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Gene: CLCA1 |
Gene summary for CLCA1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CLCA1 | Gene ID | 1179 |
| Gene name | chloride channel accessory 1 | |
| Gene Alias | CACC | |
| Cytomap | 1p22.3 | |
| Gene Type | protein-coding | GO ID | GO:0001666 | UniProtAcc | A8K7I4 |
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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 |
| 1179 | CLCA1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.43e-07 | 1.98e-01 | 0.0155 |
| 1179 | CLCA1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 9.24e-09 | 2.69e+00 | -0.0811 |
| 1179 | CLCA1 | HTA11_78_2000001011 | Human | Colorectum | AD | 2.47e-20 | 3.52e+00 | -0.1088 |
| 1179 | CLCA1 | HTA11_3361_2000001011 | Human | Colorectum | AD | 7.55e-26 | 2.48e+00 | -0.1207 |
| 1179 | CLCA1 | HTA11_83_2000001011 | Human | Colorectum | SER | 2.56e-07 | 1.86e+00 | -0.1526 |
| 1179 | CLCA1 | HTA11_696_2000001011 | Human | Colorectum | AD | 7.58e-76 | 3.38e+00 | -0.1464 |
| 1179 | CLCA1 | HTA11_866_2000001011 | Human | Colorectum | AD | 8.71e-45 | 3.23e+00 | -0.1001 |
| 1179 | CLCA1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.85e-24 | 2.74e+00 | -0.059 |
| 1179 | CLCA1 | HTA11_5216_2000001011 | Human | Colorectum | SER | 2.09e-05 | 1.92e+00 | -0.1462 |
| 1179 | CLCA1 | HTA11_546_2000001011 | Human | Colorectum | AD | 3.98e-07 | 2.71e+00 | -0.0842 |
| 1179 | CLCA1 | HTA11_866_3004761011 | Human | Colorectum | AD | 2.68e-43 | 9.19e-01 | 0.096 |
| 1179 | CLCA1 | HTA11_7663_2000001011 | Human | Colorectum | SER | 3.29e-02 | 4.28e-01 | 0.0131 |
| 1179 | CLCA1 | HTA11_6801_2000001011 | Human | Colorectum | SER | 5.37e-05 | 5.49e-01 | 0.0171 |
| 1179 | CLCA1 | HTA11_10711_2000001011 | Human | Colorectum | AD | 3.98e-09 | 6.31e-01 | 0.0338 |
| 1179 | CLCA1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 9.25e-20 | 4.81e-01 | 0.0674 |
| 1179 | CLCA1 | HTA11_6818_2000001011 | Human | Colorectum | AD | 6.29e-07 | 6.13e-01 | 0.0112 |
| 1179 | CLCA1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 4.61e-12 | 4.51e-01 | 0.294 |
| 1179 | CLCA1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 2.63e-17 | 4.44e-01 | 0.281 |
| 1179 | CLCA1 | A002-C-010 | Human | Colorectum | FAP | 2.13e-34 | 9.08e-01 | 0.242 |
| 1179 | CLCA1 | A002-C-201 | Human | Colorectum | FAP | 8.54e-05 | 4.23e-01 | 0.0324 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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:0070482 | Colorectum | AD | response to oxygen levels | 99/3918 | 347/18723 | 4.29e-04 | 4.82e-03 | 99 |
| GO:0071453 | Colorectum | AD | cellular response to oxygen levels | 55/3918 | 177/18723 | 9.48e-04 | 8.96e-03 | 55 |
| GO:0001666 | Colorectum | AD | response to hypoxia | 86/3918 | 307/18723 | 1.77e-03 | 1.46e-02 | 86 |
| GO:0036293 | Colorectum | AD | response to decreased oxygen levels | 88/3918 | 322/18723 | 3.42e-03 | 2.49e-02 | 88 |
| GO:0015698 | Colorectum | AD | inorganic anion transport | 52/3918 | 180/18723 | 6.83e-03 | 4.22e-02 | 52 |
| GO:00704821 | Colorectum | SER | response to oxygen levels | 79/2897 | 347/18723 | 1.99e-04 | 3.64e-03 | 79 |
| GO:00016661 | Colorectum | SER | response to hypoxia | 69/2897 | 307/18723 | 7.07e-04 | 9.39e-03 | 69 |
| GO:00362931 | Colorectum | SER | response to decreased oxygen levels | 71/2897 | 322/18723 | 1.04e-03 | 1.22e-02 | 71 |
| GO:00714531 | Colorectum | SER | cellular response to oxygen levels | 41/2897 | 177/18723 | 4.48e-03 | 3.56e-02 | 41 |
| GO:00704822 | Colorectum | MSS | response to oxygen levels | 85/3467 | 347/18723 | 3.08e-03 | 2.34e-02 | 85 |
| GO:00714532 | Colorectum | MSS | cellular response to oxygen levels | 47/3467 | 177/18723 | 5.13e-03 | 3.52e-02 | 47 |
| GO:00016662 | Colorectum | MSS | response to hypoxia | 75/3467 | 307/18723 | 5.56e-03 | 3.78e-02 | 75 |
| GO:00704823 | Colorectum | FAP | response to oxygen levels | 77/2622 | 347/18723 | 2.08e-05 | 5.05e-04 | 77 |
