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Gene: ARMT1 |
Gene summary for ARMT1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ARMT1 | Gene ID | 79624 |
| Gene name | acidic residue methyltransferase 1 | |
| Gene Alias | C6orf211 | |
| Cytomap | 6q25.1 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | B4DPT6 |
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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 |
| 79624 | ARMT1 | GSM4909289 | Human | Breast | IDC | 4.68e-06 | 6.17e-01 | 0.1064 |
| 79624 | ARMT1 | GSM4909293 | Human | Breast | IDC | 6.92e-68 | 1.04e+00 | 0.1581 |
| 79624 | ARMT1 | GSM4909296 | Human | Breast | IDC | 3.78e-06 | -1.11e-01 | 0.1524 |
| 79624 | ARMT1 | GSM4909297 | Human | Breast | IDC | 2.69e-03 | -5.44e-02 | 0.1517 |
| 79624 | ARMT1 | GSM4909304 | Human | Breast | IDC | 6.04e-39 | 7.51e-01 | 0.1636 |
| 79624 | ARMT1 | GSM4909306 | Human | Breast | IDC | 1.63e-13 | 5.03e-01 | 0.1564 |
| 79624 | ARMT1 | GSM4909311 | Human | Breast | IDC | 1.15e-07 | 7.37e-02 | 0.1534 |
| 79624 | ARMT1 | GSM4909312 | Human | Breast | IDC | 4.99e-14 | 4.67e-01 | 0.1552 |
| 79624 | ARMT1 | GSM4909315 | Human | Breast | IDC | 2.67e-15 | 5.67e-01 | 0.21 |
| 79624 | ARMT1 | GSM4909316 | Human | Breast | IDC | 3.57e-07 | 5.80e-01 | 0.21 |
| 79624 | ARMT1 | GSM4909319 | Human | Breast | IDC | 1.50e-07 | -7.44e-02 | 0.1563 |
| 79624 | ARMT1 | M1 | Human | Breast | IDC | 3.86e-09 | 4.77e-01 | 0.1577 |
| 79624 | ARMT1 | P1 | Human | Breast | IDC | 6.53e-05 | 2.10e-01 | 0.1527 |
| 79624 | ARMT1 | DCIS2 | Human | Breast | DCIS | 3.44e-15 | -1.19e-02 | 0.0085 |
| 79624 | ARMT1 | LZE4T | Human | Esophagus | ESCC | 3.29e-04 | 1.40e-01 | 0.0811 |
| 79624 | ARMT1 | LZE8T | Human | Esophagus | ESCC | 7.31e-03 | 1.03e-01 | 0.067 |
| 79624 | ARMT1 | LZE24T | Human | Esophagus | ESCC | 1.13e-09 | 2.06e-01 | 0.0596 |
| 79624 | ARMT1 | P2T-E | Human | Esophagus | ESCC | 3.25e-19 | 3.87e-01 | 0.1177 |
| 79624 | ARMT1 | P4T-E | Human | Esophagus | ESCC | 3.04e-18 | 5.12e-01 | 0.1323 |
| 79624 | ARMT1 | P5T-E | Human | Esophagus | ESCC | 8.29e-17 | 2.50e-01 | 0.1327 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| 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:200102013 | Breast | IDC | regulation of response to DNA damage stimulus | 30/1434 | 219/18723 | 1.36e-03 | 1.40e-02 | 30 |
| GO:200102023 | Breast | DCIS | regulation of response to DNA damage stimulus | 30/1390 | 219/18723 | 8.32e-04 | 9.47e-03 | 30 |
| GO:00434143 | Esophagus | ESCC | macromolecule methylation | 199/8552 | 316/18723 | 3.44e-10 | 9.57e-09 | 199 |
| GO:2001020110 | Esophagus | ESCC | regulation of response to DNA damage stimulus | 145/8552 | 219/18723 | 5.97e-10 | 1.50e-08 | 145 |
| GO:001631110 | Esophagus | ESCC | dephosphorylation | 251/8552 | 417/18723 | 1.26e-09 | 2.99e-08 | 251 |
| GO:00322592 | Esophagus | ESCC | methylation | 222/8552 | 364/18723 | 2.26e-09 | 5.09e-08 | 222 |
| GO:000647914 | Esophagus | ESCC | protein methylation | 115/8552 | 181/18723 | 9.07e-07 | 1.16e-05 | 115 |
| GO:000821314 | Esophagus | ESCC | protein alkylation | 115/8552 | 181/18723 | 9.07e-07 | 1.16e-05 | 115 |
| GO:200102011 | Liver | Cirrhotic | regulation of response to DNA damage stimulus | 75/4634 | 219/18723 | 9.75e-04 | 6.89e-03 | 75 |
| GO:001631111 | Liver | Cirrhotic | dephosphorylation | 130/4634 | 417/18723 | 1.58e-03 | 1.03e-02 | 130 |
