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Gene: ENSG00000132840 |
Summary for BHMT2 |
 Gene summary |
| Gene information | Ensembl ID | ENSG00000132840 | Gene symbol | BHMT2 |
| Gene name | betaine--homocysteine S-methyltransferase 2 | |
| HGNC | 1048 | |
| Entrez ID | 23743 | |
| Gene type | protein_coding | |
| Synonyms | BHMT2| | |
| UniProtAcc | Q9H2M3 |
| Drugs associated with this gene(DrugBank). |
| Gene ID | Gene Symbol | Drug ID | Drug Name | Drug Type |
| ENSG00000132840 | BHMT2 | DB00134 | Methionine | SmallMoleculeDrug |
| Cancer therapeutic drugs associated with this gene(NCI). |
| Gene ID | Gene Name | Drug ID | Drug Name | Drug Type | Cancer |
Top |
Structure and expression level for BHMT2 |
| AS events and RNA A-to-I editing events of the gene in TCGA based on Genvode V22 structure. ∗For more information on exon skipping events please check the ExonskipDB database. ∗For more information on exon skipping events please check the CAeditome database. |
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| Landscape of gene expressions across multiple cancer types. |
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| Differentially expressed gene analysis between tumor male and tumor female samples. |
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| Coding Name | Base Mean | log2FoldChange | lfcSE | Stat | P value | P.adjust Value | Cancer Type |
| BHMT2 | 2.15e+02 | -1.11e+00 | 3.88e-01 | -2.86e+00 | 4.24e-03 | 3.17e-02 | BRCA |
| Differentially expressed gene analysis between tumor male and normal male samples. |
 |
| Coding Name | Base Mean | log2FoldChange | lfcSE | Stat | P value | P.adjust Value | Cancer Type |
| BHMT2 | 7.74e+03 | -5.59e+00 | 8.23e-01 | -6.80e+00 | 1.05e-11 | 2.22e-10 | CHOL |
| Differentially expressed gene analysis between tumor female and normal female samples. |
 |
| Coding Name | Base Mean | log2FoldChange | lfcSE | Stat | P value | P.adjust Value | Cancer Type |
| BHMT2 | 1.03e+02 | -1.01e+00 | 4.66e-01 | -2.17e+00 | 2.97e-02 | 4.89e-02 | LUSC |
| BHMT2 | 1.19e+04 | -1.12e+00 | 3.11e-01 | -3.61e+00 | 3.07e-04 | 8.84e-04 | LIHC |
| BHMT2 | 3.70e+02 | -3.12e+00 | 1.34e-01 | -2.33e+01 | 1.01e-119 | 6.17e-118 | BRCA |
Top |
Sex-biased somatic mutation for BHMT2 |
| ∗For more information on exon skipping events please check the ExonskipDB database. |
| Gene ID | Cancer Type | Hugo Symbol | Male | Female | pval | or | ci.up | ci.low | adjPval |
Top |
DNA methylation with beta values for BHMT2 |
| Landscape of DNA methylation across multiple cancer types. |
 |
| Differentially expressed CpG sites between male tumor and female tumor patients. |
| Cancer Type | CpG Site | Position | CpG Island | Position to Gene | ave1 | ave2 | wilcoxon.w | wilcoxon.p | padj | dBeta |
| LIHC | cg17213304 | chr5:79068946 | CGI:chr5:79069475-79069888 | promoter | 7.01e-01 | 5.86e-01 | 4.65e+00 | 3.30e-06 | 4.13e-05 | 1.15e-01 |
| SARC | cg06501366 | chr5:79069864 | CGI:chr5:79069475-79069888 | promoter,gene body | 4.06e-01 | 2.83e-01 | 3.27e+00 | 1.09e-03 | 3.72e-03 | 1.23e-01 |
| SARC | cg08328513 | chr5:79069868 | CGI:chr5:79069475-79069888 | promoter,gene body | 3.33e-01 | 2.16e-01 | 2.83e+00 | 4.65e-03 | 1.09e-02 | 1.17e-01 |
| SARC | cg01856645 | chr5:79069824 | CGI:chr5:79069475-79069888 | promoter,gene body | 2.51e-01 | 1.36e-01 | 3.40e+00 | 6.80e-04 | 2.58e-03 | 1.14e-01 |
