80e-01 | 0.3859 |
5140 | PDE3B | HTA11_99999973899_84307 | Human | Colorectum | MSS | 4.91e-05 | -5.90e-01 | 0.2585 |
5140 | PDE3B | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.05e-26 | -7.38e-01 | 0.3005 |
5140 | PDE3B | A001-C-207 | Human | Colorectum | FAP | 2.83e-03 | 1.29e-01 | 0.1278 |
5140 | PDE3B | A015-C-203 | Human | Colorectum | FAP | 1.08e-21 | -3.98e-03 | -0.1294 |
5140 | PDE3B | A015-C-204 | Human | Colorectum | FAP | 5.42e-05 | 1.55e-01 | -0.0228 |
5140 | PDE3B | A014-C-040 | Human | Colorectum | FAP | 8.52e-03 | 8.75e-02 | -0.1184 |
5140 | PDE3B | A002-C-201 | Human | Colorectum | FAP | 8.71e-10 | -2.87e-03 | 0.0324 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0009895 | Colorectum | AD | negative regulation of catabolic process | 124/3918 | 320/18723 | 1.66e-13 | 3.35e-11 | 124 |
GO:0032868 | Colorectum | AD | response to insulin | 91/3918 | 264/18723 | 2.02e-07 | 8.48e-06 | 91 |
GO:1901653 | Colorectum | AD | cellular response to peptide | 114/3918 | 359/18723 | 8.32e-07 | 2.88e-05 | 114 |
GO:0032869 | Colorectum | AD | cellular response to insulin stimulus | 72/3918 | 203/18723 | 1.10e-06 | 3.68e-05 | 72 |
GO:0071375 | Colorectum | AD | cellular response to peptide hormone stimulus | 95/3918 | 290/18723 | 1.50e-06 | 4.66e-05 | 95 |
GO:0043434 | Colorectum | AD | response to peptide hormone | 126/3918 | 414/18723 | 2.70e-06 | 7.86e-05 | 126 |
GO:0016042 | Colorectum | AD | lipid catabolic process | 97/3918 | 320/18723 | 4.31e-05 | 7.56e-04 | 97 |
GO:00098951 | Colorectum | SER | negative regulation of catabolic process | 84/2897 | 320/18723 | 3.93e-07 | 2.06e-05 | 84 |
GO:00160421 | Colorectum | SER | lipid catabolic process | 77/2897 | 320/18723 | 3.52e-05 | 9.18e-04 | 77 |
GO:00328681 | Colorectum | SER | response to insulin | 65/2897 | 264/18723 | 6.70e-05 | 1.53e-03 | 65 |
GO:19016531 | Colorectum | SER | cellular response to peptide | 83/2897 | 359/18723 | 8.03e-05 | 1.77e-03 | 83 |
GO:00434341 | Colorectum | SER | response to peptide hormone | 93/2897 | 414/18723 | 9.61e-05 | 2.04e-03 | 93 |
GO:00713751 | Colorectum | SER | cellular response to peptide hormone stimulus | 68/2897 | 290/18723 | 2.20e-04 | 3.89e-03 | 68 |
GO:00328691 | Colorectum | SER | cellular response to insulin stimulus | 51/2897 | 203/18723 | 2.30e-04 | 3.96e-03 | 51 |
GO:0007162 | Colorectum | SER | negative regulation of cell adhesion | 68/2897 | 303/18723 | 8.02e-04 | 1.01e-02 | 68 |
GO:00098952 | Colorectum | MSS | negative regulation of catabolic process | 110/3467 | 320/18723 | 7.88e-12 | 1.20e-09 | 110 |
GO:00434342 | Colorectum | MSS | response to peptide hormone | 104/3467 | 414/18723 | 4.58e-04 | 5.43e-03 | 104 |
GO:19016532 | Colorectum | MSS | cellular response to peptide | 91/3467 | 359/18723 | 7.38e-04 | 7.88e-03 | 91 |
GO:00328692 | Colorectum | MSS | cellular response to insulin stimulus | 56/3467 | 203/18723 | 9.41e-04 | 9.50e-03 | 56 |
GO:00713752 | Colorectum | MSS | cellular response to peptide hormone stimulus | 75/3467 | 290/18723 | 1.14e-03 | 1.12e-02 | 75 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04922 | Colorectum | AD | Glucagon signaling pathway | 41/2092 | 107/8465 | 1.18e-03 | 7.75e-03 | 4.94e-03 | 41 |
hsa049221 | Colorectum | AD | Glucagon signaling pathway | 41/2092 | 107/8465 | 1.18e-03 | 7.75e-03 | 4.94e-03 | 41 |
hsa049222 | Colorectum | SER | Glucagon signaling pathway | 38/1580 | 107/8465 | 2.57e-05 | 3.28e-04 | 2.38e-04 | 38 |
hsa049223 | Colorectum | SER | Glucagon signaling pathway | 38/1580 | 107/8465 | 2.57e-05 | 3.28e-04 | 2.38e-04 | 38 |
hsa049224 | Colorectum | MSS | Glucagon signaling pathway | 39/1875 | 107/8465 | 5.00e-04 | 3.45e-03 | 2.11e-03 | 39 |
hsa04022 | Colorectum | MSS | cGMP-PKG signaling pathway | 51/1875 | 167/8465 | 6.83e-03 | 2.73e-02 | 1.67e-02 | 51 |
hsa04910 | Colorectum | MSS | Insulin signaling pathway | 43/1875 | 137/8465 | 7.37e-03 | 2.84e-02 | 1.74e-02 | 43 |
hsa049225 | Colorectum | MSS | Glucagon signaling pathway | 39/1875 | 107/8465 | 5.00e-04 | 3.45e-03 | 2.11e-03 | 39 |
hsa040221 | Colorectum | MSS | cGMP-PKG signaling pathway | 51/1875 | 167/8465 | 6.83e-03 | 2.73e-02 | 1.67e-02 | 51 |
hsa049101 | Colorectum | MSS | Insulin signaling pathway | 43/1875 | 137/8465 | 7.37e-03 | 2.84e-02 | 1.74e-02 | 43 |
