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Gene: CDH13 |
Gene summary for CDH13 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CDH13 | Gene ID | 1012 |
| Gene name | cadherin 13 | |
| Gene Alias | CDHH | |
| Cytomap | 16q23.3 | |
| Gene Type | protein-coding | GO ID | GO:0000278 | UniProtAcc | B7Z9B1 |
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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 |
| 1012 | CDH13 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.52e-04 | 4.83e-01 | -0.0811 |
| 1012 | CDH13 | HTA11_78_2000001011 | Human | Colorectum | AD | 5.36e-10 | 5.65e-01 | -0.1088 |
| 1012 | CDH13 | HTA11_347_2000001011 | Human | Colorectum | AD | 5.78e-16 | 8.56e-01 | -0.1954 |
| 1012 | CDH13 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.04e-02 | 3.78e-01 | -0.1207 |
| 1012 | CDH13 | HTA11_696_2000001011 | Human | Colorectum | AD | 9.44e-05 | 3.62e-01 | -0.1464 |
| 1012 | CDH13 | HTA11_866_2000001011 | Human | Colorectum | AD | 9.35e-05 | 4.47e-01 | -0.1001 |
| 1012 | CDH13 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.17e-09 | 5.27e-01 | 0.294 |
| 1012 | CDH13 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 4.32e-09 | 1.64e+00 | 0.3487 |
| 1012 | CDH13 | A002-C-203 | Human | Colorectum | FAP | 8.13e-03 | -8.89e-02 | 0.2786 |
| 1012 | CDH13 | LZE2T | Human | Esophagus | ESCC | 3.62e-02 | 3.09e-01 | 0.082 |
| 1012 | CDH13 | LZE4T | Human | Esophagus | ESCC | 7.36e-21 | 6.58e-01 | 0.0811 |
| 1012 | CDH13 | LZE7T | Human | Esophagus | ESCC | 1.17e-07 | 3.85e-01 | 0.0667 |
| 1012 | CDH13 | LZE22T | Human | Esophagus | ESCC | 4.76e-02 | 2.02e-01 | 0.068 |
| 1012 | CDH13 | LZE21T | Human | Esophagus | ESCC | 1.71e-06 | 7.78e-01 | 0.0655 |
| 1012 | CDH13 | P2T-E | Human | Esophagus | ESCC | 4.83e-07 | 2.20e-01 | 0.1177 |
| 1012 | CDH13 | P4T-E | Human | Esophagus | ESCC | 3.11e-03 | -4.77e-03 | 0.1323 |
| 1012 | CDH13 | P5T-E | Human | Esophagus | ESCC | 1.36e-12 | 1.19e-01 | 0.1327 |
| 1012 | CDH13 | P9T-E | Human | Esophagus | ESCC | 3.96e-07 | 1.40e-01 | 0.1131 |
| 1012 | CDH13 | P10T-E | Human | Esophagus | ESCC | 5.19e-33 | 8.07e-01 | 0.116 |
| 1012 | CDH13 | P11T-E | Human | Esophagus | ESCC | 9.51e-16 | 6.51e-01 | 0.1426 |
| Page: 1 2 3 4 5 |
| 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 | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| 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:0038127 | Colorectum | AD | ERBB signaling pathway | 55/3918 | 121/18723 | 1.19e-09 | 8.85e-08 | 55 |
| GO:0007173 | Colorectum | AD | epidermal growth factor receptor signaling pathway | 50/3918 | 108/18723 | 3.08e-09 | 2.07e-07 | 50 |
| GO:0010811 | Colorectum | AD | positive regulation of cell-substrate adhesion | 53/3918 | 123/18723 | 2.30e-08 | 1.27e-06 | 53 |
| GO:0010810 | Colorectum | AD | regulation of cell-substrate adhesion | 81/3918 | 221/18723 | 4.80e-08 | 2.55e-06 | 81 |
| GO:0031589 | Colorectum | AD | cell-substrate adhesion | 116/3918 | 363/18723 | 4.68e-07 | 1.76e-05 | 116 |
| GO:0001952 | Colorectum | AD | regulation of cell-matrix adhesion | 50/3918 | 128/18723 | 2.05e-06 | 6.05e-05 | 50 |
| GO:1901184 | Colorectum | AD | regulation of ERBB signaling pathway | 34/3918 | 79/18723 | 7.46e-06 | 1.82e-04 | 34 |
| GO:0007265 | Colorectum | AD | Ras protein signal transduction | 104/3918 | 337/18723 | 1.01e-05 | 2.35e-04 | 104 |
| GO:0001954 | Colorectum | AD | positive regulation of cell-matrix adhesion | 27/3918 | 58/18723 | 1.12e-05 | 2.55e-04 | 27 |
| GO:0001667 | Colorectum | AD | ameboidal-type cell migration | 137/3918 | 475/18723 | 2.17e-05 | 4.33e-04 | 137 |
