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Gene: KCND3 |
Gene summary for KCND3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | KCND3 | Gene ID | 3752 |
| Gene name | potassium voltage-gated channel subfamily D member 3 | |
| Gene Alias | BRGDA9 | |
| Cytomap | 1p13.2 | |
| Gene Type | protein-coding | GO ID | GO:0001508 | UniProtAcc | Q9UK17 |
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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 |
| 3752 | KCND3 | 048752_1579-all-cells | Human | Prostate | BPH | 5.04e-18 | 4.25e-01 | 0.1008 |
| 3752 | KCND3 | 052095_1628-all-cells | Human | Prostate | BPH | 9.33e-11 | 3.24e-01 | 0.1032 |
| 3752 | KCND3 | 052097_1595-all-cells | Human | Prostate | BPH | 1.40e-12 | 3.79e-01 | 0.0972 |
| 3752 | KCND3 | 052099_1652-all-cells | Human | Prostate | BPH | 1.18e-13 | 3.97e-01 | 0.1038 |
| 3752 | KCND3 | GSM5353223_PA_PB2B_Pool_2_S26_L001 | Human | Prostate | Tumor | 3.88e-03 | 3.82e-01 | 0.1604 |
| 3752 | KCND3 | GSM5353237_PA_PR5251_T2_S8_L001 | Human | Prostate | Tumor | 1.57e-02 | 5.08e-01 | 0.1622 |
| 3752 | KCND3 | GSM5353240_PA_PR5254_T1_S15_L001 | Human | Prostate | Tumor | 1.90e-05 | 3.71e-01 | 0.1575 |
| 3752 | KCND3 | GSM5353243_PA_PR5261_T1_S23_L002 | Human | Prostate | Tumor | 7.85e-03 | 3.05e-01 | 0.1545 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| ∗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:00300489 | Prostate | BPH | actin filament-based movement | 38/3107 | 127/18723 | 1.31e-04 | 1.18e-03 | 38 |
| GO:00030127 | Prostate | BPH | muscle system process | 103/3107 | 452/18723 | 3.54e-04 | 2.62e-03 | 103 |
| GO:00860018 | Prostate | BPH | cardiac muscle cell action potential | 21/3107 | 76/18723 | 1.05e-02 | 4.39e-02 | 21 |
| GO:000301214 | Prostate | Tumor | muscle system process | 105/3246 | 452/18723 | 7.44e-04 | 5.14e-03 | 105 |
| GO:003004815 | Prostate | Tumor | actin filament-based movement | 36/3246 | 127/18723 | 1.38e-03 | 8.62e-03 | 36 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0501720 | Prostate | BPH | Spinocerebellar ataxia | 55/1718 | 143/8465 | 3.63e-07 | 3.74e-06 | 2.32e-06 | 55 |
| hsa05017110 | Prostate | BPH | Spinocerebellar ataxia | 55/1718 | 143/8465 | 3.63e-07 | 3.74e-06 | 2.32e-06 | 55 |
| hsa0501724 | Prostate | Tumor | Spinocerebellar ataxia | 54/1791 | 143/8465 | 3.50e-06 | 3.13e-05 | 1.94e-05 | 54 |
| hsa0501734 | Prostate | Tumor | Spinocerebellar ataxia | 54/1791 | 143/8465 | 3.50e-06 | 3.13e-05 | 1.94e-05 | 54 |
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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 |
| KCND3 | SNV | Missense_Mutation | c.1329N>G | p.His443Gln | p.H443Q | Q9UK17 | protein_coding | tolerated(1) | benign(0) | TCGA-A1-A0SO-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | SD | ||
| KCND3 | SNV | Missense_Mutation | rs761950312 | c.1186N>C | p.Ala396Pro | p.A396P | Q9UK17 | protein_coding | deleterious(0.01) | possibly_damaging(0.617) | TCGA-A2-A0CS-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozole | SD |
| KCND3 | SNV | Missense_Mutation | rs761950312 | c.1186G>C | p.Ala396Pro | p.A396P | Q9UK17 | protein_coding | deleterious(0.01) | possibly_damaging(0.617) | TCGA-A8-A06R-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| KCND3 | SNV | Missense_Mutation | rs761950312 | c.1186G>C | p.Ala396Pro | p.A396P | Q9UK17 | protein_coding | deleterious(0.01) | possibly_damaging(0.617) | TCGA-BH-A0HO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| KCND3 | SNV | Missense_Mutation | rs760710842 | c.1876N>A | p.Glu626Lys | p.E626K | Q9UK17 | protein_coding | deleterious_low_confidence(0.01) | benign(0.37) | TCGA-BH-A2L8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | CR |
| KCND3 | SNV | Missense_Mutation | c.1515C>G | p.Ile505Met | p.I505M | Q9UK17 | protein_coding | tolerated_low_confidence(0.14) | benign(0.001) | TCGA-C8-A26X-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| KCND3 | SNV | Missense_Mutation | c.1242N>C | p.Gln414His | p.Q414H | Q9UK17 | protein_coding | deleterious(0.03) | probably_damaging(0.993) | TCGA-EW-A1PB-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| KCND3 | SNV | Missense_Mutation | novel | c.82C>T | p.Pro28Ser | p.P28S | Q9UK17 | protein_coding | deleterious(0.02) | possibly_damaging(0.886) | TCGA-LL-A73Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | taxotere | SD |
| KCND3 | SNV | Missense_Mutation | rs200212002 | c.1703N>A | p.Arg568His | p.R568H | Q9UK17 | protein_coding | tolerated_low_confidence(0.16) | benign(0.003) | TCGA-S3-AA0Z-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Ancillary | neulasta | CR |
| KCND3 | SNV | Missense_Mutation | novel | c.1652G>A | p.Ser551Asn | p.S551N | Q9UK17 | protein_coding | tolerated_low_confidence(0.56) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | 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 |
| 3752 | KCND3 | ION CHANNEL, DRUGGABLE GENOME | blocker | CHEMBL1200728 | GUANIDINE HYDROCHLORIDE | |
| 3752 | KCND3 | ION CHANNEL, DRUGGABLE GENOME | blocker | CHEMBL284348 | DALFAMPRIDINE | |
| 3752 | KCND3 | ION CHANNEL, DRUGGABLE GENOME | blocker | CHEMBL113461 | TEDISAMIL | |
| 3752 | KCND3 | ION CHANNEL, DRUGGABLE GENOME | Sodium bicarbonate | |||
| 3752 | KCND3 | ION CHANNEL, DRUGGABLE GENOME | blocker | CHEMBL2107762 | NERISPIRDINE |
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