hsa049226 | Colorectum | FAP | Glucagon signaling pathway | 32/1404 | 107/8465 | 4.08e-04 | 3.10e-03 | 1.89e-03 | 32 |
hsa049102 | Colorectum | FAP | Insulin signaling pathway | 36/1404 | 137/8465 | 2.51e-03 | 1.18e-02 | 7.18e-03 | 36 |
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 |
hsa049227 | Colorectum | FAP | Glucagon signaling pathway | 32/1404 | 107/8465 | 4.08e-04 | 3.10e-03 | 1.89e-03 | 32 |
hsa049103 | Colorectum | FAP | Insulin signaling pathway | 36/1404 | 137/8465 | 2.51e-03 | 1.18e-02 | 7.18e-03 | 36 |
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 |
hsa049104 | Colorectum | CRC | Insulin signaling pathway | 31/1091 | 137/8465 | 1.07e-03 | 8.91e-03 | 6.03e-03 | 31 |
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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 |
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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. |
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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 |
PDE3B | SNV | Missense_Mutation | novel | c.2064N>T | p.Met688Ile | p.M688I | Q13370 | protein_coding | tolerated(0.41) | benign(0.22) | TCGA-05-4396-01 | Lung | lung adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
PDE3B | SNV | Missense_Mutation | novel | c.2980N>A | p.His994Asn | p.H994N | Q13370 | protein_coding | deleterious(0.04) | probably_damaging(0.998) | TCGA-05-4396-01 | Lung | lung adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
PDE3B | SNV | Missense_Mutation | c.2476N>A | p.Pro826Thr | p.P826T | Q13370 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-49-AAR2-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Chemotherapy | taxol | CR | |
PDE3B | SNV | Missense_Mutation | novel | c.2573N>T | p.Ala858Val | p.A858V | Q13370 | protein_coding | deleterious(0.02) | probably_damaging(0.999) | TCGA-50-5935-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PDE3B | SNV | Missense_Mutation | c.1520N>G | p.Ala507Gly | p.A507G | Q13370 | protein_coding | tolerated(0.05) | benign(0.079) | TCGA-53-7624-01 | Lung | lung adenocarcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | PD | |
PDE3B | SNV | Missense_Mutation | novel | c.2461N>A | p.His821Asn | p.H821N | Q13370 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-55-7574-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
PDE3B | SNV | Missense_Mutation | c.2264N>T | p.Arg755Leu | p.R755L | Q13370 | protein_coding | deleterious(0) | probably_damaging(0.922) | TCGA-64-5779-01 | Lung | lung adenocarcinoma | Male | <65 | III/IV | Chemotherapy | cisplatin | PD | |
PDE3B | SNV | Missense_Mutation | c.839N>A | p.Ser280Asn | p.S280N | Q13370 | protein_coding | tolerated(0.16) | benign(0.3) | TCGA-69-7763-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
PDE3B | SNV | Missense_Mutation | c.463N>A | p.Leu155Met | p.L155M | Q13370 | protein_coding | deleterious(0) | possibly_damaging(0.881) | TCGA-80-5611-01 | Lung | lung adenocarcinoma | Male | Unknown | I/II | Unknown | Unknown | SD | |
PDE3B | SNV | Missense_Mutation | c.1874C>A | p.Thr625Lys | p.T625K | Q13370 | protein_coding | tolerated(0.63) | benign(0.003) | TCGA-86-A4D0-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Chemotherapy | etoposide | CR |
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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 |
5140 | PDE3B | ENZYME, DRUGGABLE GENOME | inhibitor | CHEMBL190 | THEOPHYLLINE | |
5140 | PDE3B | ENZYME, DRUGGABLE GENOME | inhibitor | 178103723 | CILOSTAZOL | |
5140 | PDE3B | ENZYME, DRUGGABLE GENOME | US8741907-compound-3 | |||
5140 | PDE3B | ENZYME, DRUGGABLE GENOME | inhibitor | CHEMBL628 | PENTOXIFYLLINE | |
5140 | PDE3B | ENZYME, DRUGGABLE GENOME | inhibitor | CHEMBL932 | DIPYRIDAMOLE | |
5140 | PDE3B | ENZYME, DRUGGABLE GENOME | inhibitor | 178101910 | MILRINONE | |
5140 | PDE3B | ENZYME, DRUGGABLE GENOME | inhibitor | CHEMBL1200759 | ANAGRELIDE HYDROCHLORIDE | |
5140 | PDE3B | ENZYME, DRUGGABLE GENOME | inhibitor | 178103777 | INAMRINONE | |
5140 | PDE3B | ENZYME, DRUGGABLE GENOME | inhibitor | CHEMBL1370561 | AMINOPHYLLINE | |
5140 | PDE3B | ENZYME, DRUGGABLE GENOME | inhibitor | CHEMBL1200434 | OXTRIPHYLLINE |
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