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Gene: BHMT |
Gene summary for BHMT |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | BHMT | Gene ID | 635 |
| Gene name | betaine--homocysteine S-methyltransferase | |
| Gene Alias | BHMT1 | |
| Cytomap | 5q14.1 | |
| Gene Type | protein-coding | GO ID | GO:0000096 | UniProtAcc | Q93088 |
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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 |
| 635 | BHMT | NAFLD1 | Human | Liver | NAFLD | 1.78e-09 | 1.24e+00 | -0.04 |
| 635 | BHMT | HCC2_Meng | Human | Liver | HCC | 4.33e-03 | -1.86e-01 | 0.0107 |
| 635 | BHMT | cirrhotic3 | Human | Liver | Cirrhotic | 2.51e-02 | -1.87e-01 | 0.0215 |
| 635 | BHMT | HCC1 | Human | Liver | HCC | 1.46e-25 | 3.96e+00 | 0.5336 |
| 635 | BHMT | HCC2 | Human | Liver | HCC | 6.21e-05 | 2.14e+00 | 0.5341 |
| 635 | BHMT | Pt14.b | Human | Liver | HCC | 8.57e-08 | 3.63e-01 | 0.018 |
| 635 | BHMT | S014 | Human | Liver | HCC | 6.14e-13 | 7.75e-01 | 0.2254 |
| 635 | BHMT | S015 | Human | Liver | HCC | 3.14e-15 | 1.16e+00 | 0.2375 |
| 635 | BHMT | S016 | Human | Liver | HCC | 1.62e-12 | 6.57e-01 | 0.2243 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:00160535 | Liver | NAFLD | organic acid biosynthetic process | 77/1882 | 316/18723 | 1.03e-13 | 6.69e-11 | 77 |
| GO:00463945 | Liver | NAFLD | carboxylic acid biosynthetic process | 75/1882 | 314/18723 | 6.37e-13 | 3.39e-10 | 75 |
| GO:00442707 | Liver | NAFLD | cellular nitrogen compound catabolic process | 93/1882 | 451/18723 | 1.04e-11 | 4.34e-09 | 93 |
| GO:00065203 | Liver | NAFLD | cellular amino acid metabolic process | 63/1882 | 284/18723 | 1.14e-09 | 2.17e-07 | 63 |
| GO:00086523 | Liver | NAFLD | cellular amino acid biosynthetic process | 26/1882 | 76/18723 | 1.00e-08 | 1.33e-06 | 26 |
| GO:19016053 | Liver | NAFLD | alpha-amino acid metabolic process | 46/1882 | 195/18723 | 2.74e-08 | 2.86e-06 | 46 |
| GO:19016073 | Liver | NAFLD | alpha-amino acid biosynthetic process | 22/1882 | 68/18723 | 4.13e-07 | 2.62e-05 | 22 |
| GO:00620125 | Liver | NAFLD | regulation of small molecule metabolic process | 63/1882 | 334/18723 | 6.55e-07 | 3.79e-05 | 63 |
| GO:00067904 | Liver | NAFLD | sulfur compound metabolic process | 58/1882 | 339/18723 | 3.79e-05 | 9.38e-04 | 58 |
| GO:0009066 | Liver | NAFLD | aspartate family amino acid metabolic process | 15/1882 | 49/18723 | 5.88e-05 | 1.30e-03 | 15 |
| GO:0000096 | Liver | NAFLD | sulfur amino acid metabolic process | 12/1882 | 34/18723 | 6.82e-05 | 1.45e-03 | 12 |
| GO:0009067 | Liver | NAFLD | aspartate family amino acid biosynthetic process | 9/1882 | 21/18723 | 9.81e-05 | 1.97e-03 | 9 |
| GO:0006555 | Liver | NAFLD | methionine metabolic process | 7/1882 | 16/18723 | 5.17e-04 | 7.15e-03 | 7 |
| GO:00064793 | Liver | NAFLD | protein methylation | 33/1882 | 181/18723 | 5.36e-04 | 7.35e-03 | 33 |
| GO:00082133 | Liver | NAFLD | protein alkylation | 33/1882 | 181/18723 | 5.36e-04 | 7.35e-03 | 33 |
| GO:0009086 | Liver | NAFLD | methionine biosynthetic process | 6/1882 | 12/18723 | 5.54e-04 | 7.46e-03 | 6 |
| GO:0044272 | Liver | NAFLD | sulfur compound biosynthetic process | 28/1882 | 148/18723 | 7.52e-04 | 9.52e-03 | 28 |
