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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 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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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 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
CDH13 | SNV | Missense_Mutation | novel | c.571C>T | p.Pro191Ser | p.P191S | P55290 | protein_coding | deleterious(0.01) | benign(0.007) | TCGA-CV-7102-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CDH13 | SNV | Missense_Mutation | rs756724897 | c.1883A>G | p.Asn628Ser | p.N628S | P55290 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-CV-7425-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
CDH13 | SNV | Missense_Mutation | novel | c.545N>A | p.Arg182Lys | p.R182K | P55290 | protein_coding | deleterious(0) | probably_damaging(0.969) | TCGA-CV-7568-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CDH13 | SNV | Missense_Mutation | novel | c.925N>G | p.Thr309Ala | p.T309A | P55290 | protein_coding | deleterious(0) | benign(0.106) | TCGA-F7-A624-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
CDH13 | SNV | Missense_Mutation | novel | c.1199T>A | p.Ile400Asn | p.I400N | P55290 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-YL-A8SB-01 | Prostate | prostate adenocarcinoma | Male | <65 | 9 | Hormone Therapy | casodex | PD |
CDH13 | SNV | Missense_Mutation | c.607N>T | p.Pro203Ser | p.P203S | P55290 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-BR-4257-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
CDH13 | SNV | Missense_Mutation | c.1285N>G | p.Asn429Asp | p.N429D | P55290 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-BR-6452-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
CDH13 | SNV | Missense_Mutation | c.519N>T | p.Lys173Asn | p.K173N | P55290 | protein_coding | tolerated(0.34) | benign(0.429) | TCGA-BR-8059-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
CDH13 | SNV | Missense_Mutation | novel | c.546A>T | p.Arg182Ser | p.R182S | P55290 | protein_coding | deleterious(0) | probably_damaging(0.985) | TCGA-BR-8381-01 | Stomach | stomach adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
CDH13 | SNV | Missense_Mutation | rs771613971 | c.901G>A | p.Val301Ile | p.V301I | P55290 | protein_coding | tolerated(0.14) | benign(0.247) | TCGA-BR-8487-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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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 |
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