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Gene: AFDN |
Gene summary for AFDN |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | AFDN | Gene ID | 4301 |
| Gene name | afadin, adherens junction formation factor | |
| Gene Alias | AF6 | |
| Cytomap | 6q27 | |
| Gene Type | protein-coding | GO ID | GO:0001885 | UniProtAcc | P55196 |
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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 |
| 4301 | AFDN | HSIL_HPV_2 | Human | Cervix | HSIL_HPV | 9.10e-03 | 2.68e-01 | 0.0208 |
| 4301 | AFDN | CCI_1 | Human | Cervix | CC | 4.73e-07 | 1.50e+00 | 0.528 |
| 4301 | AFDN | CCI_2 | Human | Cervix | CC | 4.61e-06 | 7.08e-01 | 0.5249 |
| 4301 | AFDN | CCI_3 | Human | Cervix | CC | 5.65e-07 | 6.05e-01 | 0.516 |
| 4301 | AFDN | Tumor | Human | Cervix | CC | 1.95e-08 | -2.36e-01 | 0.1241 |
| 4301 | AFDN | sample3 | Human | Cervix | CC | 3.46e-03 | 2.16e-01 | 0.1387 |
| 4301 | AFDN | H2 | Human | Cervix | HSIL_HPV | 7.75e-28 | 6.95e-01 | 0.0632 |
| 4301 | AFDN | T3 | Human | Cervix | CC | 6.20e-05 | 2.78e-01 | 0.1389 |
| 4301 | AFDN | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.10e-37 | -8.17e-01 | 0.0155 |
| 4301 | AFDN | HTA11_2487_2000001011 | Human | Colorectum | SER | 9.98e-11 | -5.44e-01 | -0.1808 |
| 4301 | AFDN | HTA11_2951_2000001011 | Human | Colorectum | AD | 1.07e-08 | -9.23e-01 | 0.0216 |
| 4301 | AFDN | HTA11_1938_2000001011 | Human | Colorectum | AD | 4.46e-05 | -3.98e-01 | -0.0811 |
| 4301 | AFDN | HTA11_3361_2000001011 | Human | Colorectum | AD | 3.96e-15 | -8.16e-01 | -0.1207 |
| 4301 | AFDN | HTA11_83_2000001011 | Human | Colorectum | SER | 3.19e-12 | -5.92e-01 | -0.1526 |
| 4301 | AFDN | HTA11_696_2000001011 | Human | Colorectum | AD | 2.37e-14 | -4.33e-01 | -0.1464 |
| 4301 | AFDN | HTA11_866_2000001011 | Human | Colorectum | AD | 1.22e-14 | -5.35e-01 | -0.1001 |
| 4301 | AFDN | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.27e-04 | -4.30e-01 | -0.059 |
| 4301 | AFDN | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.59e-09 | -4.86e-01 | -0.1706 |
| 4301 | AFDN | HTA11_546_2000001011 | Human | Colorectum | AD | 1.64e-02 | -3.88e-01 | -0.0842 |
| 4301 | AFDN | HTA11_9341_2000001011 | Human | Colorectum | SER | 4.37e-05 | -1.01e+00 | -0.00410000000000005 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| 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 | ||
| 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 | ||
| 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:0090150 | Colorectum | AD | establishment of protein localization to membrane | 100/3918 | 260/18723 | 6.01e-11 | 6.33e-09 | 100 |
| GO:0045216 | Colorectum | AD | cell-cell junction organization | 80/3918 | 200/18723 | 5.57e-10 | 4.58e-08 | 80 |
| GO:0034329 | Colorectum | AD | cell junction assembly | 136/3918 | 420/18723 | 2.02e-08 | 1.15e-06 | 136 |
| GO:0061951 | Colorectum | AD | establishment of protein localization to plasma membrane | 31/3918 | 60/18723 | 1.37e-07 | 6.42e-06 | 31 |
| GO:0007043 | Colorectum | AD | cell-cell junction assembly | 57/3918 | 146/18723 | 4.18e-07 | 1.61e-05 | 57 |