| UVM | cg03400060 | chr5:79069978 | CGI:chr5:79069475-79069888 | promoter,gene body | 5.43e-01 | 4.21e-01 | 2.30e+00 | 2.13e-02 | 3.50e-02 | 1.22e-01 |
| Differentially expressed CpG sites between male tumor and male normal patients. |
| Cancer Type | CpG Site | Position | CpG Island | Position to Gene | ave1 | ave2 | wilcoxon.w | wilcoxon.p | padj | dBeta |
| THCA | cg15089314 | chr5:79069432 | CGI:chr5:79069475-79069888 | promoter | 6.54e-01 | 7.75e-01 | -2.34e+00 | 1.92e-02 | 2.62e-02 | -1.21e-01 |
| LUSC | cg06501366 | chr5:79069864 | CGI:chr5:79069475-79069888 | promoter,gene body | 6.14e-01 | 3.32e-01 | 3.71e+00 | 2.10e-04 | 9.96e-04 | 2.82e-01 |
| LUSC | cg08328513 | chr5:79069868 | CGI:chr5:79069475-79069888 | promoter,gene body | 5.46e-01 | 2.16e-01 | 3.79e+00 | 1.52e-04 | 8.45e-04 | 3.29e-01 |
| LUSC | cg01856645 | chr5:79069824 | CGI:chr5:79069475-79069888 | promoter,gene body | 3.70e-01 | 7.42e-02 | 3.85e+00 | 1.17e-04 | 7.46e-04 | 2.96e-01 |
| LUSC | cg01902605 | chr5:79070253 | CGI:chr5:79069475-79069888 | promoter,gene body | 6.79e-01 | 5.00e-01 | 3.90e+00 | 9.43e-05 | 6.81e-04 | 1.79e-01 |
| LUSC | cg23911707 | chr5:79069887 | CGI:chr5:79069475-79069888 | promoter,gene body | 4.92e-01 | 2.70e-01 | 3.61e+00 | 3.03e-04 | 1.23e-03 | 2.22e-01 |
| LUSC | cg03400060 | chr5:79069978 | CGI:chr5:79069475-79069888 | promoter,gene body | 5.69e-01 | 3.66e-01 | 4.02e+00 | 5.76e-05 | 5.76e-04 | 2.02e-01 |
| BLCA | cg15089314 | chr5:79069432 | CGI:chr5:79069475-79069888 | promoter | 7.12e-01 | 5.29e-01 | 3.97e+00 | 7.21e-05 | 3.17e-04 | 1.83e-01 |
| LIHC | cg06501366 | chr5:79069864 | CGI:chr5:79069475-79069888 | promoter,gene body | 2.60e-01 | 3.93e-01 | -4.43e+00 | 9.43e-06 | 2.60e-05 | -1.33e-01 |
| LIHC | cg01902605 | chr5:79070253 | CGI:chr5:79069475-79069888 | promoter,gene body | 3.10e-01 | 4.22e-01 | -4.31e+00 | 1.63e-05 | 4.20e-05 | -1.12e-01 |
| KIRP | cg15089314 | chr5:79069432 | CGI:chr5:79069475-79069888 | promoter | 1.63e-01 | 2.82e-01 | -4.56e+00 | 5.04e-06 | 2.10e-05 | -1.20e-01 |
| CHOL | cg15089314 | chr5:79069432 | CGI:chr5:79069475-79069888 | promoter | 5.92e-01 | 1.84e-01 | 3.46e+00 | 5.30e-04 | 8.63e-03 | 4.08e-01 |
| CHOL | cg06501366 | chr5:79069864 | CGI:chr5:79069475-79069888 | promoter,gene body | 5.18e-01 | 3.05e-01 | 2.14e+00 | 3.25e-02 | 3.87e-02 | 2.13e-01 |
| CHOL | cg08328513 | chr5:79069868 | CGI:chr5:79069475-79069888 | promoter,gene body | 4.52e-01 | 2.16e-01 | 2.06e+00 | 3.90e-02 | 4.26e-02 | 2.37e-01 |
| CHOL | cg01902605 | chr5:79070253 | CGI:chr5:79069475-79069888 | promoter,gene body | 6.04e-01 | 3.87e-01 | 2.43e+00 | 1.50e-02 | 2.65e-02 | 2.16e-01 |
| CHOL | cg17213304 | chr5:79068946 | CGI:chr5:79069475-79069888 | promoter | 8.98e-01 | 4.81e-01 | 3.54e+00 | 4.02e-04 | 8.32e-03 | 4.17e-01 |
| CHOL | cg23911707 | chr5:79069887 | CGI:chr5:79069475-79069888 | promoter,gene body | 4.27e-01 | 2.42e-01 | 2.21e+00 | 2.70e-02 | 3.50e-02 | 1.85e-01 |
| CHOL | cg03400060 | chr5:79069978 | CGI:chr5:79069475-79069888 | promoter,gene body | 4.96e-01 | 3.01e-01 | 2.65e+00 | 7.96e-03 | 1.92e-02 | 1.95e-01 |
| Differentially expressed CpG sites between female tumor and female normal patients. |
| Cancer Type | CpG Site | Position | CpG Island | Position to Gene | ave1 | ave2 | wilcoxon.w | wilcoxon.p | padj | dBeta |
