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Gene: ENSG00000092621 |
Summary for PHGDH |
 Gene summary |
| Gene information | Ensembl ID | ENSG00000092621 | Gene symbol | PHGDH |
| Gene name | phosphoglycerate dehydrogenase | |
| HGNC | 8923 | |
| Entrez ID | 26227 | |
| Gene type | protein_coding | |
| Synonyms | PHGDH|SERA|PGDH|PDG | |
| UniProtAcc | O43175 |
| Drugs associated with this gene(DrugBank). |
| Gene ID | Gene Symbol | Drug ID | Drug Name | Drug Type |
| ENSG00000092621 | PHGDH | DB00157 | NADH | SmallMoleculeDrug |
| Cancer therapeutic drugs associated with this gene(NCI). |
| Gene ID | Gene Name | Drug ID | Drug Name | Drug Type | Cancer |
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Structure and expression level for PHGDH |
| 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 |
| PHGDH | 5.32e+03 | -1.93e+00 | 4.79e-01 | -4.04e+00 | 5.38e-05 | 1.27e-03 | BRCA |
| Differentially expressed gene analysis between tumor male and normal male samples. |
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| Coding Name | Base Mean | log2FoldChange | lfcSE | Stat | P value | P.adjust Value | Cancer Type |
| PHGDH | 2.16e+03 | -1.68e+00 | 3.27e-01 | -5.13e+00 | 2.84e-07 | 1.10e-06 | KIRP |
| PHGDH | 5.31e+03 | -2.02e+00 | 5.67e-01 | -3.57e+00 | 3.56e-04 | 1.36e-03 | CHOL |
| Differentially expressed gene analysis between tumor female and normal female samples. |
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| Coding Name | Base Mean | log2FoldChange | lfcSE | Stat | P value | P.adjust Value | Cancer Type |
| PHGDH | 2.55e+03 | -1.13e+00 | 3.57e-01 | -3.16e+00 | 1.56e-03 | 6.11e-03 | HNSC |
| PHGDH | 2.76e+03 | -1.22e+00 | 4.71e-01 | -2.59e+00 | 9.55e-03 | 1.71e-02 | KICH |
| PHGDH | 2.69e+03 | 1.71e+00 | 5.14e-01 | 3.33e+00 | 8.67e-04 | 3.07e-03 | READ |
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Sex-biased somatic mutation for PHGDH |
| ∗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 |
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DNA methylation with beta values for PHGDH |
| Landscape of DNA methylation across multiple cancer types. |
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| 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 |
| 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 |
| 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 |
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Exon skipping events with PSI in TCGA for PHGDH |
| ∗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 |
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RNA A-to-I editing events in TCGA for PHGDH |
| ∗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 PHGDH |
| TFs related to PHGDH. ∗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. |
| Cancer Type | TF | Target Gene | Male Edge Score | Male Edge Threshold | Female Edge Score | Female Edge Threshold | Type |
| PHGDH 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 PHGDH |
| RBPs related to ES in PHGDH. ∗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 |
| STAD | FXR1 | exon_skip_9173 | 9.19e+00 | 9.89e-01 | 8.81e+00 | 7.53e-03 | Male-biased |
| UVM | FXR1 | exon_skip_9173 | 9.00e+00 | 3.35e-03 | 9.39e+00 | 9.93e-01 | Female-biased |
