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Gene: CALD1 |
Gene summary for CALD1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CALD1 | Gene ID | 800 |
| Gene name | caldesmon 1 | |
| Gene Alias | CDM | |
| Cytomap | 7q33 | |
| Gene Type | protein-coding | GO ID | GO:0001525 | UniProtAcc | A0A140VKA0 |
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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 |
| 800 | CALD1 | GSM4909281 | Human | Breast | IDC | 2.99e-08 | 4.29e-01 | 0.21 |
| 800 | CALD1 | GSM4909285 | Human | Breast | IDC | 1.87e-05 | -1.50e-02 | 0.21 |
| 800 | CALD1 | GSM4909286 | Human | Breast | IDC | 5.94e-08 | 1.41e-02 | 0.1081 |
| 800 | CALD1 | GSM4909291 | Human | Breast | IDC | 1.62e-09 | -5.95e-01 | 0.1753 |
| 800 | CALD1 | GSM4909293 | Human | Breast | IDC | 1.11e-17 | -5.29e-01 | 0.1581 |
| 800 | CALD1 | GSM4909294 | Human | Breast | IDC | 3.20e-14 | -5.03e-01 | 0.2022 |
| 800 | CALD1 | GSM4909296 | Human | Breast | IDC | 2.61e-20 | -5.80e-01 | 0.1524 |
| 800 | CALD1 | GSM4909297 | Human | Breast | IDC | 4.43e-24 | -5.86e-01 | 0.1517 |
| 800 | CALD1 | GSM4909299 | Human | Breast | IDC | 3.78e-08 | 4.52e-01 | 0.035 |
| 800 | CALD1 | GSM4909301 | Human | Breast | IDC | 2.82e-27 | -6.45e-01 | 0.1577 |
| 800 | CALD1 | GSM4909304 | Human | Breast | IDC | 3.59e-37 | -6.63e-01 | 0.1636 |
| 800 | CALD1 | GSM4909306 | Human | Breast | IDC | 1.86e-07 | -4.38e-01 | 0.1564 |
| 800 | CALD1 | GSM4909307 | Human | Breast | IDC | 3.87e-11 | -7.93e-02 | 0.1569 |
| 800 | CALD1 | GSM4909308 | Human | Breast | IDC | 8.47e-14 | -5.72e-01 | 0.158 |
| 800 | CALD1 | GSM4909311 | Human | Breast | IDC | 1.32e-24 | -4.46e-01 | 0.1534 |
| 800 | CALD1 | GSM4909312 | Human | Breast | IDC | 4.96e-34 | -6.68e-01 | 0.1552 |
| 800 | CALD1 | GSM4909315 | Human | Breast | IDC | 1.54e-26 | -6.21e-01 | 0.21 |
| 800 | CALD1 | GSM4909316 | Human | Breast | IDC | 1.57e-07 | -6.65e-01 | 0.21 |
| 800 | CALD1 | GSM4909318 | Human | Breast | IDC | 5.14e-05 | -6.77e-01 | 0.2031 |
| 800 | CALD1 | GSM4909319 | Human | Breast | IDC | 1.53e-30 | -6.61e-01 | 0.1563 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| 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 | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:0061572210 | Thyroid | ATC | actin filament bundle organization | 86/6293 | 161/18723 | 1.68e-07 | 2.69e-06 | 86 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa042704 | Oral cavity | NEOLP | Vascular smooth muscle contraction | 30/1112 | 134/8465 | 2.06e-03 | 8.97e-03 | 5.64e-03 | 30 |
| hsa0427011 | Oral cavity | NEOLP | Vascular smooth muscle contraction | 30/1112 | 134/8465 | 2.06e-03 | 8.97e-03 | 5.64e-03 | 30 |
| Page: 1 |
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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 |
| CALD1 | SNV | Missense_Mutation | c.1384N>A | p.Glu462Lys | p.E462K | Q05682 | protein_coding | deleterious_low_confidence(0.05) | possibly_damaging(0.732) | TCGA-A2-A0EX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| CALD1 | SNV | Missense_Mutation | c.56N>A | p.Arg19Gln | p.R19Q | Q05682 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-A2-A0EY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| CALD1 | SNV | Missense_Mutation | c.1315N>C | p.Glu439Gln | p.E439Q | Q05682 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.898) | TCGA-A2-A0EY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| CALD1 | SNV | Missense_Mutation | c.1450C>G | p.Arg484Gly | p.R484G | Q05682 | protein_coding | tolerated(0.24) | benign(0) | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| CALD1 | SNV | Missense_Mutation | c.232N>A | p.Glu78Lys | p.E78K | Q05682 | protein_coding | deleterious(0.01) | possibly_damaging(0.652) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CALD1 | SNV | Missense_Mutation | novel | c.1622N>T | p.Arg541Leu | p.R541L | Q05682 | protein_coding | deleterious(0) | possibly_damaging(0.845) | TCGA-B6-A1KI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CALD1 | SNV | Missense_Mutation | c.2026N>C | p.Asp676His | p.D676H | Q05682 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-D8-A1J9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| CALD1 | SNV | Missense_Mutation | novel | c.1065N>T | p.Glu355Asp | p.E355D | Q05682 | protein_coding | tolerated_low_confidence(0.37) | benign(0.096) | TCGA-E9-A54Y-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| CALD1 | SNV | Missense_Mutation | novel | c.2128N>G | p.Arg710Gly | p.R710G | Q05682 | protein_coding | deleterious(0.01) | probably_damaging(0.992) | TCGA-JL-A3YW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CALD1 | SNV | Missense_Mutation | novel | c.2090C>T | p.Pro697Leu | p.P697L | Q05682 | protein_coding | deleterious(0) | possibly_damaging(0.874) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
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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 |
| Page: 1 |
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