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Gene: CDH1 |
Gene summary for CDH1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CDH1 | Gene ID | 999 |
| Gene name | cadherin 1 | |
| Gene Alias | Arc-1 | |
| Cytomap | 16q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | B3GN61 |
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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 |
| 999 | CDH1 | CA_HPV_1 | Human | Cervix | CC | 5.82e-12 | -3.26e-01 | 0.0264 |
| 999 | CDH1 | N_HPV_1 | Human | Cervix | N_HPV | 1.70e-05 | -3.24e-01 | 0.0079 |
| 999 | CDH1 | CCI_2 | Human | Cervix | CC | 1.78e-11 | 1.25e+00 | 0.5249 |
| 999 | CDH1 | CCI_3 | Human | Cervix | CC | 6.15e-04 | 7.33e-01 | 0.516 |
| 999 | CDH1 | sample3 | Human | Cervix | CC | 6.67e-08 | 3.01e-01 | 0.1387 |
| 999 | CDH1 | T2 | Human | Cervix | CC | 2.26e-02 | 3.74e-01 | 0.0709 |
| 999 | CDH1 | T3 | Human | Cervix | CC | 3.64e-06 | 2.92e-01 | 0.1389 |
| 999 | CDH1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 8.02e-14 | 1.08e+00 | -0.1808 |
| 999 | CDH1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.42e-28 | 1.38e+00 | -0.0811 |
| 999 | CDH1 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.55e-10 | 8.78e-01 | -0.1088 |
| 999 | CDH1 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.90e-48 | 1.39e+00 | -0.1954 |
| 999 | CDH1 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.12e-08 | 1.57e+00 | -0.2602 |
| 999 | CDH1 | HTA11_2112_2000001011 | Human | Colorectum | SER | 4.57e-16 | 1.59e+00 | -0.2196 |
| 999 | CDH1 | HTA11_83_2000001011 | Human | Colorectum | SER | 3.78e-16 | 9.47e-01 | -0.1526 |
| 999 | CDH1 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.75e-16 | 8.64e-01 | -0.1464 |
| 999 | CDH1 | HTA11_866_2000001011 | Human | Colorectum | AD | 5.47e-05 | 5.19e-01 | -0.1001 |
| 999 | CDH1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.94e-10 | 8.75e-01 | -0.059 |
| 999 | CDH1 | HTA11_2992_2000001011 | Human | Colorectum | SER | 8.84e-05 | 7.30e-01 | -0.1706 |
| 999 | CDH1 | HTA11_5212_2000001011 | Human | Colorectum | AD | 4.24e-10 | 9.93e-01 | -0.2061 |
| 999 | CDH1 | HTA11_5216_2000001011 | Human | Colorectum | SER | 1.75e-07 | 8.31e-01 | -0.1462 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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:00615648 | Endometrium | AEH | axon development | 88/2100 | 467/18723 | 6.39e-07 | 2.38e-05 | 88 |
| GO:004873216 | Endometrium | AEH | gland development | 83/2100 | 436/18723 | 8.62e-07 | 3.11e-05 | 83 |
| GO:003315710 | Endometrium | AEH | regulation of intracellular protein transport | 51/2100 | 229/18723 | 1.13e-06 | 3.75e-05 | 51 |
| GO:00015038 | Endometrium | AEH | ossification | 78/2100 | 408/18723 | 1.54e-06 | 4.85e-05 | 78 |
| GO:003238810 | Endometrium | AEH | positive regulation of intracellular transport | 46/2100 | 202/18723 | 1.96e-06 | 5.93e-05 | 46 |
| GO:00323869 | Endometrium | AEH | regulation of intracellular transport | 66/2100 | 337/18723 | 4.18e-06 | 1.10e-04 | 66 |
| GO:00343299 | Endometrium | AEH | cell junction assembly | 78/2100 | 420/18723 | 4.80e-06 | 1.24e-04 | 78 |
| GO:00903168 | Endometrium | AEH | positive regulation of intracellular protein transport | 38/2100 | 160/18723 | 5.22e-06 | 1.33e-04 | 38 |
| GO:19001828 | Endometrium | AEH | positive regulation of protein localization to nucleus | 25/2100 | 87/18723 | 6.36e-06 | 1.55e-04 | 25 |
| GO:00303364 | Endometrium | AEH | negative regulation of cell migration | 65/2100 | 344/18723 | 1.65e-05 | 3.42e-04 | 65 |
| GO:00345049 | Endometrium | AEH | protein localization to nucleus | 57/2100 | 290/18723 | 1.65e-05 | 3.42e-04 | 57 |
| GO:20001464 | Endometrium | AEH | negative regulation of cell motility | 67/2100 | 359/18723 | 1.86e-05 | 3.77e-04 | 67 |
| GO:00512714 | Endometrium | AEH | negative regulation of cellular component movement | 68/2100 | 367/18723 | 2.06e-05 | 4.11e-04 | 68 |