| UVM | IGF2BP1 | exon_skip_9173 | 7.08e+00 | 6.88e-03 | 7.41e+00 | 9.82e-01 | Female-biased |
| LIHC | SAMD4A | exon_skip_9191 | 8.62e+00 | 9.82e-01 | 8.25e+00 | 1.21e-02 | Male-biased |
| LUSC | SRSF9 | exon_skip_9160 | 7.82e+00 | 6.92e-03 | 8.21e+00 | 9.86e-01 | Female-biased |
| CHOL | SNRPA | exon_skip_9197 | 7.29e+00 | 9.81e-01 | 6.83e+00 | 6.43e-03 | Male-biased |
| READ | FXR1 | exon_skip_9173 | 9.10e+00 | 9.86e-01 | 8.77e+00 | 1.03e-02 | Male-biased |
| MESO | FXR1 | exon_skip_9173 | 8.86e+00 | 8.43e-03 | 9.23e+00 | 9.88e-01 | Female-biased |
| MESO | IGF2BP1 | exon_skip_9173 | 7.09e+00 | 7.53e-03 | 7.46e+00 | 9.82e-01 | Female-biased |
| MESO | SAMD4A | exon_skip_9191 | 8.36e+00 | 9.91e-01 | 7.85e+00 | 2.38e-03 | Male-biased |
| GBM | FXR1 | exon_skip_9173 | 9.25e+00 | 9.94e-01 | 8.79e+00 | 2.62e-03 | Male-biased |
| PAAD | FXR1 | exon_skip_9173 | 9.12e+00 | 9.84e-01 | 8.83e+00 | 1.22e-02 | Male-biased |
| KIRC | FXR1 | exon_skip_9173 | 8.85e+00 | 6.54e-03 | 9.20e+00 | 9.90e-01 | Female-biased |
| KIRC | SAMD4A | exon_skip_9191 | 8.21e+00 | 2.07e-03 | 8.68e+00 | 9.92e-01 | Female-biased |
| KICH | SAMD4A | exon_skip_9191 | 8.07e+00 | 1.83e-03 | 8.55e+00 | 9.92e-01 | Female-biased |
| HNSC | FXR1 | exon_skip_9173 | 8.82e+00 | 1.07e-02 | 9.15e+00 | 9.86e-01 | Female-biased |
| HNSC | SAMD4A | exon_skip_9191 | 8.68e+00 | 9.89e-01 | 8.27e+00 | 5.28e-03 | Male-biased |
| SARC | SAMD4A | exon_skip_9191 | 7.99e+00 | 5.67e-04 | 8.71e+00 | 9.94e-01 | Female-biased |
| PHGDH 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 |
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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 |
| rs1182215 | chr1:116821054:G:A | - | 0.116847709897553 | 0.0374908175188215 | COAD | Female-baised eQTL |
| Female-specific eQTL regulation. |
| SNP ID | SNP Info | Position to Gene | Effect Score | FDR | Cancer Type | Biased Type |
| rs2843025 | chr1:119886173:A:G | - | -0.0473928840793829 | 0.000950346562585351 | LUSC | Male-baised eQTL |
| rs12408572 | chr1:110448996:C:T | - | 0.0376940602842767 | 0.00528539669231881 | LUSC | Male-baised eQTL |
| rs4839392 | chr1:110451762:T:C | - | 0.0372617218386614 | 0.00579354822972909 | LUSC | Male-baised eQTL |
| rs4839391 | chr1:110451368:G:A | - | 0.0367813705089416 | 0.00662806411762013 | LUSC | Male-baised eQTL |
| rs12131713 | chr1:116240882:A:G | - | 0.0689721292595382 | 0.0337420875053697 | KIRC | Male-baised eQTL |
| rs7553700 | chr1:111579013:A:T | - | -0.0781000561419359 | 0.0340649734835414 | KIRC | Male-baised eQTL |
| rs2493389 | chr1:119931555:C:T | - | 0.035525353296693 | 0.0184124151583444 | BLCA | Male-baised eQTL |
| rs113599901 | chr1:111086498:C:T | - | 0.030911301798027 | 0.0389884369662479 | BLCA | Male-baised eQTL |
| rs1264893 | chr1:111426810:C:G | - | 0.132701579725486 | 0.00236351287153045 | LUAD | Male-baised eQTL |
| rs1264901 | chr1:111444413:C:T | - | 0.130169274181839 | 0.00288936675487703 | LUAD | Male-baised eQTL |
| rs1264896 | chr1:111452946:G:A | - | 0.130135777623359 | 0.00292401721221747 | LUAD | Male-baised eQTL |
| rs1264910 | chr1:111435410:G:A | - | 0.114402990334923 | 0.00497482291304524 | LUAD | Male-baised eQTL |
