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Gene: AMN |
Gene summary for AMN |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | AMN | Gene ID | 81693 |
| Gene name | amnion associated transmembrane protein | |
| Gene Alias | IGS2 | |
| Cytomap | 14q32.32 | |
| Gene Type | protein-coding | GO ID | GO:0003008 | UniProtAcc | Q9BXJ7 |
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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 |
| 81693 | AMN | HTA11_3410_2000001011 | Human | Colorectum | AD | 6.23e-03 | -1.69e-01 | 0.0155 |
| 81693 | AMN | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.96e-12 | 7.66e-01 | -0.1808 |
| 81693 | AMN | HTA11_347_2000001011 | Human | Colorectum | AD | 1.42e-14 | 6.06e-01 | -0.1954 |
| 81693 | AMN | HTA11_411_2000001011 | Human | Colorectum | SER | 5.86e-03 | 1.01e+00 | -0.2602 |
| 81693 | AMN | HTA11_83_2000001011 | Human | Colorectum | SER | 3.34e-03 | 3.38e-01 | -0.1526 |
| 81693 | AMN | HTA11_696_2000001011 | Human | Colorectum | AD | 2.27e-05 | 3.43e-01 | -0.1464 |
| 81693 | AMN | HTA11_866_2000001011 | Human | Colorectum | AD | 5.19e-03 | 2.82e-01 | -0.1001 |
| 81693 | AMN | HTA11_866_3004761011 | Human | Colorectum | AD | 8.43e-03 | -2.19e-01 | 0.096 |
| 81693 | AMN | HTA11_7469_2000001011 | Human | Colorectum | AD | 8.55e-03 | 4.03e-01 | -0.0124 |
| 81693 | AMN | HTA11_99999971662_82457 | Human | Colorectum | MSS | 2.65e-02 | -2.99e-01 | 0.3859 |
| 81693 | AMN | A015-C-203 | Human | Colorectum | FAP | 2.05e-07 | 9.29e-02 | -0.1294 |
| 81693 | AMN | A001-C-119 | Human | Colorectum | FAP | 5.52e-04 | -3.55e-01 | -0.1557 |
| 81693 | AMN | A001-C-108 | Human | Colorectum | FAP | 1.54e-06 | -2.83e-01 | -0.0272 |
| 81693 | AMN | A002-C-205 | Human | Colorectum | FAP | 3.81e-03 | -1.75e-01 | -0.1236 |
| 81693 | AMN | A015-C-104 | Human | Colorectum | FAP | 1.47e-06 | -5.64e-02 | -0.1899 |
| 81693 | AMN | A002-C-016 | Human | Colorectum | FAP | 2.88e-03 | 7.74e-02 | 0.0521 |
| 81693 | AMN | A002-C-116 | Human | Colorectum | FAP | 7.76e-07 | -2.10e-01 | -0.0452 |
| 81693 | AMN | F034 | Human | Colorectum | FAP | 1.07e-05 | -2.66e-01 | -0.0665 |
| 81693 | AMN | LZE20T | Human | Esophagus | ESCC | 2.37e-09 | 2.58e-01 | 0.0662 |
| 81693 | AMN | LZE22T | Human | Esophagus | ESCC | 1.54e-04 | 2.94e-01 | 0.068 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:004819318 | Esophagus | ESCC | Golgi vesicle transport | 231/8552 | 296/18723 | 1.82e-30 | 9.63e-28 | 231 |
| GO:0090150110 | Esophagus | ESCC | establishment of protein localization to membrane | 182/8552 | 260/18723 | 1.27e-15 | 8.19e-14 | 182 |
| GO:0072659110 | Esophagus | ESCC | protein localization to plasma membrane | 193/8552 | 284/18723 | 1.95e-14 | 1.03e-12 | 193 |
| GO:199077819 | Esophagus | ESCC | protein localization to cell periphery | 217/8552 | 333/18723 | 4.08e-13 | 1.88e-11 | 217 |
| GO:000689215 | Esophagus | ESCC | post-Golgi vesicle-mediated transport | 82/8552 | 104/18723 | 4.00e-12 | 1.55e-10 | 82 |
| GO:009887615 | Esophagus | ESCC | vesicle-mediated transport to the plasma membrane | 99/8552 | 136/18723 | 1.13e-10 | 3.39e-09 | 99 |
| GO:000689315 | Esophagus | ESCC | Golgi to plasma membrane transport | 48/8552 | 60/18723 | 5.11e-08 | 9.16e-07 | 48 |
| GO:004300114 | Esophagus | ESCC | Golgi to plasma membrane protein transport | 34/8552 | 40/18723 | 3.00e-07 | 4.27e-06 | 34 |
| GO:006195114 | Esophagus | ESCC | establishment of protein localization to plasma membrane | 44/8552 | 60/18723 | 1.25e-05 | 1.15e-04 | 44 |
| GO:000689818 | Esophagus | ESCC | receptor-mediated endocytosis | 142/8552 | 244/18723 | 5.22e-05 | 4.05e-04 | 142 |
