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Gene: CARM1 |
Gene summary for CARM1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CARM1 | Gene ID | 10498 |
| Gene name | coactivator associated arginine methyltransferase 1 | |
| Gene Alias | PRMT4 | |
| Cytomap | 19p13.2 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | Q86X55 |
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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 |
| 10498 | CARM1 | LZE4T | Human | Esophagus | ESCC | 1.63e-02 | 6.60e-02 | 0.0811 |
| 10498 | CARM1 | LZE7T | Human | Esophagus | ESCC | 4.62e-09 | 3.55e-01 | 0.0667 |
| 10498 | CARM1 | LZE20T | Human | Esophagus | ESCC | 7.59e-05 | 1.11e-01 | 0.0662 |
| 10498 | CARM1 | LZE22T | Human | Esophagus | ESCC | 3.69e-02 | 1.47e-01 | 0.068 |
| 10498 | CARM1 | LZE24T | Human | Esophagus | ESCC | 6.71e-10 | 2.41e-01 | 0.0596 |
| 10498 | CARM1 | LZE21T | Human | Esophagus | ESCC | 2.86e-05 | 3.74e-01 | 0.0655 |
| 10498 | CARM1 | P1T-E | Human | Esophagus | ESCC | 1.17e-03 | 3.23e-01 | 0.0875 |
| 10498 | CARM1 | P2T-E | Human | Esophagus | ESCC | 3.63e-11 | 1.02e-01 | 0.1177 |
| 10498 | CARM1 | P4T-E | Human | Esophagus | ESCC | 4.22e-17 | 3.28e-01 | 0.1323 |
| 10498 | CARM1 | P5T-E | Human | Esophagus | ESCC | 1.67e-18 | 2.18e-01 | 0.1327 |
| 10498 | CARM1 | P8T-E | Human | Esophagus | ESCC | 5.31e-19 | 2.99e-01 | 0.0889 |
| 10498 | CARM1 | P9T-E | Human | Esophagus | ESCC | 1.06e-18 | 3.37e-01 | 0.1131 |
| 10498 | CARM1 | P10T-E | Human | Esophagus | ESCC | 1.29e-22 | 3.95e-01 | 0.116 |
| 10498 | CARM1 | P12T-E | Human | Esophagus | ESCC | 1.59e-17 | 3.76e-01 | 0.1122 |
| 10498 | CARM1 | P15T-E | Human | Esophagus | ESCC | 1.57e-08 | 1.66e-01 | 0.1149 |
| 10498 | CARM1 | P16T-E | Human | Esophagus | ESCC | 1.24e-10 | 6.52e-02 | 0.1153 |
| 10498 | CARM1 | P17T-E | Human | Esophagus | ESCC | 5.39e-06 | 1.78e-01 | 0.1278 |
| 10498 | CARM1 | P20T-E | Human | Esophagus | ESCC | 6.89e-06 | 7.70e-02 | 0.1124 |
| 10498 | CARM1 | P21T-E | Human | Esophagus | ESCC | 4.19e-16 | 2.21e-01 | 0.1617 |
| 10498 | CARM1 | P22T-E | Human | Esophagus | ESCC | 1.43e-18 | 2.12e-01 | 0.1236 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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:001657015 | Esophagus | ESCC | histone modification | 323/8552 | 463/18723 | 2.61e-26 | 7.88e-24 | 323 |
| GO:0051098111 | Esophagus | ESCC | regulation of binding | 251/8552 | 363/18723 | 6.73e-20 | 8.46e-18 | 251 |
| GO:00434143 | Esophagus | ESCC | macromolecule methylation | 199/8552 | 316/18723 | 3.44e-10 | 9.57e-09 | 199 |
| GO:0030522110 | Esophagus | ESCC | intracellular receptor signaling pathway | 170/8552 | 265/18723 | 8.58e-10 | 2.09e-08 | 170 |
| GO:00322592 | Esophagus | ESCC | methylation | 222/8552 | 364/18723 | 2.26e-09 | 5.09e-08 | 222 |
| GO:0048545111 | Esophagus | ESCC | response to steroid hormone | 204/8552 | 339/18723 | 4.47e-08 | 8.11e-07 | 204 |
| GO:000756820 | Esophagus | ESCC | aging | 201/8552 | 339/18723 | 2.64e-07 | 3.94e-06 | 201 |
| 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:0071383110 | Esophagus | ESCC | cellular response to steroid hormone stimulus | 127/8552 | 204/18723 | 1.26e-06 | 1.55e-05 | 127 |
| GO:003051819 | Esophagus | ESCC | intracellular steroid hormone receptor signaling pathway | 76/8552 | 116/18723 | 1.25e-05 | 1.15e-04 | 76 |
| GO:004340119 | Esophagus | ESCC | steroid hormone mediated signaling pathway | 87/8552 | 136/18723 | 1.25e-05 | 1.15e-04 | 87 |
| GO:00165718 | Esophagus | ESCC | histone methylation | 89/8552 | 141/18723 | 2.17e-05 | 1.87e-04 | 89 |
| GO:00454449 | Esophagus | ESCC | fat cell differentiation | 135/8552 | 229/18723 | 3.38e-05 | 2.78e-04 | 135 |
| GO:00456007 | Esophagus | ESCC | positive regulation of fat cell differentiation | 46/8552 | 66/18723 | 6.72e-05 | 5.11e-04 | 46 |
| GO:19052142 | Esophagus | ESCC | regulation of RNA binding | 12/8552 | 12/18723 | 8.21e-05 | 6.01e-04 | 12 |
| GO:00331438 | Esophagus | ESCC | regulation of intracellular steroid hormone receptor signaling pathway | 50/8552 | 74/18723 | 1.16e-04 | 8.04e-04 | 50 |
