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Gene: GDE1 |
Gene summary for GDE1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GDE1 | Gene ID | 51573 |
| Gene name | glycerophosphodiester phosphodiesterase 1 | |
| Gene Alias | 363E6.2 | |
| Cytomap | 16p12.3 | |
| Gene Type | protein-coding | GO ID | GO:0006066 | UniProtAcc | A0A024QYU1 |
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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 |
| 51573 | GDE1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.24e-05 | 4.02e-01 | -0.1808 |
| 51573 | GDE1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.76e-06 | 5.09e-01 | -0.0811 |
| 51573 | GDE1 | HTA11_78_2000001011 | Human | Colorectum | AD | 3.18e-02 | 3.31e-01 | -0.1088 |
| 51573 | GDE1 | HTA11_347_2000001011 | Human | Colorectum | AD | 5.09e-20 | 6.31e-01 | -0.1954 |
| 51573 | GDE1 | HTA11_2112_2000001011 | Human | Colorectum | SER | 5.57e-07 | 8.71e-01 | -0.2196 |
| 51573 | GDE1 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.13e-04 | 3.36e-01 | -0.1464 |
| 51573 | GDE1 | HTA11_866_2000001011 | Human | Colorectum | AD | 3.03e-05 | 2.73e-01 | -0.1001 |
| 51573 | GDE1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.82e-06 | 4.64e-01 | -0.059 |
| 51573 | GDE1 | HTA11_10623_2000001011 | Human | Colorectum | AD | 2.60e-02 | 4.11e-01 | -0.0177 |
| 51573 | GDE1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 3.64e-08 | 5.53e-01 | 0.281 |
| 51573 | GDE1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.70e-04 | 3.39e-01 | 0.3859 |
| 51573 | GDE1 | A002-C-201 | Human | Colorectum | FAP | 1.13e-03 | -1.41e-01 | 0.0324 |
| 51573 | GDE1 | A002-C-205 | Human | Colorectum | FAP | 1.42e-02 | -1.13e-01 | -0.1236 |
| 51573 | GDE1 | A015-C-006 | Human | Colorectum | FAP | 1.19e-03 | -1.66e-01 | -0.0994 |
| 51573 | GDE1 | A002-C-114 | Human | Colorectum | FAP | 2.15e-02 | -1.31e-01 | -0.1561 |
| 51573 | GDE1 | A015-C-104 | Human | Colorectum | FAP | 5.13e-03 | -1.41e-01 | -0.1899 |
| 51573 | GDE1 | A001-C-203 | Human | Colorectum | FAP | 2.47e-02 | -1.20e-01 | -0.0481 |
| 51573 | GDE1 | A002-C-116 | Human | Colorectum | FAP | 1.79e-02 | -1.23e-01 | -0.0452 |
| 51573 | GDE1 | A014-C-008 | Human | Colorectum | FAP | 2.99e-03 | -1.66e-01 | -0.191 |
| 51573 | GDE1 | A018-E-020 | Human | Colorectum | FAP | 1.31e-03 | -1.50e-01 | -0.2034 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:0006066 | Colorectum | AD | alcohol metabolic process | 106/3918 | 353/18723 | 3.02e-05 | 5.57e-04 | 106 |
| GO:0016042 | Colorectum | AD | lipid catabolic process | 97/3918 | 320/18723 | 4.31e-05 | 7.56e-04 | 97 |
| GO:0044242 | Colorectum | AD | cellular lipid catabolic process | 66/3918 | 214/18723 | 3.96e-04 | 4.50e-03 | 66 |
| GO:0034308 | Colorectum | AD | primary alcohol metabolic process | 35/3918 | 102/18723 | 1.16e-03 | 1.05e-02 | 35 |
| GO:0006650 | Colorectum | AD | glycerophospholipid metabolic process | 83/3918 | 306/18723 | 5.40e-03 | 3.55e-02 | 83 |
| GO:0006644 | Colorectum | AD | phospholipid metabolic process | 101/3918 | 383/18723 | 5.80e-03 | 3.67e-02 | 101 |
| GO:00160421 | Colorectum | SER | lipid catabolic process | 77/2897 | 320/18723 | 3.52e-05 | 9.18e-04 | 77 |
| GO:00060661 | Colorectum | SER | alcohol metabolic process | 79/2897 | 353/18723 | 3.50e-04 | 5.50e-03 | 79 |
| GO:00442421 | Colorectum | SER | cellular lipid catabolic process | 51/2897 | 214/18723 | 8.60e-04 | 1.05e-02 | 51 |
| GO:0046486 | Colorectum | SER | glycerolipid metabolic process | 82/2897 | 392/18723 | 2.26e-03 | 2.17e-02 | 82 |
