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Gene: MTHFR |
Gene summary for MTHFR |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MTHFR | Gene ID | 4524 |
| Gene name | methylenetetrahydrofolate reductase | |
| Gene Alias | MTHFR | |
| Cytomap | 1p36.22 | |
| Gene Type | protein-coding | GO ID | GO:0000096 | UniProtAcc | P42898 |
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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 |
| 4524 | MTHFR | LZE4T | Human | Esophagus | ESCC | 7.78e-03 | 7.10e-02 | 0.0811 |
| 4524 | MTHFR | LZE7T | Human | Esophagus | ESCC | 9.25e-04 | 1.67e-01 | 0.0667 |
| 4524 | MTHFR | LZE20T | Human | Esophagus | ESCC | 4.13e-02 | 6.77e-02 | 0.0662 |
| 4524 | MTHFR | LZE22T | Human | Esophagus | ESCC | 4.49e-02 | 1.94e-01 | 0.068 |
| 4524 | MTHFR | LZE24T | Human | Esophagus | ESCC | 3.31e-05 | 1.70e-01 | 0.0596 |
| 4524 | MTHFR | P1T-E | Human | Esophagus | ESCC | 1.97e-07 | 2.67e-01 | 0.0875 |
| 4524 | MTHFR | P2T-E | Human | Esophagus | ESCC | 7.02e-09 | 1.35e-01 | 0.1177 |
| 4524 | MTHFR | P4T-E | Human | Esophagus | ESCC | 1.90e-10 | 1.01e-01 | 0.1323 |
| 4524 | MTHFR | P5T-E | Human | Esophagus | ESCC | 4.32e-04 | 8.17e-02 | 0.1327 |
| 4524 | MTHFR | P8T-E | Human | Esophagus | ESCC | 3.82e-11 | 2.24e-01 | 0.0889 |
| 4524 | MTHFR | P9T-E | Human | Esophagus | ESCC | 4.37e-06 | 9.33e-02 | 0.1131 |
| 4524 | MTHFR | P10T-E | Human | Esophagus | ESCC | 7.70e-05 | 1.21e-01 | 0.116 |
| 4524 | MTHFR | P15T-E | Human | Esophagus | ESCC | 3.12e-09 | 1.29e-01 | 0.1149 |
| 4524 | MTHFR | P16T-E | Human | Esophagus | ESCC | 2.32e-06 | 7.47e-02 | 0.1153 |
| 4524 | MTHFR | P20T-E | Human | Esophagus | ESCC | 7.12e-06 | 8.59e-02 | 0.1124 |
| 4524 | MTHFR | P21T-E | Human | Esophagus | ESCC | 5.55e-17 | 1.33e-01 | 0.1617 |
| 4524 | MTHFR | P23T-E | Human | Esophagus | ESCC | 2.42e-07 | 8.25e-02 | 0.108 |
| 4524 | MTHFR | P24T-E | Human | Esophagus | ESCC | 9.19e-06 | 4.99e-02 | 0.1287 |
| 4524 | MTHFR | P26T-E | Human | Esophagus | ESCC | 2.71e-05 | 4.24e-02 | 0.1276 |
| 4524 | MTHFR | P27T-E | Human | Esophagus | ESCC | 2.68e-05 | 1.78e-01 | 0.1055 |
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| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:0031667111 | Esophagus | ESCC | response to nutrient levels | 289/8552 | 474/18723 | 9.25e-12 | 3.47e-10 | 289 |
| GO:0070482111 | Esophagus | ESCC | response to oxygen levels | 218/8552 | 347/18723 | 6.91e-11 | 2.17e-09 | 218 |
| GO:00434143 | Esophagus | ESCC | macromolecule methylation | 199/8552 | 316/18723 | 3.44e-10 | 9.57e-09 | 199 |
| GO:0036293111 | Esophagus | ESCC | response to decreased oxygen levels | 201/8552 | 322/18723 | 8.37e-10 | 2.04e-08 | 201 |
| GO:003105614 | Esophagus | ESCC | regulation of histone modification | 106/8552 | 152/18723 | 1.52e-09 | 3.55e-08 | 106 |
| GO:0001666111 | Esophagus | ESCC | response to hypoxia | 192/8552 | 307/18723 | 1.59e-09 | 3.69e-08 | 192 |
| GO:00322592 | Esophagus | ESCC | methylation | 222/8552 | 364/18723 | 2.26e-09 | 5.09e-08 | 222 |
| GO:000184115 | Esophagus | ESCC | neural tube formation | 75/8552 | 102/18723 | 9.68e-09 | 1.95e-07 | 75 |
| GO:000184314 | Esophagus | ESCC | neural tube closure | 66/8552 | 88/18723 | 1.98e-08 | 3.82e-07 | 66 |
| GO:001402014 | Esophagus | ESCC | primary neural tube formation | 69/8552 | 94/18723 | 4.22e-08 | 7.76e-07 | 69 |
| GO:006060614 | Esophagus | ESCC | tube closure | 66/8552 | 89/18723 | 4.24e-08 | 7.76e-07 | 66 |
| GO:000758410 | Esophagus | ESCC | response to nutrient | 114/8552 | 174/18723 | 9.43e-08 | 1.56e-06 | 114 |
| GO:00219159 | Esophagus | ESCC | neural tube development | 101/8552 | 152/18723 | 1.78e-07 | 2.79e-06 | 101 |
| GO:00163316 | Esophagus | ESCC | morphogenesis of embryonic epithelium | 98/8552 | 147/18723 | 2.12e-07 | 3.27e-06 | 98 |
| GO:00067906 | Esophagus | ESCC | sulfur compound metabolic process | 201/8552 | 339/18723 | 2.64e-07 | 3.94e-06 | 201 |
| GO:000183814 | Esophagus | ESCC | embryonic epithelial tube formation | 83/8552 | 121/18723 | 2.78e-07 | 4.08e-06 | 83 |
