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Gene: PKD2 |
Gene summary for PKD2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PKD2 | Gene ID | 5311 |
| Gene name | polycystin 2, transient receptor potential cation channel | |
| Gene Alias | APKD2 | |
| Cytomap | 4q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q13563 |
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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 |
| 5311 | PKD2 | HCC1_Meng | Human | Liver | HCC | 1.01e-26 | -8.42e-03 | 0.0246 |
| 5311 | PKD2 | HCC2_Meng | Human | Liver | HCC | 5.97e-04 | -3.47e-02 | 0.0107 |
| 5311 | PKD2 | cirrhotic3 | Human | Liver | Cirrhotic | 9.98e-04 | 7.40e-02 | 0.0215 |
| 5311 | PKD2 | HCC1 | Human | Liver | HCC | 8.63e-05 | 8.80e-01 | 0.5336 |
| 5311 | PKD2 | HCC2 | Human | Liver | HCC | 3.59e-06 | 2.05e+00 | 0.5341 |
| 5311 | PKD2 | Pt13.b | Human | Liver | HCC | 2.29e-03 | 1.75e-02 | 0.0251 |
| 5311 | PKD2 | S027 | Human | Liver | HCC | 1.46e-02 | 3.13e-01 | 0.2446 |
| 5311 | PKD2 | S028 | Human | Liver | HCC | 4.86e-07 | 3.02e-01 | 0.2503 |
| 5311 | PKD2 | RNA-P17T-P17T-4 | Human | Lung | IAC | 2.39e-03 | 5.27e-01 | 0.343 |
| 5311 | PKD2 | RNA-P17T-P17T-6 | Human | Lung | IAC | 1.19e-03 | 5.20e-01 | 0.3385 |
| 5311 | PKD2 | RNA-P17T-P17T-8 | Human | Lung | IAC | 9.56e-04 | 5.85e-01 | 0.3329 |
| 5311 | PKD2 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 7.77e-03 | 2.92e-01 | -0.2116 |
| 5311 | PKD2 | RNA-P6T2-P6T2-1 | Human | Lung | IAC | 7.68e-03 | 2.27e-01 | -0.0166 |
| 5311 | PKD2 | RNA-P6T2-P6T2-3 | Human | Lung | IAC | 5.31e-06 | 2.84e-01 | -0.013 |
| 5311 | PKD2 | HTA12-15-2 | Human | Pancreas | PDAC | 4.09e-08 | 3.83e-01 | 0.2315 |
| 5311 | PKD2 | HTA12-23-1 | Human | Pancreas | PDAC | 2.93e-09 | 8.09e-01 | 0.3405 |
| 5311 | PKD2 | HTA12-25-1 | Human | Pancreas | PDAC | 3.33e-07 | 5.69e-01 | 0.313 |
| 5311 | PKD2 | HTA12-26-1 | Human | Pancreas | PDAC | 5.25e-22 | 8.82e-01 | 0.3728 |
| 5311 | PKD2 | HTA12-29-1 | Human | Pancreas | PDAC | 1.83e-50 | 9.34e-01 | 0.3722 |
| 5311 | PKD2 | HTA12-30-1 | Human | Pancreas | PDAC | 3.91e-06 | 1.05e+00 | 0.3671 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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:00447721 | Liver | Cirrhotic | mitotic cell cycle phase transition | 139/4634 | 424/18723 | 1.02e-04 | 1.06e-03 | 139 |
| GO:00712417 | Liver | Cirrhotic | cellular response to inorganic substance | 81/4634 | 226/18723 | 1.21e-04 | 1.20e-03 | 81 |
| GO:00011013 | Liver | Cirrhotic | response to acid chemical | 52/4634 | 135/18723 | 2.65e-04 | 2.36e-03 | 52 |
| GO:00516517 | Liver | Cirrhotic | maintenance of location in cell | 76/4634 | 214/18723 | 2.66e-04 | 2.37e-03 | 76 |
| GO:1901990 | Liver | Cirrhotic | regulation of mitotic cell cycle phase transition | 100/4634 | 299/18723 | 4.13e-04 | 3.41e-03 | 100 |
| GO:00512202 | Liver | Cirrhotic | cytoplasmic sequestering of protein | 13/4634 | 22/18723 | 6.27e-04 | 4.80e-03 | 13 |
| GO:00018925 | Liver | Cirrhotic | embryonic placenta development | 34/4634 | 82/18723 | 6.36e-04 | 4.85e-03 | 34 |
| GO:200105712 | Liver | Cirrhotic | reactive nitrogen species metabolic process | 34/4634 | 82/18723 | 6.36e-04 | 4.85e-03 | 34 |
| GO:005159112 | Liver | Cirrhotic | response to cAMP | 37/4634 | 93/18723 | 9.58e-04 | 6.78e-03 | 37 |
| GO:000697011 | Liver | Cirrhotic | response to osmotic stress | 34/4634 | 84/18723 | 1.06e-03 | 7.40e-03 | 34 |
| GO:004620912 | Liver | Cirrhotic | nitric oxide metabolic process | 33/4634 | 81/18723 | 1.09e-03 | 7.59e-03 | 33 |
