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Gene: GPD1 |
Gene summary for GPD1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GPD1 | Gene ID | 2819 |
| Gene name | glycerol-3-phosphate dehydrogenase 1 | |
| Gene Alias | GPD-C | |
| Cytomap | 12q13.12 | |
| Gene Type | protein-coding | GO ID | GO:0005975 | UniProtAcc | P21695 |
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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 |
| 2819 | GPD1 | HCC1 | Human | Liver | HCC | 3.66e-02 | 1.97e+00 | 0.5336 |
| 2819 | GPD1 | HCC2 | Human | Liver | HCC | 8.41e-29 | 3.67e+00 | 0.5341 |
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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:1903829 | Colorectum | AD | positive regulation of cellular protein localization | 110/3918 | 276/18723 | 4.58e-13 | 8.44e-11 | 110 |
| GO:0010563 | Colorectum | AD | negative regulation of phosphorus metabolic process | 130/3918 | 442/18723 | 1.26e-05 | 2.76e-04 | 130 |
| GO:0045936 | Colorectum | AD | negative regulation of phosphate metabolic process | 129/3918 | 441/18723 | 1.81e-05 | 3.76e-04 | 129 |
| GO:0002028 | Colorectum | AD | regulation of sodium ion transport | 36/3918 | 90/18723 | 2.89e-05 | 5.37e-04 | 36 |
| GO:0042326 | Colorectum | AD | negative regulation of phosphorylation | 112/3918 | 385/18723 | 8.02e-05 | 1.27e-03 | 112 |
| GO:0001933 | Colorectum | AD | negative regulation of protein phosphorylation | 101/3918 | 342/18723 | 9.39e-05 | 1.42e-03 | 101 |
| GO:0030048 | Colorectum | AD | actin filament-based movement | 44/3918 | 127/18723 | 2.31e-04 | 2.99e-03 | 44 |
| GO:0010765 | Colorectum | AD | positive regulation of sodium ion transport | 17/3918 | 35/18723 | 2.48e-04 | 3.13e-03 | 17 |
| GO:1902305 | Colorectum | AD | regulation of sodium ion transmembrane transport | 27/3918 | 68/18723 | 3.19e-04 | 3.80e-03 | 27 |
| GO:0019674 | Colorectum | AD | NAD metabolic process | 15/3918 | 30/18723 | 3.85e-04 | 4.39e-03 | 15 |
| GO:2000649 | Colorectum | AD | regulation of sodium ion transmembrane transporter activity | 23/3918 | 58/18723 | 8.82e-04 | 8.53e-03 | 23 |
| GO:0018105 | Colorectum | AD | peptidyl-serine phosphorylation | 88/3918 | 315/18723 | 1.73e-03 | 1.43e-02 | 88 |
| GO:0018209 | Colorectum | AD | peptidyl-serine modification | 92/3918 | 338/18723 | 3.19e-03 | 2.36e-02 | 92 |
| GO:0034394 | Colorectum | AD | protein localization to cell surface | 24/3918 | 68/18723 | 4.33e-03 | 2.97e-02 | 24 |
| GO:19038292 | Colorectum | MSS | positive regulation of cellular protein localization | 103/3467 | 276/18723 | 1.12e-13 | 2.67e-11 | 103 |
| GO:00300482 | Colorectum | MSS | actin filament-based movement | 44/3467 | 127/18723 | 1.11e-05 | 2.64e-04 | 44 |
| GO:00105632 | Colorectum | MSS | negative regulation of phosphorus metabolic process | 118/3467 | 442/18723 | 1.18e-05 | 2.77e-04 | 118 |
| GO:00459362 | Colorectum | MSS | negative regulation of phosphate metabolic process | 117/3467 | 441/18723 | 1.74e-05 | 3.84e-04 | 117 |
| GO:00423262 | Colorectum | MSS | negative regulation of phosphorylation | 103/3467 | 385/18723 | 3.76e-05 | 7.17e-04 | 103 |
| GO:00019332 | Colorectum | MSS | negative regulation of protein phosphorylation | 93/3467 | 342/18723 | 4.54e-05 | 8.35e-04 | 93 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| GPD1 | SNV | Missense_Mutation | c.991N>A | p.Glu331Lys | p.E331K | P21695 | protein_coding | tolerated(0.23) | benign(0.017) | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| GPD1 | SNV | Missense_Mutation | c.548N>T | p.Thr183Ile | p.T183I | P21695 | protein_coding | deleterious(0.02) | probably_damaging(0.992) | TCGA-B6-A0I6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| GPD1 | SNV | Missense_Mutation | novel | c.124G>A | p.Glu42Lys | p.E42K | P21695 | protein_coding | deleterious(0.01) | probably_damaging(0.969) | TCGA-PE-A5DE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
| GPD1 | deletion | Frame_Shift_Del | c.110_147delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | p.Met38AspfsTer2 | p.M38Dfs*2 | P21695 | protein_coding | TCGA-C8-A134-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |||
| GPD1 | SNV | Missense_Mutation | novel | c.485N>C | p.Cys162Ser | p.C162S | P21695 | protein_coding | tolerated(0.44) | possibly_damaging(0.804) | TCGA-ZJ-AAXT-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
| GPD1 | SNV | Missense_Mutation | c.343N>T | p.Gly115Cys | p.G115C | P21695 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| GPD1 | SNV | Missense_Mutation | rs755956209 | c.689N>C | p.Leu230Pro | p.L230P | P21695 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AY-6197-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| GPD1 | SNV | Missense_Mutation | c.569T>C | p.Val190Ala | p.V190A | P21695 | protein_coding | deleterious(0.04) | probably_damaging(0.943) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| GPD1 | SNV | Missense_Mutation | novel | c.864N>T | p.Glu288Asp | p.E288D | P21695 | protein_coding | deleterious(0.01) | possibly_damaging(0.702) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| GPD1 | SNV | Missense_Mutation | novel | c.140G>A | p.Gly47Asp | p.G47D | P21695 | protein_coding | deleterious(0.03) | possibly_damaging(0.655) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <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 |
| Page: 1 |
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