| GO:001097516 | Esophagus | ESCC | regulation of neuron projection development | 240/8552 | 445/18723 | 2.48e-04 | 1.53e-03 | 240 |
| GO:000975516 | Esophagus | ESCC | hormone-mediated signaling pathway | 106/8552 | 190/18723 | 3.13e-03 | 1.30e-02 | 106 |
| GO:003052014 | Esophagus | ESCC | intracellular estrogen receptor signaling pathway | 35/8552 | 54/18723 | 3.55e-03 | 1.45e-02 | 35 |
| Page: 1 2 3 4 5 6 7 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa015227 | Esophagus | ESCC | Endocrine resistance | 63/4205 | 98/8465 | 2.38e-03 | 6.58e-03 | 3.37e-03 | 63 |
| hsa0152215 | Esophagus | ESCC | Endocrine resistance | 63/4205 | 98/8465 | 2.38e-03 | 6.58e-03 | 3.37e-03 | 63 |
| hsa01522 | Liver | HCC | Endocrine resistance | 58/4020 | 98/8465 | 1.28e-02 | 3.19e-02 | 1.78e-02 | 58 |
| hsa015221 | Liver | HCC | Endocrine resistance | 58/4020 | 98/8465 | 1.28e-02 | 3.19e-02 | 1.78e-02 | 58 |
| hsa015226 | Oral cavity | OSCC | Endocrine resistance | 63/3704 | 98/8465 | 3.09e-05 | 1.31e-04 | 6.67e-05 | 63 |
| hsa0152214 | Oral cavity | OSCC | Endocrine resistance | 63/3704 | 98/8465 | 3.09e-05 | 1.31e-04 | 6.67e-05 | 63 |
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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 |
| CARM1 | SNV | Missense_Mutation | novel | c.687C>A | p.Asn229Lys | p.N229K | Q86X55 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-A8-A08S-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD |
| CARM1 | SNV | Missense_Mutation | c.608N>T | p.Ala203Val | p.A203V | Q86X55 | protein_coding | tolerated(0.74) | benign(0.111) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CARM1 | SNV | Missense_Mutation | c.1560N>C | p.Leu520Phe | p.L520F | Q86X55 | protein_coding | deleterious_low_confidence(0.05) | probably_damaging(0.991) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CARM1 | SNV | Missense_Mutation | c.950N>T | p.Ser317Phe | p.S317F | Q86X55 | protein_coding | deleterious(0.02) | probably_damaging(0.969) | TCGA-E9-A1RG-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | tamoxiphen | SD | |
| CARM1 | insertion | Nonsense_Mutation | novel | c.377_378insACAGGCATAAGCCACCGTGCCCGGCTTATTATTTCTTGTAGAGA | p.Cys127GlnfsTer3 | p.C127Qfs*3 | Q86X55 | protein_coding | TCGA-A2-A0EQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| CARM1 | SNV | Missense_Mutation | novel | c.1255N>T | p.Arg419Trp | p.R419W | Q86X55 | protein_coding | deleterious(0.01) | possibly_damaging(0.771) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CARM1 | SNV | Missense_Mutation | c.330N>C | p.Gln110His | p.Q110H | Q86X55 | protein_coding | tolerated(0.09) | benign(0.106) | TCGA-JW-A5VI-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | topotecan | PD | |
| CARM1 | SNV | Missense_Mutation | rs765573504 | c.1204N>A | p.Val402Met | p.V402M | Q86X55 | protein_coding | deleterious(0.01) | probably_damaging(0.957) | TCGA-A6-2672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| CARM1 | SNV | Missense_Mutation | c.1430C>T | p.Thr477Met | p.T477M | Q86X55 | protein_coding | deleterious(0.01) | possibly_damaging(0.814) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| CARM1 | SNV | Missense_Mutation | c.1134N>T | p.Met378Ile | p.M378I | Q86X55 | protein_coding | tolerated(0.35) | benign(0.035) | TCGA-DM-A1HB-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | 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 |
| 10498 | CARM1 | ENZYME, METHYL TRANSFERASE, DRUGGABLE GENOME | inhibitor | 336446915 | ||
| 10498 | CARM1 | ENZYME, METHYL TRANSFERASE, DRUGGABLE GENOME | EOSIN | EOSIN | 18348515 | |
| 10498 | CARM1 | ENZYME, METHYL TRANSFERASE, DRUGGABLE GENOME | inhibitor | 178103610 | ||
| 10498 | CARM1 | ENZYME, METHYL TRANSFERASE, DRUGGABLE GENOME | inhibitor | 310264736 | ||
| 10498 | CARM1 | ENZYME, METHYL TRANSFERASE, DRUGGABLE GENOME | inhibitor | 315661334 | ||
| 10498 | CARM1 | ENZYME, METHYL TRANSFERASE, DRUGGABLE GENOME | inhibitor | 178103609 | ||
| 10498 | CARM1 | ENZYME, METHYL TRANSFERASE, DRUGGABLE GENOME | inhibitor | 315661333 | BIIB021 |
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