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Gene: CAPN3 |
Gene summary for CAPN3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CAPN3 | Gene ID | 825 |
| Gene name | calpain 3 | |
| Gene Alias | CANP3 | |
| Cytomap | 15q15.1 | |
| Gene Type | protein-coding | GO ID | GO:0001775 | UniProtAcc | P20807 |
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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 |
| 825 | CAPN3 | RNA-P10T2-P10T2-2 | Human | Lung | AAH | 3.17e-04 | 6.29e-01 | -0.1406 |
| 825 | CAPN3 | RNA-P10T2-P10T2-3 | Human | Lung | AAH | 1.22e-02 | 5.04e-01 | -0.1408 |
| 825 | CAPN3 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 1.17e-04 | 3.06e-01 | -0.2116 |
| 825 | CAPN3 | RNA-P25T1-P25T1-2 | Human | Lung | AIS | 2.37e-02 | 4.00e-01 | -0.1941 |
| 825 | CAPN3 | RNA-P25T1-P25T1-4 | Human | Lung | AIS | 2.81e-06 | 4.37e-01 | -0.2119 |
| 825 | CAPN3 | RNA-P6T2-P6T2-1 | Human | Lung | IAC | 3.36e-06 | 2.96e-01 | -0.0166 |
| 825 | CAPN3 | RNA-P6T2-P6T2-2 | Human | Lung | IAC | 1.06e-02 | 1.82e-01 | -0.0132 |
| 825 | CAPN3 | RNA-P6T2-P6T2-3 | Human | Lung | IAC | 4.72e-02 | 1.55e-01 | -0.013 |
| 825 | CAPN3 | RNA-P6T2-P6T2-4 | Human | Lung | IAC | 1.85e-04 | 2.32e-01 | -0.0121 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:19033208 | Lung | IAC | regulation of protein modification by small protein conjugation or removal | 64/2061 | 242/18723 | 1.38e-11 | 4.83e-09 | 64 |
| GO:00458628 | Lung | IAC | positive regulation of proteolysis | 80/2061 | 372/18723 | 2.62e-09 | 4.21e-07 | 80 |
| GO:00310327 | Lung | IAC | actomyosin structure organization | 46/2061 | 196/18723 | 4.70e-07 | 3.10e-05 | 46 |
| GO:00316478 | Lung | IAC | regulation of protein stability | 62/2061 | 298/18723 | 5.37e-07 | 3.32e-05 | 62 |
| GO:19033218 | Lung | IAC | negative regulation of protein modification by small protein conjugation or removal | 28/2061 | 95/18723 | 7.08e-07 | 4.08e-05 | 28 |
| GO:00072495 | Lung | IAC | I-kappaB kinase/NF-kappaB signaling | 56/2061 | 281/18723 | 7.39e-06 | 2.62e-04 | 56 |
| GO:00431226 | Lung | IAC | regulation of I-kappaB kinase/NF-kappaB signaling | 51/2061 | 249/18723 | 8.41e-06 | 2.87e-04 | 51 |
| GO:00621978 | Lung | IAC | cellular response to chemical stress | 64/2061 | 337/18723 | 8.92e-06 | 3.01e-04 | 64 |
| GO:00510903 | Lung | IAC | regulation of DNA-binding transcription factor activity | 76/2061 | 440/18723 | 4.44e-05 | 1.05e-03 | 76 |
| GO:00510914 | Lung | IAC | positive regulation of DNA-binding transcription factor activity | 50/2061 | 260/18723 | 5.87e-05 | 1.29e-03 | 50 |
| GO:00316483 | Lung | IAC | protein destabilization | 15/2061 | 46/18723 | 7.40e-05 | 1.55e-03 | 15 |
| GO:00459276 | Lung | IAC | positive regulation of growth | 49/2061 | 259/18723 | 1.06e-04 | 2.05e-03 | 49 |
| GO:00486385 | Lung | IAC | regulation of developmental growth | 59/2061 | 330/18723 | 1.17e-04 | 2.22e-03 | 59 |
| GO:00512357 | Lung | IAC | maintenance of location | 58/2061 | 327/18723 | 1.66e-04 | 2.96e-03 | 58 |
| GO:0051092 | Lung | IAC | positive regulation of NF-kappaB transcription factor activity | 32/2061 | 152/18723 | 2.25e-04 | 3.90e-03 | 32 |
| GO:00712146 | Lung | IAC | cellular response to abiotic stimulus | 58/2061 | 331/18723 | 2.30e-04 | 3.96e-03 | 58 |
| GO:01040046 | Lung | IAC | cellular response to environmental stimulus | 58/2061 | 331/18723 | 2.30e-04 | 3.96e-03 | 58 |
| GO:0042692 | Lung | IAC | muscle cell differentiation | 65/2061 | 384/18723 | 2.75e-04 | 4.54e-03 | 65 |
| GO:00486394 | Lung | IAC | positive regulation of developmental growth | 35/2061 | 174/18723 | 2.96e-04 | 4.79e-03 | 35 |
| GO:00515924 | Lung | IAC | response to calcium ion | 31/2061 | 149/18723 | 3.47e-04 | 5.42e-03 | 31 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| CAPN3 | SNV | Missense_Mutation | c.311A>G | p.Glu104Gly | p.E104G | P20807 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A2-A0CW-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
| CAPN3 | SNV | Missense_Mutation | rs772580081 | c.46G>A | p.Glu16Lys | p.E16K | P20807 | protein_coding | tolerated(0.17) | benign(0.001) | TCGA-BH-A1F8-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| CAPN3 | SNV | Missense_Mutation | c.1328N>T | p.Ser443Phe | p.S443F | P20807 | protein_coding | deleterious(0) | benign(0.33) | TCGA-GM-A2DO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | CR | |
| CAPN3 | deletion | Frame_Shift_Del | novel | c.1004delN | p.Tyr336ThrfsTer16 | p.Y336Tfs*16 | P20807 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| CAPN3 | SNV | Missense_Mutation | c.610C>G | p.Leu204Val | p.L204V | P20807 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| CAPN3 | SNV | Missense_Mutation | rs398123145 | c.2218N>A | p.Gly740Ser | p.G740S | P20807 | protein_coding | deleterious(0.03) | possibly_damaging(0.446) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| CAPN3 | SNV | Missense_Mutation | rs142004418 | c.1621N>T | p.Arg541Trp | p.R541W | P20807 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-EA-A5ZF-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| CAPN3 | SNV | Missense_Mutation | c.1024N>C | p.Asp342His | p.D342H | P20807 | protein_coding | deleterious(0.01) | benign(0.409) | TCGA-EK-A2R8-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| CAPN3 | SNV | Missense_Mutation | c.433C>T | p.Leu145Phe | p.L145F | P20807 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-LP-A7HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| CAPN3 | SNV | Missense_Mutation | rs587780290 | c.2243N>A | p.Arg748Gln | p.R748Q | P20807 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
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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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