| 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:003514815 | Esophagus | ESCC | tube formation | 96/8552 | 148/18723 | 1.86e-06 | 2.16e-05 | 96 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa015232 | Esophagus | ESCC | Antifolate resistance | 22/4205 | 30/8465 | 7.23e-03 | 1.76e-02 | 8.99e-03 | 22 |
| hsa0152311 | Esophagus | ESCC | Antifolate resistance | 22/4205 | 30/8465 | 7.23e-03 | 1.76e-02 | 8.99e-03 | 22 |
| hsa006702 | Liver | HCC | One carbon pool by folate | 17/4020 | 20/8465 | 6.04e-04 | 2.50e-03 | 1.39e-03 | 17 |
| hsa01523 | Liver | HCC | Antifolate resistance | 21/4020 | 30/8465 | 1.06e-02 | 2.71e-02 | 1.51e-02 | 21 |
| hsa0067011 | Liver | HCC | One carbon pool by folate | 17/4020 | 20/8465 | 6.04e-04 | 2.50e-03 | 1.39e-03 | 17 |
| hsa015231 | Liver | HCC | Antifolate resistance | 21/4020 | 30/8465 | 1.06e-02 | 2.71e-02 | 1.51e-02 | 21 |
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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 |
| MTHFR | SNV | Missense_Mutation | c.632G>A | p.Gly211Glu | p.G211E | P42898 | protein_coding | tolerated(0.18) | benign(0.01) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| MTHFR | SNV | Missense_Mutation | rs757268352 | c.1390N>A | p.Glu464Lys | p.E464K | P42898 | protein_coding | tolerated(0.21) | benign(0.013) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| MTHFR | SNV | Missense_Mutation | c.1681G>C | p.Glu561Gln | p.E561Q | P42898 | protein_coding | tolerated(0.08) | possibly_damaging(0.623) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| MTHFR | SNV | Missense_Mutation | c.1585A>G | p.Ile529Val | p.I529V | P42898 | protein_coding | tolerated(1) | benign(0.003) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| MTHFR | SNV | Missense_Mutation | c.1499N>T | p.Pro500Leu | p.P500L | P42898 | protein_coding | tolerated(0.07) | possibly_damaging(0.741) | TCGA-C5-A1M9-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD | |
| MTHFR | SNV | Missense_Mutation | rs772932189 | c.596N>A | p.Gly199Glu | p.G199E | P42898 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-C5-A1MH-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | PD |
| MTHFR | SNV | Missense_Mutation | rs121434297 | c.1091N>C | p.Leu364Pro | p.L364P | P42898 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-C5-A3HL-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| MTHFR | SNV | Missense_Mutation | c.456N>A | p.Met152Ile | p.M152I | P42898 | protein_coding | tolerated(0.19) | benign(0.001) | TCGA-EK-A2R7-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| MTHFR | SNV | Missense_Mutation | c.139A>G | p.Arg47Gly | p.R47G | P42898 | protein_coding | tolerated_low_confidence(0.07) | benign(0) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| MTHFR | SNV | Missense_Mutation | novel | c.867N>G | p.Ile289Met | p.I289M | P42898 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-ZJ-AB0I-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | 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 |
| 4524 | MTHFR | ENZYME, CLINICALLY ACTIONABLE | pravastatin | PRAVASTATIN | 18622257 | |
| 4524 | MTHFR | ENZYME, CLINICALLY ACTIONABLE | sulfasalazine | SULFASALAZINE | 12083967 | |
| 4524 | MTHFR | ENZYME, CLINICALLY ACTIONABLE | ETHANOL | ALCOHOL | 15894672 | |
| 4524 | MTHFR | ENZYME, CLINICALLY ACTIONABLE | olanzapine | OLANZAPINE | 24725652 | |
| 4524 | MTHFR | ENZYME, CLINICALLY ACTIONABLE | ALBUMIN | ALBUMIN HUMAN | 11531629 | |
| 4524 | MTHFR | ENZYME, CLINICALLY ACTIONABLE | leucovorin | LEUCOVORIN | 18245544,17700593,29845393,27864592,20819423,29134491,25331073,20385995,27557140,24980946,23407049 | |
| 4524 | MTHFR | ENZYME, CLINICALLY ACTIONABLE | l-methylfolate | 27035272,27520898,31058543 | ||
| 4524 | MTHFR | ENZYME, CLINICALLY ACTIONABLE | cisplatin | CISPLATIN | 21605004,29662106,27995989,20634689,19159907,19307503 | |
| 4524 | MTHFR | ENZYME, CLINICALLY ACTIONABLE | Vitamin B-complex, Incl. Combinations | 27035272,27520898,31058543 | ||
| 4524 | MTHFR | ENZYME, CLINICALLY ACTIONABLE | pemetrexed | PEMETREXED | 29662106,24732178,20634689,19307503 |
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