| GO:000680912 | Liver | Cirrhotic | nitric oxide biosynthetic process | 31/4634 | 76/18723 | 1.49e-03 | 9.87e-03 | 31 |
| GO:001407411 | Liver | Cirrhotic | response to purine-containing compound | 53/4634 | 148/18723 | 1.70e-03 | 1.08e-02 | 53 |
| GO:2000045 | Liver | Cirrhotic | regulation of G1/S transition of mitotic cell cycle | 51/4634 | 142/18723 | 1.91e-03 | 1.20e-02 | 51 |
| GO:00000821 | Liver | Cirrhotic | G1/S transition of mitotic cell cycle | 72/4634 | 214/18723 | 2.07e-03 | 1.28e-02 | 72 |
| GO:00614585 | Liver | Cirrhotic | reproductive system development | 132/4634 | 427/18723 | 2.07e-03 | 1.28e-02 | 132 |
| GO:004542812 | Liver | Cirrhotic | regulation of nitric oxide biosynthetic process | 26/4634 | 62/18723 | 2.18e-03 | 1.34e-02 | 26 |
| GO:00486085 | Liver | Cirrhotic | reproductive structure development | 131/4634 | 424/18723 | 2.19e-03 | 1.34e-02 | 131 |
| GO:008016412 | Liver | Cirrhotic | regulation of nitric oxide metabolic process | 26/4634 | 64/18723 | 3.69e-03 | 2.03e-02 | 26 |
| GO:0071229 | Liver | Cirrhotic | cellular response to acid chemical | 31/4634 | 80/18723 | 3.83e-03 | 2.10e-02 | 31 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
| PKD2 | SNV | Missense_Mutation | rs748241808 | c.2615N>A | p.Arg872Gln | p.R872Q | Q13563 | protein_coding | deleterious(0.05) | benign(0.007) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PKD2 | SNV | Missense_Mutation | rs757656223 | c.1870N>A | p.Asp624Asn | p.D624N | Q13563 | protein_coding | tolerated(0.27) | benign(0.07) | TCGA-AR-A1AI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | PD |
| PKD2 | SNV | Missense_Mutation | rs770609334 | c.2668N>A | p.Glu890Lys | p.E890K | Q13563 | protein_coding | tolerated(0.07) | probably_damaging(0.981) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| PKD2 | SNV | Missense_Mutation | c.1637C>T | p.Pro546Leu | p.P546L | Q13563 | protein_coding | deleterious(0) | benign(0.122) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PKD2 | SNV | Missense_Mutation | c.2355N>C | p.Glu785Asp | p.E785D | Q13563 | protein_coding | deleterious(0.03) | benign(0.214) | TCGA-E9-A1R4-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | SD | |
| PKD2 | SNV | Missense_Mutation | rs761597786 | c.2449N>A | p.Asp817Asn | p.D817N | Q13563 | protein_coding | tolerated(0.16) | benign(0.02) | TCGA-LL-A740-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| PKD2 | SNV | Missense_Mutation | rs144590958 | c.2729N>A | p.Arg910His | p.R910H | Q13563 | protein_coding | deleterious(0) | probably_damaging(0.925) | TCGA-WT-AB44-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| PKD2 | SNV | Missense_Mutation | c.1069N>T | p.Pro357Ser | p.P357S | Q13563 | protein_coding | tolerated(0.35) | benign(0.115) | TCGA-EK-A3GJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PKD2 | SNV | Missense_Mutation | rs755031837 | c.2534G>A | p.Arg845Gln | p.R845Q | Q13563 | protein_coding | tolerated(0.07) | probably_damaging(0.978) | TCGA-A6-6781-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD |
| PKD2 | SNV | Missense_Mutation | c.1904C>T | p.Thr635Ile | p.T635I | Q13563 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
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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 |
| 5311 | PKD2 | DRUGGABLE GENOME, TUMOR SUPPRESSOR, ION CHANNEL, TRANSPORTER | allopurinol | ALLOPURINOL | 30924126 |
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