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Gene: CACNA1D |
Gene summary for CACNA1D |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CACNA1D | Gene ID | 776 |
| Gene name | calcium voltage-gated channel subunit alpha1 D | |
| Gene Alias | CACH3 | |
| Cytomap | 3p21.1 | |
| Gene Type | protein-coding | GO ID | GO:0001508 | UniProtAcc | Q01668 |
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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 |
| 776 | CACNA1D | GSM4909298 | Human | Breast | IDC | 1.51e-09 | 1.99e-01 | 0.1551 |
| 776 | CACNA1D | GSM4909302 | Human | Breast | IDC | 2.01e-11 | 3.43e-01 | 0.1545 |
| 776 | CACNA1D | GSM4909304 | Human | Breast | IDC | 1.76e-04 | 1.79e-01 | 0.1636 |
| 776 | CACNA1D | GSM4909307 | Human | Breast | IDC | 1.95e-02 | 1.72e-01 | 0.1569 |
| 776 | CACNA1D | GSM4909308 | Human | Breast | IDC | 6.26e-04 | 1.63e-01 | 0.158 |
| 776 | CACNA1D | M5 | Human | Breast | IDC | 2.79e-05 | 5.21e-01 | 0.1598 |
| 776 | CACNA1D | P3 | Human | Breast | IDC | 7.09e-13 | 6.67e-01 | 0.1542 |
| 776 | CACNA1D | HTA11_3410_2000001011 | Human | Colorectum | AD | 9.80e-15 | -4.95e-01 | 0.0155 |
| 776 | CACNA1D | HTA11_3361_2000001011 | Human | Colorectum | AD | 5.69e-05 | -6.24e-01 | -0.1207 |
| 776 | CACNA1D | HTA11_696_2000001011 | Human | Colorectum | AD | 6.91e-08 | -4.56e-01 | -0.1464 |
| 776 | CACNA1D | HTA11_866_2000001011 | Human | Colorectum | AD | 1.46e-09 | -5.11e-01 | -0.1001 |
| 776 | CACNA1D | HTA11_5212_2000001011 | Human | Colorectum | AD | 4.22e-02 | -6.81e-01 | -0.2061 |
| 776 | CACNA1D | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.94e-06 | -5.91e-01 | 0.0338 |
| 776 | CACNA1D | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.36e-08 | -4.36e-01 | 0.294 |
| 776 | CACNA1D | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 1.04e-09 | 1.17e+00 | 0.3487 |
| 776 | CACNA1D | HTA11_99999974143_84620 | Human | Colorectum | MSS | 6.38e-08 | -3.71e-01 | 0.3005 |
| 776 | CACNA1D | F007 | Human | Colorectum | FAP | 3.54e-10 | -5.83e-01 | 0.1176 |
| 776 | CACNA1D | A001-C-207 | Human | Colorectum | FAP | 3.72e-05 | -3.31e-01 | 0.1278 |
| 776 | CACNA1D | A015-C-203 | Human | Colorectum | FAP | 1.15e-32 | -6.85e-01 | -0.1294 |
| 776 | CACNA1D | A015-C-204 | Human | Colorectum | FAP | 5.78e-05 | -2.85e-01 | -0.0228 |
| Page: 1 2 3 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma |
| ∗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:001095913 | Breast | IDC | regulation of metal ion transport | 52/1434 | 406/18723 | 1.76e-04 | 2.97e-03 | 52 |
| GO:008606511 | Breast | IDC | cell communication involved in cardiac conduction | 13/1434 | 58/18723 | 3.59e-04 | 5.18e-03 | 13 |
| GO:00432703 | Breast | IDC | positive regulation of ion transport | 36/1434 | 275/18723 | 1.11e-03 | 1.22e-02 | 36 |
| GO:002289812 | Breast | IDC | regulation of transmembrane transporter activity | 36/1434 | 278/18723 | 1.35e-03 | 1.40e-02 | 36 |
| GO:00613373 | Breast | IDC | cardiac conduction | 16/1434 | 98/18723 | 3.06e-03 | 2.60e-02 | 16 |
| GO:0051924 | Breast | IDC | regulation of calcium ion transport | 32/1434 | 255/18723 | 3.94e-03 | 3.22e-02 | 32 |
| GO:00423912 | Breast | IDC | regulation of membrane potential | 49/1434 | 434/18723 | 4.04e-03 | 3.25e-02 | 49 |
| GO:00324125 | Breast | IDC | regulation of ion transmembrane transporter activity | 33/1434 | 267/18723 | 4.38e-03 | 3.40e-02 | 33 |
| GO:00324096 | Breast | IDC | regulation of transporter activity | 37/1434 | 310/18723 | 4.77e-03 | 3.66e-02 | 37 |
| GO:00860015 | Breast | IDC | cardiac muscle cell action potential | 13/1434 | 76/18723 | 4.81e-03 | 3.67e-02 | 13 |