| GO:000963610 | Endometrium | AEH | response to toxic substance | 52/2100 | 262/18723 | 2.89e-05 | 5.40e-04 | 52 |
| GO:002240714 | Endometrium | AEH | regulation of cell-cell adhesion | 79/2100 | 448/18723 | 2.90e-05 | 5.40e-04 | 79 |
| GO:19001809 | Endometrium | AEH | regulation of protein localization to nucleus | 32/2100 | 136/18723 | 3.42e-05 | 6.06e-04 | 32 |
| GO:004521610 | Endometrium | AEH | cell-cell junction organization | 42/2100 | 200/18723 | 4.26e-05 | 7.20e-04 | 42 |
| GO:00400134 | Endometrium | AEH | negative regulation of locomotion | 70/2100 | 391/18723 | 4.95e-05 | 8.05e-04 | 70 |
| GO:009730510 | Endometrium | AEH | response to alcohol | 48/2100 | 253/18723 | 1.80e-04 | 2.31e-03 | 48 |
| GO:001003816 | Endometrium | AEH | response to metal ion | 65/2100 | 373/18723 | 2.02e-04 | 2.54e-03 | 65 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0452020 | Cervix | CC | Adherens junction | 33/1267 | 93/8465 | 6.99e-07 | 7.31e-06 | 4.32e-06 | 33 |
| hsa0401512 | Cervix | CC | Rap1 signaling pathway | 56/1267 | 210/8465 | 6.23e-06 | 5.61e-05 | 3.32e-05 | 56 |
| hsa052197 | Cervix | CC | Bladder cancer | 16/1267 | 41/8465 | 1.45e-04 | 9.05e-04 | 5.35e-04 | 16 |
| hsa043908 | Cervix | CC | Hippo signaling pathway | 40/1267 | 157/8465 | 3.64e-04 | 1.82e-03 | 1.07e-03 | 40 |
| hsa0510020 | Cervix | CC | Bacterial invasion of epithelial cells | 23/1267 | 77/8465 | 6.25e-04 | 2.93e-03 | 1.73e-03 | 23 |
| hsa0521310 | Cervix | CC | Endometrial cancer | 18/1267 | 58/8465 | 1.46e-03 | 6.30e-03 | 3.73e-03 | 18 |
| hsa045147 | Cervix | CC | Cell adhesion molecules | 36/1267 | 157/8465 | 4.94e-03 | 1.67e-02 | 9.86e-03 | 36 |
| hsa04520110 | Cervix | CC | Adherens junction | 33/1267 | 93/8465 | 6.99e-07 | 7.31e-06 | 4.32e-06 | 33 |
| hsa0401513 | Cervix | CC | Rap1 signaling pathway | 56/1267 | 210/8465 | 6.23e-06 | 5.61e-05 | 3.32e-05 | 56 |
| hsa0521914 | Cervix | CC | Bladder cancer | 16/1267 | 41/8465 | 1.45e-04 | 9.05e-04 | 5.35e-04 | 16 |
| hsa0439013 | Cervix | CC | Hippo signaling pathway | 40/1267 | 157/8465 | 3.64e-04 | 1.82e-03 | 1.07e-03 | 40 |
| hsa05100110 | Cervix | CC | Bacterial invasion of epithelial cells | 23/1267 | 77/8465 | 6.25e-04 | 2.93e-03 | 1.73e-03 | 23 |
| hsa0521313 | Cervix | CC | Endometrial cancer | 18/1267 | 58/8465 | 1.46e-03 | 6.30e-03 | 3.73e-03 | 18 |
| hsa0451412 | Cervix | CC | Cell adhesion molecules | 36/1267 | 157/8465 | 4.94e-03 | 1.67e-02 | 9.86e-03 | 36 |
| hsa0510025 | Cervix | N_HPV | Bacterial invasion of epithelial cells | 10/349 | 77/8465 | 1.17e-03 | 7.93e-03 | 6.20e-03 | 10 |
| hsa0510035 | Cervix | N_HPV | Bacterial invasion of epithelial cells | 10/349 | 77/8465 | 1.17e-03 | 7.93e-03 | 6.20e-03 | 10 |
| hsa05100 | Colorectum | AD | Bacterial invasion of epithelial cells | 44/2092 | 77/8465 | 1.13e-09 | 2.22e-08 | 1.42e-08 | 44 |
| hsa04520 | Colorectum | AD | Adherens junction | 50/2092 | 93/8465 | 1.52e-09 | 2.83e-08 | 1.81e-08 | 50 |
| hsa05213 | Colorectum | AD | Endometrial cancer | 29/2092 | 58/8465 | 2.69e-05 | 2.57e-04 | 1.64e-04 | 29 |
| hsa05216 | Colorectum | AD | Thyroid cancer | 21/2092 | 37/8465 | 3.05e-05 | 2.76e-04 | 1.76e-04 | 21 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
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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 |
| CDH1 | ITGA2_ITGB1 | CDH1_ITGA1_ITGB1 | CDH1 | Breast | ADJ |
| CDH1 | CDH1 | CDH1_CDH1 | CDH | Breast | ADJ |
| ANGPTL4 | CDH11 | ANGPTL4_CDH11 | ANGPTL | Breast | DCIS |
| CDH1 | ITGA2_ITGB1 | CDH1_ITGA1_ITGB1 | CDH1 | Breast | DCIS |
| CDH1 | ITGAE_ITGB7 | CDH1_ITGAE_ITGB7 | CDH1 | Breast | DCIS |
| CDH1 | KLRG1 | CDH1_KLRG1 | CDH1 | Breast | DCIS |
| CDH1 | CDH1 | CDH1_CDH1 | CDH | Breast | DCIS |
| ANGPTL4 | CDH11 | ANGPTL4_CDH11 | ANGPTL | Breast | Healthy |