| BRCA | cg15089314 | chr5:79069432 | CGI:chr5:79069475-79069888 | promoter | 5.69e-01 | 4.20e-01 | 3.58e+00 | 3.46e-04 | 4.83e-04 | 1.49e-01 |
| BRCA | cg06501366 | chr5:79069864 | CGI:chr5:79069475-79069888 | promoter,gene body | 4.91e-01 | 2.57e-01 | 9.79e+00 | 1.24e-22 | 8.41e-22 | 2.34e-01 |
| BRCA | cg08328513 | chr5:79069868 | CGI:chr5:79069475-79069888 | promoter,gene body | 4.04e-01 | 1.45e-01 | 9.93e+00 | 3.09e-23 | 2.22e-22 | 2.59e-01 |
| BRCA | cg01856645 | chr5:79069824 | CGI:chr5:79069475-79069888 | promoter,gene body | 2.78e-01 | 7.34e-02 | 9.81e+00 | 1.03e-22 | 7.06e-22 | 2.05e-01 |
| BRCA | cg01902605 | chr5:79070253 | CGI:chr5:79069475-79069888 | promoter,gene body | 7.00e-01 | 5.08e-01 | 1.24e+01 | 1.50e-35 | 4.84e-34 | 1.91e-01 |
| BRCA | cg23911707 | chr5:79069887 | CGI:chr5:79069475-79069888 | promoter,gene body | 3.73e-01 | 2.09e-01 | 9.35e+00 | 9.18e-21 | 5.30e-20 | 1.64e-01 |
| BRCA | cg03400060 | chr5:79069978 | CGI:chr5:79069475-79069888 | promoter,gene body | 5.60e-01 | 3.81e-01 | 1.04e+01 | 3.24e-25 | 2.81e-24 | 1.78e-01 |
| LUAD | cg03400060 | chr5:79069978 | CGI:chr5:79069475-79069888 | promoter,gene body | 5.07e-01 | 4.00e-01 | 2.82e+00 | 4.80e-03 | 9.35e-03 | 1.06e-01 |
| LIHC | cg17213304 | chr5:79068946 | CGI:chr5:79069475-79069888 | promoter | 7.01e-01 | 4.81e-01 | 3.60e+00 | 3.17e-04 | 9.27e-04 | 2.20e-01 |
Top |
Exon skipping events with PSI in TCGA for BHMT2 |
| ∗Please access ExonSkipDB for exon skipping annotation. |
| Landscape of exon skipping events across multiple cancer types. |
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| Differentially expressed exon skipping events between male tumor and female tumor patients. |
| Cancer Type | Exon Skipping | ave.female_T | ave.female_N | wilcoxon.w | wilcoxon.p | padj | dPSI |
| Differentially expressed exon skipping events between male tumor and male normal patients. |
| Cancer Type | Exon Skipping | ave.female_T | ave.female_N | wilcoxon.w | wilcoxon.p | padj | dPSI |
| Differentially expressed exon skipping events between female tumor and female normal patients. |
| Cancer Type | Exon Skipping | ave.female_T | ave.female_N | wilcoxon.w | wilcoxon.p | padj | dPSI |
Top |
RNA A-to-I editing events in TCGA for BHMT2 |
| ∗Please access CAeditome for RNA editing annotation. |
| Differentially expressed RNA editing events between male tumor and female tumor patients. |
| Cancer Type | Transcript | Editing | ave.male_T | ave.female_T | wilcoxon.w | wilcoxon.p | p_adj | dFre |
| Differentially expressed RNA editing events between male tumor and male normal patients. |
| Cancer Type | Transcript | Editing | ave.male_T | ave.female_T | wilcoxon.w | wilcoxon.p | p_adj | dFre |
| Differentially expressed RNA editing events between female tumor and female normal patients. |
| Cancer Type | Transcript | Editing | ave.male_T | ave.female_T | wilcoxon.w | wilcoxon.p | p_adj | dFre |
| Protein coding RNA editing(s). |
| Editing Position | Variant Type | Gene Symbol | Transcript ID | NTchange | AAchange |
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Sex-biased TF-Gene network for BHMT2 |
| TFs related to BHMT2. ∗The female-biased TF-gene edges were identified if Female_Edge_threshold>0.98 and Male_Edge_threshold<=0.98. ∗The male-biased TF-gene edges were identified if Male_Edge_threshold>0.98 and Female_Edge_threshold<=0.98. |