| GO:00064791 | Liver | Cirrhotic | protein methylation | 61/4634 | 181/18723 | 4.13e-03 | 2.21e-02 | 61 |
| GO:00082131 | Liver | Cirrhotic | protein alkylation | 61/4634 | 181/18723 | 4.13e-03 | 2.21e-02 | 61 |
| GO:00434141 | Liver | HCC | macromolecule methylation | 183/7958 | 316/18723 | 2.00e-08 | 4.72e-07 | 183 |
| GO:0032259 | Liver | HCC | methylation | 206/7958 | 364/18723 | 3.35e-08 | 7.53e-07 | 206 |
| GO:001631121 | Liver | HCC | dephosphorylation | 230/7958 | 417/18723 | 1.00e-07 | 1.96e-06 | 230 |
| GO:00064792 | Liver | HCC | protein methylation | 111/7958 | 181/18723 | 2.36e-07 | 4.18e-06 | 111 |
| GO:00082132 | Liver | HCC | protein alkylation | 111/7958 | 181/18723 | 2.36e-07 | 4.18e-06 | 111 |
| GO:200102021 | Liver | HCC | regulation of response to DNA damage stimulus | 128/7958 | 219/18723 | 1.31e-06 | 1.90e-05 | 128 |
| GO:200102017 | Oral cavity | OSCC | regulation of response to DNA damage stimulus | 131/7305 | 219/18723 | 3.21e-10 | 8.72e-09 | 131 |
| GO:00163119 | Oral cavity | OSCC | dephosphorylation | 220/7305 | 417/18723 | 6.33e-09 | 1.34e-07 | 220 |
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| 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 |
| ARMT1 | SNV | Missense_Mutation | c.22C>G | p.Leu8Val | p.L8V | Q9H993 | protein_coding | deleterious(0.03) | benign(0.197) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| ARMT1 | deletion | Frame_Shift_Del | c.429_430delNN | p.Lys144ArgfsTer26 | p.K144Rfs*26 | Q9H993 | protein_coding | TCGA-EW-A1IZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxotere | SD | |||
| ARMT1 | SNV | Missense_Mutation | rs778214484 | c.602N>A | p.Gly201Glu | p.G201E | Q9H993 | protein_coding | deleterious(0) | possibly_damaging(0.612) | TCGA-C5-A1BQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | CR |
| ARMT1 | SNV | Missense_Mutation | c.772G>C | p.Glu258Gln | p.E258Q | Q9H993 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| ARMT1 | SNV | Missense_Mutation | rs560894715 | c.181C>A | p.Leu61Ile | p.L61I | Q9H993 | protein_coding | tolerated(0.19) | benign(0.139) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| ARMT1 | SNV | Missense_Mutation | novel | c.168N>T | p.Lys56Asn | p.K56N | Q9H993 | protein_coding | deleterious(0) | probably_damaging(0.927) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| ARMT1 | SNV | Missense_Mutation | novel | c.70A>G | p.Arg24Gly | p.R24G | Q9H993 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-AA-A00O-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| ARMT1 | SNV | Missense_Mutation | c.922A>G | p.Asn308Asp | p.N308D | Q9H993 | protein_coding | tolerated(0.16) | benign(0.017) | TCGA-AA-A02R-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| ARMT1 | SNV | Missense_Mutation | c.92N>G | p.Lys31Arg | p.K31R | Q9H993 | protein_coding | tolerated(0.21) | benign(0.053) | TCGA-D5-6530-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| ARMT1 | SNV | Missense_Mutation | novel | c.1193N>A | p.Cys398Tyr | p.C398Y | Q9H993 | protein_coding | deleterious(0) | probably_damaging(0.962) | TCGA-G4-6302-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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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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