| GO:00020271 | Breast | IDC | regulation of heart rate | 16/1434 | 103/18723 | 5.06e-03 | 3.79e-02 | 16 |
| GO:0051928 | Breast | IDC | positive regulation of calcium ion transport | 18/1434 | 122/18723 | 5.35e-03 | 3.95e-02 | 18 |
| GO:00030125 | Breast | IDC | muscle system process | 50/1434 | 452/18723 | 5.52e-03 | 4.05e-02 | 50 |
| GO:00015082 | Breast | IDC | action potential | 19/1434 | 134/18723 | 6.62e-03 | 4.62e-02 | 19 |
| GO:0030048 | Colorectum | AD | actin filament-based movement | 44/3918 | 127/18723 | 2.31e-04 | 2.99e-03 | 44 |
| GO:00300482 | Colorectum | MSS | actin filament-based movement | 44/3467 | 127/18723 | 1.11e-05 | 2.64e-04 | 44 |
| GO:0086001 | Colorectum | MSS | cardiac muscle cell action potential | 26/3467 | 76/18723 | 8.18e-04 | 8.59e-03 | 26 |
| GO:0086065 | Colorectum | MSS | cell communication involved in cardiac conduction | 21/3467 | 58/18723 | 1.11e-03 | 1.09e-02 | 21 |
| GO:00324091 | Colorectum | MSS | regulation of transporter activity | 78/3467 | 310/18723 | 2.09e-03 | 1.78e-02 | 78 |
| GO:0086091 | Colorectum | MSS | regulation of heart rate by cardiac conduction | 15/3467 | 39/18723 | 2.80e-03 | 2.19e-02 | 15 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0502023 | Breast | IDC | Prion disease | 102/867 | 273/8465 | 3.70e-34 | 4.01e-32 | 3.00e-32 | 102 |
| hsa0501023 | Breast | IDC | Alzheimer disease | 107/867 | 384/8465 | 1.70e-23 | 7.88e-22 | 5.90e-22 | 107 |
| hsa0502223 | Breast | IDC | Pathways of neurodegeneration - multiple diseases | 116/867 | 476/8465 | 3.63e-20 | 1.18e-18 | 8.82e-19 | 116 |
| hsa0453024 | Breast | IDC | Tight junction | 38/867 | 169/8465 | 2.07e-06 | 3.20e-05 | 2.39e-05 | 38 |
| hsa0421824 | Breast | IDC | Cellular senescence | 35/867 | 156/8465 | 5.49e-06 | 7.43e-05 | 5.56e-05 | 35 |
| hsa0472323 | Breast | IDC | Retrograde endocannabinoid signaling | 31/867 | 148/8465 | 7.62e-05 | 7.50e-04 | 5.61e-04 | 31 |
| hsa050312 | Breast | IDC | Amphetamine addiction | 18/867 | 69/8465 | 1.42e-04 | 1.36e-03 | 1.01e-03 | 18 |
| hsa0502033 | Breast | IDC | Prion disease | 102/867 | 273/8465 | 3.70e-34 | 4.01e-32 | 3.00e-32 | 102 |
| hsa0501033 | Breast | IDC | Alzheimer disease | 107/867 | 384/8465 | 1.70e-23 | 7.88e-22 | 5.90e-22 | 107 |
| hsa0502233 | Breast | IDC | Pathways of neurodegeneration - multiple diseases | 116/867 | 476/8465 | 3.63e-20 | 1.18e-18 | 8.82e-19 | 116 |
| hsa0453034 | Breast | IDC | Tight junction | 38/867 | 169/8465 | 2.07e-06 | 3.20e-05 | 2.39e-05 | 38 |
| hsa0421834 | Breast | IDC | Cellular senescence | 35/867 | 156/8465 | 5.49e-06 | 7.43e-05 | 5.56e-05 | 35 |
| hsa0472333 | Breast | IDC | Retrograde endocannabinoid signaling | 31/867 | 148/8465 | 7.62e-05 | 7.50e-04 | 5.61e-04 | 31 |
| hsa050313 | Breast | IDC | Amphetamine addiction | 18/867 | 69/8465 | 1.42e-04 | 1.36e-03 | 1.01e-03 | 18 |
| hsa05010 | Colorectum | AD | Alzheimer disease | 174/2092 | 384/8465 | 1.82e-19 | 9.26e-18 | 5.91e-18 | 174 |
| hsa05020 | Colorectum | AD | Prion disease | 133/2092 | 273/8465 | 2.47e-18 | 8.29e-17 | 5.29e-17 | 133 |
| hsa05022 | Colorectum | AD | Pathways of neurodegeneration - multiple diseases | 201/2092 | 476/8465 | 4.54e-18 | 1.27e-16 | 8.09e-17 | 201 |
| hsa04530 | Colorectum | AD | Tight junction | 76/2092 | 169/8465 | 5.49e-09 | 9.69e-08 | 6.18e-08 | 76 |
| hsa04723 | Colorectum | AD | Retrograde endocannabinoid signaling | 59/2092 | 148/8465 | 2.94e-05 | 2.73e-04 | 1.74e-04 | 59 |
| hsa04912 | Colorectum | AD | GnRH signaling pathway | 35/2092 | 93/8465 | 3.69e-03 | 1.90e-02 | 1.21e-02 | 35 |
| Page: 1 2 3 4 5 6 7 8 9 |
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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 |