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| Cancer Type | TF | Target Gene | Male Edge Score | Male Edge Threshold | Female Edge Score | Female Edge Threshold | Type |
| CHOL | ZNF225 | BHMT2 | 4.09e+00 | 9.85e-01 | 2.97e+00 | 5.52e-03 | Male-biased |
| CHOL | ZNF567 | BHMT2 | 4.03e+00 | 9.80e-01 | 3.02e+00 | 8.47e-03 | Male-biased |
| CHOL | ZNF613 | BHMT2 | 3.96e+00 | 9.82e-01 | 2.84e+00 | 5.22e-03 | Male-biased |
| DLBC | ZNF770 | BHMT2 | 4.38e+00 | 9.82e-01 | 3.50e+00 | 9.26e-03 | Male-biased |
| BHMT2 related gene. ∗Only the gene encode TF might with this result. ∗For more information please check Sex-biased TF-Coding gene network. |
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Sex-biased RBP-ES network for BHMT2 |
| RBPs related to ES in BHMT2. ∗The female-biased RBP-ES edges were identified if Female_Edge_threshold>0.98 and Male_Edge_threshold<=0.98. ∗The male-biased RBP-ES edges were identified if Male_Edge_threshold>0.98 and Female_Edge_threshold<=0.98. |
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| Cancer Type | RBP | Target ES | Male Edge Score | Male Edge Threshold | Female Edge Score | Female Edge Threshold | Type |
| KIRP | ZFP36 | exon_skip_435900 | 7.53e+00 | 9.84e-01 | 7.15e+00 | 5.52e-03 | Male-biased |
| BHMT2 related ES. ∗Only the gene encode RBP might with this result. ∗For more information please check Sex-biased RBP-ES network in cancer. |
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Sex-biased CeRNA regulation of gene |
| Sex-biased CeRNA regulation of gene. |
| Gene ID | ceRNA(lncRNA-miRNA-mRNA) | Group | Cancer Type |
Top |
Sex-biased eQTL regulation of gene |
| Sex-biased eQTL regulation of gene (The figures only show the pairs with FDR <1e-5. For more information please check the below table). |
| eQTL | Description |
| Male-specific eQTL regulation. |
| SNP ID | SNP Info | Position to Gene | Effect Score | FDR | Cancer Type | Biased Type |
| rs78504707 | chr5:79007950:G:A | - | 0.305533122665033 | 0.0364888356132402 | KIRP | Female-baised eQTL |
| rs2386071 | chr5:82756182:C:T | - | -0.163010290524214 | 0.0104953510205843 | LIHC | Female-baised eQTL |
| rs73141362 | chr5:82751455:C:T | - | -0.159841064307021 | 0.0274893382244063 | LIHC | Female-baised eQTL |
| rs6891004 | chr5:87878339:G:A | - | 0.0808610968083102 | 0.00822569067533975 | KIRC | Female-baised eQTL |
| rs6859479 | chr5:87956045:A:C | - | 0.0681973413264206 | 0.0474382853802072 | KIRC | Female-baised eQTL |
| rs10052220 | chr5:87956321:A:G | - | 0.0681973413264206 | 0.0474382853802072 | KIRC | Female-baised eQTL |
| rs13435982 | chr5:87956895:A:C | - | 0.0681973413264206 | 0.0474382853802072 | KIRC | Female-baised eQTL |
| rs13436524 | chr5:87956907:G:A | - | 0.0681973413264206 | 0.0474382853802072 | KIRC | Female-baised eQTL |
| rs13435984 | chr5:87957033:A:G | - | 0.0681973413264206 | 0.0474382853802072 | KIRC | Female-baised eQTL |
| rs73770013 | chr5:85218852:G:A | - | 0.118270340971476 | 0.014117317874834 | LUAD | Female-baised eQTL |
| rs4608956 | chr5:85219985:G:A | - | 0.118270340971476 | 0.014117317874834 | LUAD | Female-baised eQTL |
| Female-specific eQTL regulation. |
| SNP ID | SNP Info | Position to Gene | Effect Score | FDR | Cancer Type | Biased Type |
| rs7717956 | chr5:77668993:G:A | - | 0.266617432538329 | 0.0155313050007491 | SARC | Male-baised eQTL |