| GO:00066441 | Colorectum | SER | phospholipid metabolic process | 79/2897 | 383/18723 | 3.94e-03 | 3.24e-02 | 79 |
| GO:00343081 | Colorectum | SER | primary alcohol metabolic process | 26/2897 | 102/18723 | 5.87e-03 | 4.29e-02 | 26 |
| GO:00066501 | Colorectum | SER | glycerophospholipid metabolic process | 64/2897 | 306/18723 | 6.41e-03 | 4.60e-02 | 64 |
| GO:00060662 | Colorectum | MSS | alcohol metabolic process | 92/3467 | 353/18723 | 2.57e-04 | 3.46e-03 | 92 |
| GO:00160422 | Colorectum | MSS | lipid catabolic process | 77/3467 | 320/18723 | 7.43e-03 | 4.71e-02 | 77 |
| GO:00442422 | Colorectum | FAP | cellular lipid catabolic process | 49/2622 | 214/18723 | 2.87e-04 | 3.77e-03 | 49 |
| GO:00160423 | Colorectum | FAP | lipid catabolic process | 65/2622 | 320/18723 | 1.13e-03 | 1.08e-02 | 65 |
| GO:00066502 | Colorectum | FAP | glycerophospholipid metabolic process | 62/2622 | 306/18723 | 1.54e-03 | 1.38e-02 | 62 |
| GO:00066442 | Colorectum | FAP | phospholipid metabolic process | 74/2622 | 383/18723 | 2.24e-03 | 1.83e-02 | 74 |
| GO:00060663 | Colorectum | FAP | alcohol metabolic process | 69/2622 | 353/18723 | 2.29e-03 | 1.85e-02 | 69 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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 |
| GDE1 | SNV | Missense_Mutation | c.652C>G | p.Arg218Gly | p.R218G | Q9NZC3 | protein_coding | tolerated(0.17) | benign(0.119) | TCGA-E2-A573-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR | |
| GDE1 | insertion | Frame_Shift_Ins | novel | c.278_279insTGGTTATTCATGTAATATCAAT | p.Thr94GlyfsTer15 | p.T94Gfs*15 | Q9NZC3 | protein_coding | TCGA-AN-A049-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| GDE1 | SNV | Missense_Mutation | rs757733912 | c.652N>T | p.Arg218Trp | p.R218W | Q9NZC3 | protein_coding | deleterious(0.01) | possibly_damaging(0.606) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| GDE1 | SNV | Missense_Mutation | rs757733912 | c.652N>T | p.Arg218Trp | p.R218W | Q9NZC3 | protein_coding | deleterious(0.01) | possibly_damaging(0.606) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| GDE1 | SNV | Missense_Mutation | novel | c.779N>C | p.Ser260Thr | p.S260T | Q9NZC3 | protein_coding | tolerated(0.18) | possibly_damaging(0.725) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| GDE1 | SNV | Missense_Mutation | novel | c.752N>G | p.Val251Gly | p.V251G | Q9NZC3 | protein_coding | tolerated(0.54) | benign(0.003) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| GDE1 | SNV | Missense_Mutation | rs537541856 | c.374G>A | p.Arg125Gln | p.R125Q | Q9NZC3 | protein_coding | tolerated(0.54) | benign(0.012) | TCGA-BG-A220-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| GDE1 | SNV | Missense_Mutation | c.877N>A | p.Gly293Arg | p.G293R | Q9NZC3 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-D1-A0ZU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | SD | |
| GDE1 | SNV | Missense_Mutation | rs757733912 | c.652C>T | p.Arg218Trp | p.R218W | Q9NZC3 | protein_coding | deleterious(0.01) | possibly_damaging(0.606) | TCGA-D1-A16X-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| GDE1 | SNV | Missense_Mutation | novel | c.677N>G | p.His226Arg | p.H226R | Q9NZC3 | protein_coding | tolerated(0.19) | possibly_damaging(0.759) | TCGA-FI-A2F4-01 | Endometrium | uterine corpus endometrioid carcinoma | 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 |
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