| CACNA1D | SNV | Missense_Mutation | c.2786N>A | p.Ile929Asn | p.I929N | Q01668 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-A2-A04R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxol | SD | |
| CACNA1D | SNV | Missense_Mutation | c.1960N>G | p.Thr654Ala | p.T654A | Q01668 | protein_coding | tolerated(0.85) | benign(0) | TCGA-A2-A0SY-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | arimidex | SD | |
| CACNA1D | SNV | Missense_Mutation | rs748437057 | c.3808N>A | p.Val1270Ile | p.V1270I | Q01668 | protein_coding | tolerated(0.23) | benign(0.047) | TCGA-A2-A3XT-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | PR |
| CACNA1D | SNV | Missense_Mutation | rs763383320 | c.158N>T | p.Trp53Leu | p.W53L | Q01668 | protein_coding | deleterious_low_confidence(0.02) | probably_damaging(0.991) | TCGA-A8-A09V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| CACNA1D | SNV | Missense_Mutation | c.4330N>A | p.Glu1444Lys | p.E1444K | Q01668 | protein_coding | tolerated(0.15) | probably_damaging(0.994) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CACNA1D | SNV | Missense_Mutation | rs537189630 | c.2458G>A | p.Asp820Asn | p.D820N | Q01668 | protein_coding | tolerated(0.18) | benign(0.001) | TCGA-AC-A62Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CACNA1D | SNV | Missense_Mutation | novel | c.248N>T | p.Arg83Ile | p.R83I | Q01668 | protein_coding | deleterious(0) | possibly_damaging(0.894) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CACNA1D | SNV | Missense_Mutation | novel | c.1765N>A | p.Glu589Lys | p.E589K | Q01668 | protein_coding | deleterious(0) | probably_damaging(0.98) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CACNA1D | SNV | Missense_Mutation | c.4642T>A | p.Cys1548Ser | p.C1548S | Q01668 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-AQ-A0Y5-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | cytoxan | SD | |
| CACNA1D | SNV | Missense_Mutation | rs779080006 | c.6121C>T | p.Arg2041Cys | p.R2041C | Q01668 | protein_coding | tolerated_low_confidence(0.15) | probably_damaging(0.931) | TCGA-BH-A0H6-01 | 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 21 22 23 24 25 26 27 28 29 |
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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 |
| 776 | CACNA1D | ION CHANNEL, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | blocker | 135651305 | VERAPAMIL | |
| 776 | CACNA1D | ION CHANNEL, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | activator | 135650283 | ||
| 776 | CACNA1D | ION CHANNEL, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | FELODIPINE | FELODIPINE | ||
| 776 | CACNA1D | ION CHANNEL, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | inhibitor | 178103560 | AMLODIPINE | |
| 776 | CACNA1D | ION CHANNEL, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | blocker | CHEMBL1280 | VERAPAMIL HYDROCHLORIDE | |
| 776 | CACNA1D | ION CHANNEL, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | celecoxib | CELECOXIB | 22336956 | |
| 776 | CACNA1D | ION CHANNEL, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | blocker | CHEMBL1201729 | DRONEDARONE HYDROCHLORIDE | |
| 776 | CACNA1D | ION CHANNEL, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | modulator | CHEMBL940 | GABAPENTIN | |
| 776 | CACNA1D | ION CHANNEL, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | blocker | CHEMBL1480 | FELODIPINE | |
| 776 | CACNA1D | ION CHANNEL, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | inhibitor | 135650723 | NITRENDIPINE |
| Page: 1 2 3 4 5 |
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