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Gene: GDPD2 |
Gene summary for GDPD2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GDPD2 | Gene ID | 54857 |
| Gene name | glycerophosphodiester phosphodiesterase domain containing 2 | |
| Gene Alias | GDE3 | |
| Cytomap | Xq13.1 | |
| Gene Type | protein-coding | GO ID | GO:0001503 | UniProtAcc | Q9HCC8 |
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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 |
| 54857 | GDPD2 | C51 | Human | Oral cavity | OSCC | 1.14e-10 | 5.45e-01 | 0.2674 |
| 54857 | GDPD2 | C06 | Human | Oral cavity | OSCC | 5.29e-09 | 1.02e+00 | 0.2699 |
| 54857 | GDPD2 | C07 | Human | Oral cavity | OSCC | 2.33e-02 | 5.95e-01 | 0.2491 |
| 54857 | GDPD2 | SYSMH3 | Human | Oral cavity | OSCC | 2.60e-14 | 5.51e-01 | 0.2442 |
| 54857 | GDPD2 | SYSMH5 | Human | Oral cavity | OSCC | 3.00e-02 | 1.51e-01 | 0.0647 |
| 54857 | GDPD2 | P3_S6_AK | Human | Skin | AK | 1.79e-02 | -8.64e-02 | -0.3256 |
| 54857 | GDPD2 | P5_S10_cSCC | Human | Skin | cSCC | 3.76e-02 | -1.09e-01 | -0.299 |
| 54857 | GDPD2 | P1_cSCC | Human | Skin | cSCC | 5.39e-05 | 4.27e-01 | 0.0292 |
| 54857 | GDPD2 | P4_cSCC | Human | Skin | cSCC | 5.95e-08 | 4.11e-01 | -0.00290000000000005 |
| 54857 | GDPD2 | cSCC_p1 | Human | Skin | cSCC | 4.49e-17 | 5.55e-01 | -0.1916 |
| 54857 | GDPD2 | cSCC_p11 | Human | Skin | cSCC | 4.15e-13 | 4.23e-01 | -0.2102 |
| 54857 | GDPD2 | cSCC_p8 | Human | Skin | cSCC | 2.77e-06 | 2.46e-01 | -0.1971 |
| 54857 | GDPD2 | cSCC_p9 | Human | Skin | cSCC | 2.11e-16 | 4.14e-01 | -0.1991 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:000701520 | Oral cavity | OSCC | actin filament organization | 230/7305 | 442/18723 | 1.37e-08 | 2.77e-07 | 230 |
| GO:003153216 | Oral cavity | OSCC | actin cytoskeleton reorganization | 65/7305 | 107/18723 | 4.25e-06 | 4.93e-05 | 65 |
| GO:000150310 | Oral cavity | OSCC | ossification | 203/7305 | 408/18723 | 5.54e-06 | 6.19e-05 | 203 |
| GO:000164910 | Oral cavity | OSCC | osteoblast differentiation | 118/7305 | 229/18723 | 7.51e-05 | 5.85e-04 | 118 |
| GO:00456674 | Oral cavity | OSCC | regulation of osteoblast differentiation | 65/7305 | 132/18723 | 1.06e-02 | 3.60e-02 | 65 |
| GO:000701528 | Skin | AK | actin filament organization | 85/1910 | 442/18723 | 5.94e-09 | 4.14e-07 | 85 |
| GO:000164919 | Skin | AK | osteoblast differentiation | 52/1910 | 229/18723 | 2.27e-08 | 1.28e-06 | 52 |
| GO:000150318 | Skin | AK | ossification | 78/1910 | 408/18723 | 3.26e-08 | 1.76e-06 | 78 |
| GO:003153219 | Skin | AK | actin cytoskeleton reorganization | 23/1910 | 107/18723 | 4.20e-04 | 4.00e-03 | 23 |
| GO:00456676 | Skin | AK | regulation of osteoblast differentiation | 26/1910 | 132/18723 | 7.61e-04 | 6.39e-03 | 26 |
| GO:000701529 | Skin | cSCC | actin filament organization | 156/4864 | 442/18723 | 7.37e-06 | 1.02e-04 | 156 |
| GO:000164923 | Skin | cSCC | osteoblast differentiation | 89/4864 | 229/18723 | 1.18e-05 | 1.51e-04 | 89 |
| GO:000150323 | Skin | cSCC | ossification | 137/4864 | 408/18723 | 3.39e-04 | 2.68e-03 | 137 |
| GO:003153224 | Skin | cSCC | actin cytoskeleton reorganization | 42/4864 | 107/18723 | 1.76e-03 | 1.07e-02 | 42 |
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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 |
| GDPD2 | SNV | Missense_Mutation | novel | c.574N>A | p.Leu192Met | p.L192M | Q9HCC8 | protein_coding | tolerated(0.09) | benign(0.369) | TCGA-A8-A09E-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozole | SD |
| GDPD2 | SNV | Missense_Mutation | c.1423N>G | p.Pro475Ala | p.P475A | Q9HCC8 | protein_coding | tolerated_low_confidence(0.83) | possibly_damaging(0.539) | TCGA-B6-A0X1-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| GDPD2 | SNV | Missense_Mutation | c.237N>C | p.Trp79Cys | p.W79C | Q9HCC8 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-C8-A132-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| GDPD2 | SNV | Missense_Mutation | c.1451N>G | p.His484Arg | p.H484R | Q9HCC8 | protein_coding | tolerated_low_confidence(1) | benign(0.003) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| GDPD2 | SNV | Missense_Mutation | novel | c.521N>A | p.Pro174His | p.P174H | Q9HCC8 | protein_coding | deleterious(0.02) | possibly_damaging(0.817) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| GDPD2 | SNV | Missense_Mutation | c.595N>C | p.Val199Leu | p.V199L | Q9HCC8 | protein_coding | tolerated(0.19) | benign(0.01) | TCGA-3L-AA1B-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| GDPD2 | SNV | Missense_Mutation | novel | c.811N>T | p.His271Tyr | p.H271Y | Q9HCC8 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A6-2672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| GDPD2 | SNV | Missense_Mutation | c.820N>T | p.His274Tyr | p.H274Y | Q9HCC8 | protein_coding | tolerated(0.12) | benign(0.113) | TCGA-AA-3939-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| GDPD2 | SNV | Missense_Mutation | c.1744N>G | p.Thr582Ala | p.T582A | Q9HCC8 | protein_coding | deleterious(0) | probably_damaging(0.978) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| GDPD2 | SNV | Missense_Mutation | rs747682076 | c.1550N>T | p.Ser517Leu | p.S517L | Q9HCC8 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
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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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