| GO:0000097 | Liver | NAFLD | sulfur amino acid biosynthetic process | 7/1882 | 17/18723 | 8.03e-04 | 9.95e-03 | 7 |
| GO:00105653 | Liver | NAFLD | regulation of cellular ketone metabolic process | 25/1882 | 133/18723 | 1.54e-03 | 1.66e-02 | 25 |
| GO:00421803 | Liver | NAFLD | cellular ketone metabolic process | 35/1882 | 211/18723 | 2.09e-03 | 2.06e-02 | 35 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa00270 | Liver | Cirrhotic | Cysteine and methionine metabolism | 27/2530 | 52/8465 | 6.98e-04 | 4.15e-03 | 2.56e-03 | 27 |
| hsa00260 | Liver | Cirrhotic | Glycine, serine and threonine metabolism | 22/2530 | 40/8465 | 7.85e-04 | 4.51e-03 | 2.78e-03 | 22 |
| hsa002701 | Liver | Cirrhotic | Cysteine and methionine metabolism | 27/2530 | 52/8465 | 6.98e-04 | 4.15e-03 | 2.56e-03 | 27 |
| hsa002601 | Liver | Cirrhotic | Glycine, serine and threonine metabolism | 22/2530 | 40/8465 | 7.85e-04 | 4.51e-03 | 2.78e-03 | 22 |
| hsa002602 | Liver | HCC | Glycine, serine and threonine metabolism | 28/4020 | 40/8465 | 3.28e-03 | 1.07e-02 | 5.93e-03 | 28 |
| hsa002603 | Liver | HCC | Glycine, serine and threonine metabolism | 28/4020 | 40/8465 | 3.28e-03 | 1.07e-02 | 5.93e-03 | 28 |
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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 |
| BHMT | SNV | Missense_Mutation | rs376343021 | c.76N>A | p.Asp26Asn | p.D26N | Q93088 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| BHMT | SNV | Missense_Mutation | c.215N>C | p.Gln72Pro | p.Q72P | Q93088 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-B6-A0X5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| BHMT | insertion | In_Frame_Ins | novel | c.476_477insAGAGTACCT | p.Glu159_Tyr160insGluTyrLeu | p.E159_Y160insEYL | Q93088 | protein_coding | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| BHMT | SNV | Missense_Mutation | rs757263273 | c.362G>A | p.Gly121Glu | p.G121E | Q93088 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| BHMT | SNV | Missense_Mutation | c.607N>C | p.Val203Leu | p.V203L | Q93088 | protein_coding | tolerated(0.07) | possibly_damaging(0.501) | TCGA-ZJ-AAXF-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| BHMT | SNV | Missense_Mutation | rs758515635 | c.346N>A | p.Ala116Thr | p.A116T | Q93088 | protein_coding | tolerated(0.08) | possibly_damaging(0.839) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| BHMT | SNV | Missense_Mutation | c.213G>A | p.Met71Ile | p.M71I | Q93088 | protein_coding | tolerated(0.28) | benign(0.007) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
| BHMT | SNV | Missense_Mutation | c.101A>T | p.Glu34Val | p.E34V | Q93088 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-F4-6570-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| BHMT | SNV | Missense_Mutation | c.769N>G | p.Asn257Asp | p.N257D | Q93088 | protein_coding | tolerated(0.42) | benign(0.027) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| BHMT | SNV | Missense_Mutation | rs111297335 | c.323G>A | p.Arg108Gln | p.R108Q | Q93088 | protein_coding | tolerated(0.05) | benign(0.039) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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 |
| 635 | BHMT | DRUGGABLE GENOME, ENZYME | CHEMBL1201130 | BETAINE HYDROCHLORIDE |
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