| GO:00311461 | Esophagus | ESCC | SCF-dependent proteasomal ubiquitin-dependent protein catabolic process | 33/8552 | 49/18723 | 1.80e-03 | 8.26e-03 | 33 |
| GO:004819321 | Liver | HCC | Golgi vesicle transport | 217/7958 | 296/18723 | 2.58e-27 | 1.02e-24 | 217 |
| GO:009015012 | Liver | HCC | establishment of protein localization to membrane | 168/7958 | 260/18723 | 4.07e-13 | 2.13e-11 | 168 |
| GO:007265921 | Liver | HCC | protein localization to plasma membrane | 177/7958 | 284/18723 | 1.02e-11 | 4.18e-10 | 177 |
| GO:199077821 | Liver | HCC | protein localization to cell periphery | 200/7958 | 333/18723 | 6.07e-11 | 2.23e-09 | 200 |
| GO:000689221 | Liver | HCC | post-Golgi vesicle-mediated transport | 77/7958 | 104/18723 | 6.14e-11 | 2.24e-09 | 77 |
| GO:009887621 | Liver | HCC | vesicle-mediated transport to the plasma membrane | 92/7958 | 136/18723 | 2.57e-09 | 7.07e-08 | 92 |
| GO:000689321 | Liver | HCC | Golgi to plasma membrane transport | 44/7958 | 60/18723 | 1.24e-06 | 1.81e-05 | 44 |
| GO:004300121 | Liver | HCC | Golgi to plasma membrane protein transport | 32/7958 | 40/18723 | 1.40e-06 | 2.01e-05 | 32 |
| GO:006195111 | Liver | HCC | establishment of protein localization to plasma membrane | 41/7958 | 60/18723 | 4.65e-05 | 4.49e-04 | 41 |
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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 |
| 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. |
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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 |
| AMN | SNV | Missense_Mutation | c.391N>A | p.Asp131Asn | p.D131N | Q9BXJ7 | protein_coding | deleterious(0.01) | probably_damaging(0.989) | TCGA-AR-A24H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| AMN | deletion | Frame_Shift_Del | novel | c.409delN | p.Cys137AlafsTer62 | p.C137Afs*62 | Q9BXJ7 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| AMN | SNV | Missense_Mutation | rs866956966 | c.193N>A | p.Ala65Thr | p.A65T | Q9BXJ7 | protein_coding | tolerated(0.21) | benign(0.09) | TCGA-D5-6530-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| AMN | SNV | Missense_Mutation | c.86N>G | p.Asp29Gly | p.D29G | Q9BXJ7 | protein_coding | tolerated(0.06) | benign(0.086) | TCGA-EI-6511-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatinum+5-fu | SD | |
| AMN | SNV | Missense_Mutation | c.56N>T | p.Ala19Val | p.A19V | Q9BXJ7 | protein_coding | deleterious(0) | probably_damaging(0.95) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| AMN | SNV | Missense_Mutation | novel | c.211C>A | p.Leu71Met | p.L71M | Q9BXJ7 | protein_coding | deleterious(0.04) | probably_damaging(0.994) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| AMN | SNV | Missense_Mutation | novel | c.709N>A | p.Ala237Thr | p.A237T | Q9BXJ7 | protein_coding | tolerated(0.36) | benign(0.297) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| AMN | SNV | Missense_Mutation | novel | c.763N>A | p.Ala255Thr | p.A255T | Q9BXJ7 | protein_coding | deleterious(0) | benign(0.346) | TCGA-B5-A1MR-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| AMN | SNV | Missense_Mutation | c.401N>A | p.Arg134His | p.R134H | Q9BXJ7 | protein_coding | deleterious(0) | probably_damaging(0.933) | TCGA-D1-A103-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| AMN | SNV | Missense_Mutation | c.86N>T | p.Asp29Val | p.D29V | Q9BXJ7 | protein_coding | deleterious(0) | benign(0.39) | TCGA-D1-A2G5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
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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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