| GO:0043087 | Colorectum | AD | regulation of GTPase activity | 110/3918 | 348/18723 | 1.64e-06 | 5.03e-05 | 110 |
| GO:0043297 | Colorectum | AD | apical junction assembly | 34/3918 | 78/18723 | 5.31e-06 | 1.37e-04 | 34 |
| GO:0061028 | Colorectum | AD | establishment of endothelial barrier | 23/3918 | 46/18723 | 1.14e-05 | 2.57e-04 | 23 |
| GO:0120193 | Colorectum | AD | tight junction organization | 33/3918 | 80/18723 | 2.93e-05 | 5.42e-04 | 33 |
| GO:0120192 | Colorectum | AD | tight junction assembly | 31/3918 | 74/18723 | 3.53e-05 | 6.43e-04 | 31 |
| GO:0070830 | Colorectum | AD | bicellular tight junction assembly | 28/3918 | 70/18723 | 2.15e-04 | 2.83e-03 | 28 |
| GO:0045785 | Colorectum | AD | positive regulation of cell adhesion | 122/3918 | 437/18723 | 2.65e-04 | 3.28e-03 | 122 |
| GO:0001885 | Colorectum | AD | endothelial cell development | 26/3918 | 64/18723 | 2.67e-04 | 3.29e-03 | 26 |
| GO:0043547 | Colorectum | AD | positive regulation of GTPase activity | 75/3918 | 255/18723 | 7.95e-04 | 7.91e-03 | 75 |
| GO:0090557 | Colorectum | AD | establishment of endothelial intestinal barrier | 8/3918 | 12/18723 | 7.99e-04 | 7.91e-03 | 8 |
| GO:0003158 | Colorectum | AD | endothelium development | 44/3918 | 136/18723 | 1.20e-03 | 1.07e-02 | 44 |
| GO:0045446 | Colorectum | AD | endothelial cell differentiation | 39/3918 | 118/18723 | 1.42e-03 | 1.22e-02 | 39 |
| GO:00726591 | Colorectum | SER | protein localization to plasma membrane | 92/2897 | 284/18723 | 6.36e-13 | 1.86e-10 | 92 |
| GO:19907781 | Colorectum | SER | protein localization to cell periphery | 98/2897 | 333/18723 | 6.09e-11 | 9.57e-09 | 98 |
| GO:00452161 | Colorectum | SER | cell-cell junction organization | 63/2897 | 200/18723 | 9.15e-09 | 7.80e-07 | 63 |
| 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 |
| 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 |
| hsa0453020 | Cervix | CC | Tight junction | 49/1267 | 169/8465 | 1.87e-06 | 1.78e-05 | 1.05e-05 | 49 |
| hsa0467020 | Cervix | CC | Leukocyte transendothelial migration | 36/1267 | 114/8465 | 5.22e-06 | 4.83e-05 | 2.86e-05 | 36 |
| hsa0401512 | Cervix | CC | Rap1 signaling pathway | 56/1267 | 210/8465 | 6.23e-06 | 5.61e-05 | 3.32e-05 | 56 |
| hsa040142 | Cervix | CC | Ras signaling pathway | 51/1267 | 236/8465 | 3.55e-03 | 1.34e-02 | 7.91e-03 | 51 |
| hsa04520110 | Cervix | CC | Adherens junction | 33/1267 | 93/8465 | 6.99e-07 | 7.31e-06 | 4.32e-06 | 33 |
| hsa04530110 | Cervix | CC | Tight junction | 49/1267 | 169/8465 | 1.87e-06 | 1.78e-05 | 1.05e-05 | 49 |
| hsa04670110 | Cervix | CC | Leukocyte transendothelial migration | 36/1267 | 114/8465 | 5.22e-06 | 4.83e-05 | 2.86e-05 | 36 |
| hsa0401513 | Cervix | CC | Rap1 signaling pathway | 56/1267 | 210/8465 | 6.23e-06 | 5.61e-05 | 3.32e-05 | 56 |
| hsa0401411 | Cervix | CC | Ras signaling pathway | 51/1267 | 236/8465 | 3.55e-03 | 1.34e-02 | 7.91e-03 | 51 |
| hsa0467025 | Cervix | HSIL_HPV | Leukocyte transendothelial migration | 16/459 | 114/8465 | 4.04e-04 | 3.49e-03 | 2.82e-03 | 16 |
| hsa0467035 | Cervix | HSIL_HPV | Leukocyte transendothelial migration | 16/459 | 114/8465 | 4.04e-04 | 3.49e-03 | 2.82e-03 | 16 |
| hsa04520 | Colorectum | AD | Adherens junction | 50/2092 | 93/8465 | 1.52e-09 | 2.83e-08 | 1.81e-08 | 50 |