| GO:0042058 | Colorectum | AD | regulation of epidermal growth factor receptor signaling pathway | 31/3918 | 73/18723 | 2.56e-05 | 4.89e-04 | 31 |
| GO:0007160 | Colorectum | AD | cell-matrix adhesion | 75/3918 | 233/18723 | 3.56e-05 | 6.45e-04 | 75 |
| GO:0097581 | Colorectum | AD | lamellipodium organization | 35/3918 | 90/18723 | 7.39e-05 | 1.18e-03 | 35 |
| GO:0016601 | Colorectum | AD | Rac protein signal transduction | 20/3918 | 42/18723 | 1.02e-04 | 1.53e-03 | 20 |
| GO:0090132 | Colorectum | AD | epithelium migration | 105/3918 | 360/18723 | 1.18e-04 | 1.73e-03 | 105 |
| GO:0010631 | Colorectum | AD | epithelial cell migration | 104/3918 | 357/18723 | 1.33e-04 | 1.90e-03 | 104 |
| GO:0030100 | Colorectum | AD | regulation of endocytosis | 67/3918 | 211/18723 | 1.42e-04 | 2.01e-03 | 67 |
| GO:0090130 | Colorectum | AD | tissue migration | 105/3918 | 365/18723 | 2.10e-04 | 2.77e-03 | 105 |
| GO:0045785 | Colorectum | AD | positive regulation of cell adhesion | 122/3918 | 437/18723 | 2.65e-04 | 3.28e-03 | 122 |
| GO:0050673 | Colorectum | AD | epithelial cell proliferation | 119/3918 | 437/18723 | 8.75e-04 | 8.51e-03 | 119 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
| 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 |
| CDH13 | SNV | Missense_Mutation | novel | c.1360N>A | p.Pro454Thr | p.P454T | P55290 | protein_coding | deleterious(0.02) | benign(0.426) | TCGA-A2-A0EM-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
| CDH13 | SNV | Missense_Mutation | rs372445890 | c.1510N>A | p.Gly504Ser | p.G504S | P55290 | protein_coding | tolerated(0.73) | probably_damaging(0.997) | TCGA-A8-A08T-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| CDH13 | SNV | Missense_Mutation | novel | c.1414T>C | p.Ser472Pro | p.S472P | P55290 | protein_coding | deleterious(0.01) | probably_damaging(0.981) | TCGA-A8-A094-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CDH13 | SNV | Missense_Mutation | novel | c.1954N>C | p.Gly652Arg | p.G652R | P55290 | protein_coding | tolerated(0.14) | probably_damaging(0.999) | TCGA-D8-A73U-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
| CDH13 | insertion | Nonsense_Mutation | novel | c.1332_1333insCGGCTCAAAGGAATGTGCTAATGAAAGCTCATGAAATTCTCTATCTAT | p.Arg444_Ala445insArgLeuLysGlyMetCysTerTerLysLeuMetLysPheSerIleTyr | p.R444_A445insRLKGMC**KLMKFSIY | P55290 | protein_coding | TCGA-BH-A0EE-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | docetaxel | SD | ||
| CDH13 | SNV | Missense_Mutation | rs868363122 | c.1078T>C | p.Ser360Pro | p.S360P | P55290 | protein_coding | tolerated(0.1) | benign(0.003) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CDH13 | SNV | Missense_Mutation | novel | c.1910C>A | p.Ala637Asp | p.A637D | P55290 | protein_coding | deleterious(0.01) | probably_damaging(0.996) | TCGA-EK-A2PG-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| CDH13 | SNV | Missense_Mutation | c.2186G>A | p.Cys729Tyr | p.C729Y | P55290 | protein_coding | deleterious(0) | possibly_damaging(0.56) | TCGA-IR-A3LH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| CDH13 | SNV | Missense_Mutation | c.240N>C | p.Gln80His | p.Q80H | P55290 | protein_coding | deleterious(0.04) | benign(0.444) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| CDH13 | SNV | Missense_Mutation | novel | c.1213N>C | p.Asp405His | p.D405H | P55290 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-VS-A959-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| 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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