| rs10462518 | chr5:75490507:A:T | - | 0.0682479343808451 | 0.0433046312308346 | KIRC | Male-baised eQTL |
| Opposite sex-biased eQTL regulation. |
| SNP ID | SNP Info | Position to Gene | Male Effect | Male FDR | Female Effect | Female FDR | Sex-biased Gene in Cancer | Cancer Type |
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Sex-biased eQTM regulation of gene |
| Sex-biased eQTM regulation of gene (The figures only show the pairs with FDR<1e-5. For more information please check the below table). |
| eQTM | Description |
 | Gene ID: ENSG00000132840 |
| CpG Site: cg01902605 | |
| Position to Gene: gene,promoter | |
| Male Effect: -0.30132245761066 | |
| Female Effect: - |
| Male-specific eQTM regulation. |
| CpG Site | CpG Postion | Position to Gene | Effect Score | FDR | Cor.r | Cor.Pvalue | Cancer Type |
| cg01902605 | chr5:79070253 | gene,promoter | -0.30132245761066 | 9.69751475569579e-07 | -0.38611838458223735 | 2.422886821972468e-09 | LUAD |
| Female-specific eQTM regulation. |
| CpG Site | CpG Postion | Position to Gene | Effect Score | FDR | Cor.r | Cor.Pvalue | Cancer Type |
| Opposite sex-biased eQTM regulation. |
| CpG Site | CpG Postion | CpG Island | Position to Gene | Male Effect | Male FDR | Female Effect | Female FDR | Male Cor | Male P-value | Female Cor | Female P-value | Sex-biased Coding Gene | Cancer Type |
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Sex-biased sQTL regulation of gene |
| Sex-biased sQTL regulation of gene (The figures only show the pairs with FDR <1e-5. For more information please check the below table). |
| sQTL | Description |
| Male-specific sQTL regulation. |
| ES ID | Skipped Exon | ORF Anno | SNP ID | SNP Info | SNP Position to ES | Effect Score | FDR | Cancer Type | Biased Type |
| Female-specific sQTL regulation. |
| ES ID | Skipped Exon | ORF Anno | SNP ID | SNP Info | SNP Position to ES | Effect Score | FDR | Cancer Type | Biased Type |
| Opposite sex-biased sQTL regulation. |
| ES ID | Skipped Exon | ORF Anno | SNP ID | SNP Info | SNP Position to ES | Male Effect | Male FDR | Female Effect | Female FDR | Cancer Type |
Top |
Sex-biased sQTM regulation of gene |
| Sex-biased sQTM regulation of gene (The figures only show the pairs with FDR <1e-5. For more information please check the below table). |
| sQTM | Description |
| Male-specific sQTM regulation. |
| EX ID | Skipped Exon | CPG Site | CPG Position | Position to EX Events | Effect Score | FDR | Cor.r | Cor.Pvalue | ORF_anno | Cancer Type |
| Female-specific sQTM regulation. |
| EX ID | Skipped Exon | CPG Site | CPG Position | Position to EX Events | Effect Score | FDR | Cor.r | Cor.Pvalue | ORF_anno | Cancer Type |
| Opposite sex-biased sQTM regulation. |
| EX ID | EX Info | Skipped Exon | CPG Site | CPG Position | CPG Island | Position to EX Events | Male Effect | Male FDR | Female Effect | Female FDR | Male Correlation | Male P-value | Female Correlation | Female P-value | ORF_anno | Cancer Type |
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Related disease information of BHMT2 |
| Diseases associated with this gene (DisGeNET). |
| Gene ID | Gene Symbol | Disease ID | Disease Name | Number of PMID | Source |
| ENSG00000132840 | BHMT2 | C0008924 | Cleft upper lip | 1 | CTD_human |
| ENSG00000132840 | BHMT2 | C0008925 | Cleft Palate | 1 | CTD_human |
| ENSG00000132840 | BHMT2 | C1837218 | Cleft palate, isolated | 1 | CTD_human |