| hsa04530 | Colorectum | AD | Tight junction | 76/2092 | 169/8465 | 5.49e-09 | 9.69e-08 | 6.18e-08 | 76 |
| hsa04015 | Colorectum | AD | Rap1 signaling pathway | 71/2092 | 210/8465 | 1.72e-03 | 9.68e-03 | 6.18e-03 | 71 |
| hsa04670 | Colorectum | AD | Leukocyte transendothelial migration | 41/2092 | 114/8465 | 4.60e-03 | 2.20e-02 | 1.40e-02 | 41 |
| hsa045201 | Colorectum | AD | Adherens junction | 50/2092 | 93/8465 | 1.52e-09 | 2.83e-08 | 1.81e-08 | 50 |
| hsa045301 | Colorectum | AD | Tight junction | 76/2092 | 169/8465 | 5.49e-09 | 9.69e-08 | 6.18e-08 | 76 |
| hsa040151 | Colorectum | AD | Rap1 signaling pathway | 71/2092 | 210/8465 | 1.72e-03 | 9.68e-03 | 6.18e-03 | 71 |
| hsa046701 | Colorectum | AD | Leukocyte transendothelial migration | 41/2092 | 114/8465 | 4.60e-03 | 2.20e-02 | 1.40e-02 | 41 |
| Page: 1 2 3 4 5 6 7 8 9 |
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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 |
| AFDN | SNV | Missense_Mutation | novel | c.2237T>C | p.Phe746Ser | p.F746S | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A8-A06Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| AFDN | SNV | Missense_Mutation | c.3484G>A | p.Gly1162Arg | p.G1162R | protein_coding | deleterious_low_confidence(0) | probably_damaging(1) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | ||
| AFDN | SNV | Missense_Mutation | novel | c.4720N>C | p.Glu1574Gln | p.E1574Q | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.724) | TCGA-AC-A62X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| AFDN | SNV | Missense_Mutation | rs571941763 | c.4076N>T | p.Pro1359Leu | p.P1359L | protein_coding | tolerated_low_confidence(0.29) | benign(0.003) | TCGA-AN-A0FD-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| AFDN | SNV | Missense_Mutation | rs765437330 | c.3461N>T | p.Ala1154Val | p.A1154V | protein_coding | tolerated_low_confidence(0.1) | possibly_damaging(0.523) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| AFDN | SNV | Missense_Mutation | c.4406N>A | p.Ser1469Asn | p.S1469N | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.997) | TCGA-BH-A0B6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| AFDN | SNV | Missense_Mutation | c.4581G>C | p.Lys1527Asn | p.K1527N | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.863) | TCGA-BH-A0DZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | ||
| AFDN | SNV | Missense_Mutation | c.1568N>G | p.Ser523Cys | p.S523C | protein_coding | tolerated(0.07) | benign(0.024) | TCGA-BH-A18P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | ||
| AFDN | SNV | Missense_Mutation | novel | c.1399C>G | p.Leu467Val | p.L467V | protein_coding | tolerated(0.14) | benign(0.013) | TCGA-BH-A5IZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR | |
| AFDN | SNV | Missense_Mutation | c.2702G>T | p.Cys901Phe | p.C901F | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-C8-A12Q-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 |
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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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