| rs1264908 | chr1:111436733:C:T | - | 0.114354693309304 | 0.00502963750713822 | LUAD | Male-baised eQTL |
| rs1264905 | chr1:111439672:C:T | - | 0.113924789947453 | 0.00553558205846896 | LUAD | Male-baised eQTL |
| rs1264913 | chr1:111432313:A:G | - | 0.111239938999596 | 0.00715374756724737 | LUAD | Male-baised eQTL |
| rs1264887 | chr1:111425499:C:T | - | 0.0992128423390227 | 0.0164910309769376 | LUAD | Male-baised eQTL |
| rs1264904 | chr1:111440530:A:G | - | 0.103624421271072 | 0.0174205661796145 | LUAD | Male-baised eQTL |
| rs1264915 | chr1:111430326:A:G | - | 0.098816480439288 | 0.0175167665319127 | LUAD | Male-baised eQTL |
| rs2485321 | chr1:111438328:T:C | - | 0.0976551418919379 | 0.0190785465838514 | LUAD | 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: ENSG00000092621 |
| CpG Site: cg22872553 | |
| Position to Gene: gene | |
| Male Effect: - | |
| Female Effect: -0.45592679273135 | |
 | Gene ID: ENSG00000092621 |
| CpG Site: cg14476101 | |
| Position to Gene: gene | |
| Male Effect: - | |
| Female Effect: -0.45592679273135 | |
 | Gene ID: ENSG00000092621 |
| CpG Site: cg22872553 | |
| Position to Gene: gene | |
| Male Effect: -0.256818287923648 | |
| Female Effect: - |
| Male-specific eQTM regulation. |
| CpG Site | CpG Postion | Position to Gene | Effect Score | FDR | Cor.r | Cor.Pvalue | Cancer Type |
| cg22872553 | chr1:119674016 | gene | -0.256818287923648 | 1.93429423647386e-38 | -0.7021097195179258 | 1.3589424644955287e-38 | LUSC |
| Female-specific eQTM regulation. |
| CpG Site | CpG Postion | Position to Gene | Effect Score | FDR | Cor.r | Cor.Pvalue | Cancer Type |
| cg22872553 | chr1:119674016 | gene | -0.45592679273135 | 1.42839269049907e-11 | -0.4620832814451712 | 6.8169829636459795e-15 | LUAD |
| cg14476101 | chr1:119713369 | gene | -0.45592679273135 | 1.42839269049907e-11 | -0.4620832814451712 | 6.8169829636459795e-15 | LUAD |
| 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 |
Top |
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 PHGDH |
| Diseases associated with this gene (DisGeNET). |
| Gene ID | Gene Symbol | Disease ID | Disease Name | Number of PMID | Source |
| ENSG00000092621 | PHGDH | C0006142 | Malignant neoplasm of breast | 1 | CTD_human |
| ENSG00000092621 | PHGDH | C0007131 | Non-Small Cell Lung Carcinoma | 1 | CTD_human |
| ENSG00000092621 | PHGDH | C0007621 | Neoplastic Cell Transformation | 1 | CTD_human |
| ENSG00000092621 | PHGDH | C0023903 | Liver neoplasms | 1 | CTD_human |
| ENSG00000092621 | PHGDH | C0025202 | melanoma | 1 | CTD_human |
| ENSG00000092621 | PHGDH | C0033578 | Prostatic Neoplasms | 1 | CTD_human |
| ENSG00000092621 | PHGDH | C0265218 | Neu-Laxova syndrome | 1 | CTD_human |
| ENSG00000092621 | PHGDH | C0345904 | Malignant neoplasm of liver | 1 | CTD_human |
| ENSG00000092621 | PHGDH | C0376358 | Malignant neoplasm of prostate | 1 | CTD_human |
| ENSG00000092621 | PHGDH | C0678222 | Breast Carcinoma | 1 | CTD_human |
| ENSG00000092621 | PHGDH | C1257931 | Mammary Neoplasms, Human | 1 | CTD_human |
| ENSG00000092621 | PHGDH | C1458155 | Mammary Neoplasms | 1 | CTD_human |
| ENSG00000092621 | PHGDH | C1866174 | Phosphoglycerate Dehydrogenase Deficiency | 1 | CTD_human |
| ENSG00000092621 | PHGDH | C4704874 | Mammary Carcinoma, Human | 1 | CTD_human |