| CDH1 | ITGA2_ITGB1 | CDH1_ITGA1_ITGB1 | CDH1 | Breast | Healthy |
| CDH1 | ITGAE_ITGB7 | CDH1_ITGAE_ITGB7 | CDH1 | Breast | Healthy |
| CDH1 | KLRG1 | CDH1_KLRG1 | CDH1 | Breast | Healthy |
| CDH1 | CDH1 | CDH1_CDH1 | CDH | Breast | Healthy |
| ANGPTL4 | CDH11 | ANGPTL4_CDH11 | ANGPTL | Breast | IDC |
| CDH1 | ITGA2_ITGB1 | CDH1_ITGA1_ITGB1 | CDH1 | Breast | Precancer |
| CDH1 | CDH1 | CDH1_CDH1 | CDH | Breast | Precancer |
| CDH1 | ITGA2_ITGB1 | CDH1_ITGA1_ITGB1 | CDH1 | Cervix | ADJ |
| CDH1 | CDH1 | CDH1_CDH1 | CDH | Cervix | ADJ |
| CDH1 | ITGA2_ITGB1 | CDH1_ITGA1_ITGB1 | CDH1 | Cervix | CC |
| CDH1 | KLRG1 | CDH1_KLRG1 | CDH1 | Cervix | CC |
| CDH1 | CDH1 | CDH1_CDH1 | CDH | Cervix | CC |
| Page: 1 2 3 4 5 6 7 |
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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 |
| CDH1 | SNV | Missense_Mutation | c.727N>A | p.Glu243Lys | p.E243K | P12830 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A1-A0SE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| CDH1 | SNV | Missense_Mutation | rs587782623 | c.2600A>G | p.Asn867Ser | p.N867S | P12830 | protein_coding | tolerated(0.43) | benign(0.264) | TCGA-A2-A1G0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD |
| CDH1 | SNV | Missense_Mutation | c.727N>A | p.Glu243Lys | p.E243K | P12830 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A8-A091-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | PD | |
| CDH1 | SNV | Missense_Mutation | c.727N>A | p.Glu243Lys | p.E243K | P12830 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A8-A0A7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| CDH1 | SNV | Missense_Mutation | c.846N>T | p.Met282Ile | p.M282I | P12830 | protein_coding | tolerated(0.18) | probably_damaging(0.922) | TCGA-AC-A3W6-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| CDH1 | SNV | Missense_Mutation | novel | c.1316C>A | p.Ala439Glu | p.A439E | P12830 | protein_coding | tolerated(0.06) | benign(0.398) | TCGA-AO-A03T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| CDH1 | SNV | Missense_Mutation | rs587782024 | c.2450N>T | p.Ala817Val | p.A817V | P12830 | protein_coding | deleterious(0.04) | probably_damaging(1) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| CDH1 | SNV | Missense_Mutation | novel | c.493N>C | p.Glu165Gln | p.E165Q | P12830 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-AR-A2LJ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD |
| CDH1 | SNV | Missense_Mutation | c.832N>A | p.Gly278Arg | p.G278R | P12830 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-AR-A2LL-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| CDH1 | SNV | Missense_Mutation | c.779N>A | p.Pro260His | p.P260H | P12830 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-BH-A0BA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
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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 |
| 999 | CDH1 | CLINICALLY ACTIONABLE, DRUGGABLE GENOME | Volasertib | VOLASERTIB | 26597303 | |
| 999 | CDH1 | CLINICALLY ACTIONABLE, DRUGGABLE GENOME | Erlotinib | ERLOTINIB | 26251290 | |
| 999 | CDH1 | CLINICALLY ACTIONABLE, DRUGGABLE GENOME | Selumetinib | SELUMETINIB | 26251290 | |
| 999 | CDH1 | CLINICALLY ACTIONABLE, DRUGGABLE GENOME | N/A | 26182300,26380059 | ||
| 999 | CDH1 | CLINICALLY ACTIONABLE, DRUGGABLE GENOME | PROTEOLYTIC ENZYMES | 2211831 | ||
| 999 | CDH1 | CLINICALLY ACTIONABLE, DRUGGABLE GENOME | Capecitabine | CAPECITABINE | 26487584 | |
| 999 | CDH1 | CLINICALLY ACTIONABLE, DRUGGABLE GENOME | BI2536 | 26597303 | ||
| 999 | CDH1 | CLINICALLY ACTIONABLE, DRUGGABLE GENOME | ANTISERUM | 3880756 | ||
| 999 | CDH1 | CLINICALLY ACTIONABLE, DRUGGABLE GENOME | Lapatinib | LAPATINIB | 26487584 |
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