| GO:00714533 | Colorectum | FAP | cellular response to oxygen levels | 45/2622 | 177/18723 | 3.77e-05 | 8.13e-04 | 45 |
| GO:00016663 | Colorectum | FAP | response to hypoxia | 68/2622 | 307/18723 | 6.53e-05 | 1.25e-03 | 68 |
| GO:00362932 | Colorectum | FAP | response to decreased oxygen levels | 70/2622 | 322/18723 | 9.49e-05 | 1.61e-03 | 70 |
| GO:0036294 | Colorectum | FAP | cellular response to decreased oxygen levels | 39/2622 | 161/18723 | 3.52e-04 | 4.47e-03 | 39 |
| GO:0071456 | Colorectum | FAP | cellular response to hypoxia | 37/2622 | 151/18723 | 3.88e-04 | 4.75e-03 | 37 |
| GO:00156981 | Colorectum | FAP | inorganic anion transport | 38/2622 | 180/18723 | 5.73e-03 | 3.67e-02 | 38 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04972 | Colorectum | AD | Pancreatic secretion | 36/2092 | 102/8465 | 1.06e-02 | 3.98e-02 | 2.54e-02 | 36 |
| hsa049721 | Colorectum | AD | Pancreatic secretion | 36/2092 | 102/8465 | 1.06e-02 | 3.98e-02 | 2.54e-02 | 36 |
| hsa049722 | Colorectum | SER | Pancreatic secretion | 30/1580 | 102/8465 | 5.41e-03 | 3.28e-02 | 2.38e-02 | 30 |
| hsa049723 | Colorectum | SER | Pancreatic secretion | 30/1580 | 102/8465 | 5.41e-03 | 3.28e-02 | 2.38e-02 | 30 |
| hsa049724 | Colorectum | MSS | Pancreatic secretion | 33/1875 | 102/8465 | 1.09e-02 | 3.75e-02 | 2.30e-02 | 33 |
| hsa049725 | Colorectum | MSS | Pancreatic secretion | 33/1875 | 102/8465 | 1.09e-02 | 3.75e-02 | 2.30e-02 | 33 |
| hsa049726 | Colorectum | FAP | Pancreatic secretion | 34/1404 | 102/8465 | 2.43e-05 | 2.78e-04 | 1.69e-04 | 34 |
| hsa049727 | Colorectum | FAP | Pancreatic secretion | 34/1404 | 102/8465 | 2.43e-05 | 2.78e-04 | 1.69e-04 | 34 |
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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 |
| CLCA1 | SNV | Missense_Mutation | rs146316532 | c.1844N>A | p.Arg615His | p.R615H | A8K7I4 | protein_coding | tolerated(0.17) | benign(0.014) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CLCA1 | SNV | Missense_Mutation | novel | c.1107N>G | p.Asp369Glu | p.D369E | A8K7I4 | protein_coding | tolerated(0.71) | benign(0.02) | TCGA-AO-A0J9-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD |
| CLCA1 | SNV | Missense_Mutation | novel | c.964N>T | p.Arg322Cys | p.R322C | A8K7I4 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-AR-A5QQ-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | carboplatin | PD |
| CLCA1 | SNV | Missense_Mutation | rs368950561 | c.2081N>A | p.Gly694Glu | p.G694E | A8K7I4 | protein_coding | tolerated(0.25) | benign(0.356) | TCGA-B6-A0IH-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| CLCA1 | SNV | Missense_Mutation | c.1675G>T | p.Ala559Ser | p.A559S | A8K7I4 | protein_coding | deleterious(0) | probably_damaging(0.974) | TCGA-EW-A1P4-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | |
| CLCA1 | deletion | Frame_Shift_Del | c.798delA | p.Lys266AsnfsTer10 | p.K266Nfs*10 | A8K7I4 | protein_coding | TCGA-A2-A0D2-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |||
| CLCA1 | insertion | Nonsense_Mutation | novel | c.2740_2741insAGTTAACGCAGCCAGACGGAGAGTGATACC | p.Ala914delinsGluLeuThrGlnProAspGlyGluTerTyrPro | p.A914delinsELTQPDGE*YP | A8K7I4 | protein_coding | TCGA-A8-A0A4-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | CR | ||
| CLCA1 | insertion | Frame_Shift_Ins | novel | c.2300_2301insACCTGAAATTAATAAGGATGATGTTCAACACAAGCAAGTGTGTT | p.Ser767ArgfsTer20 | p.S767Rfs*20 | A8K7I4 | protein_coding | TCGA-BH-A0AY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | |||
| CLCA1 | deletion | Frame_Shift_Del | novel | c.2089delT | p.Tyr697ThrfsTer63 | p.Y697Tfs*63 | A8K7I4 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| CLCA1 | deletion | Frame_Shift_Del | novel | c.1420delG | p.Ala474ProfsTer21 | p.A474Pfs*21 | A8K7I4 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
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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 |
| 1179 | CLCA1 | DRUGGABLE GENOME | TALNIFLUMATE | TALNIFLUMATE |
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