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Gene: GNPDA2 |
Gene summary for GNPDA2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GNPDA2 | Gene ID | 132789 |
| Gene name | glucosamine-6-phosphate deaminase 2 | |
| Gene Alias | GNP2 | |
| Cytomap | 4p12 | |
| Gene Type | protein-coding | GO ID | GO:0005975 | UniProtAcc | Q8TDQ7 |
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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 |
| 132789 | GNPDA2 | C04 | Human | Oral cavity | OSCC | 2.45e-05 | 4.17e-01 | 0.2633 |
| 132789 | GNPDA2 | C21 | Human | Oral cavity | OSCC | 1.47e-03 | 2.55e-01 | 0.2678 |
| 132789 | GNPDA2 | C30 | Human | Oral cavity | OSCC | 4.06e-16 | 7.92e-01 | 0.3055 |
| 132789 | GNPDA2 | C43 | Human | Oral cavity | OSCC | 1.05e-18 | 1.58e-01 | 0.1704 |
| 132789 | GNPDA2 | C46 | Human | Oral cavity | OSCC | 8.02e-08 | 2.63e-01 | 0.1673 |
| 132789 | GNPDA2 | C06 | Human | Oral cavity | OSCC | 3.29e-04 | 6.09e-01 | 0.2699 |
| 132789 | GNPDA2 | C08 | Human | Oral cavity | OSCC | 4.00e-12 | 1.42e-01 | 0.1919 |
| 132789 | GNPDA2 | SYSMH1 | Human | Oral cavity | OSCC | 5.16e-08 | 7.91e-02 | 0.1127 |
| 132789 | GNPDA2 | SYSMH2 | Human | Oral cavity | OSCC | 3.89e-02 | 8.48e-02 | 0.2326 |
| 132789 | GNPDA2 | SYSMH3 | Human | Oral cavity | OSCC | 1.92e-12 | 1.32e-01 | 0.2442 |
| 132789 | GNPDA2 | SYSMH4 | Human | Oral cavity | OSCC | 4.33e-06 | 3.05e-02 | 0.1226 |
| 132789 | GNPDA2 | SYSMH5 | Human | Oral cavity | OSCC | 4.46e-04 | 1.37e-02 | 0.0647 |
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| 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 |
| ∗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:00092255 | Oral cavity | OSCC | nucleotide-sugar metabolic process | 26/7305 | 36/18723 | 5.44e-05 | 4.51e-04 | 26 |
| GO:19011361 | Oral cavity | OSCC | carbohydrate derivative catabolic process | 89/7305 | 172/18723 | 4.52e-04 | 2.73e-03 | 89 |
| GO:00442826 | Oral cavity | OSCC | small molecule catabolic process | 174/7305 | 376/18723 | 2.25e-03 | 1.00e-02 | 174 |
| GO:00092261 | Oral cavity | OSCC | nucleotide-sugar biosynthetic process | 14/7305 | 19/18723 | 2.31e-03 | 1.02e-02 | 14 |
| GO:0006040 | Oral cavity | OSCC | amino sugar metabolic process | 24/7305 | 42/18723 | 1.30e-02 | 4.34e-02 | 24 |
| GO:0006047 | Oral cavity | OSCC | UDP-N-acetylglucosamine metabolic process | 10/7305 | 14/18723 | 1.44e-02 | 4.69e-02 | 10 |
| GO:0046348 | Oral cavity | OSCC | amino sugar catabolic process | 10/7305 | 14/18723 | 1.44e-02 | 4.69e-02 | 10 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa00520 | Oral cavity | OSCC | Amino sugar and nucleotide sugar metabolism | 34/3704 | 49/8465 | 2.48e-04 | 8.08e-04 | 4.11e-04 | 34 |
| hsa005201 | Oral cavity | OSCC | Amino sugar and nucleotide sugar metabolism | 34/3704 | 49/8465 | 2.48e-04 | 8.08e-04 | 4.11e-04 | 34 |
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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 |
| GNPDA2 | SNV | Missense_Mutation | novel | c.16N>T | p.Leu6Phe | p.L6F | Q8TDQ7 | protein_coding | tolerated_low_confidence(0.51) | benign(0.005) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD |
| GNPDA2 | SNV | Missense_Mutation | c.607N>G | p.Ile203Val | p.I203V | Q8TDQ7 | protein_coding | tolerated_low_confidence(0.64) | benign(0.06) | TCGA-E9-A1RF-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD | |
| GNPDA2 | SNV | Missense_Mutation | novel | c.433G>A | p.Ala145Thr | p.A145T | Q8TDQ7 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.979) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| GNPDA2 | SNV | Missense_Mutation | c.692N>G | p.Gln231Arg | p.Q231R | Q8TDQ7 | protein_coding | tolerated_low_confidence(0.07) | benign(0.211) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| GNPDA2 | SNV | Missense_Mutation | c.582G>T | p.Met194Ile | p.M194I | Q8TDQ7 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.898) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| GNPDA2 | deletion | Frame_Shift_Del | c.282delN | p.Phe94LeufsTer6 | p.F94Lfs*6 | Q8TDQ7 | protein_coding | TCGA-AA-3845-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |||
| GNPDA2 | deletion | Frame_Shift_Del | c.282delN | p.Phe94LeufsTer6 | p.F94Lfs*6 | Q8TDQ7 | protein_coding | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
| GNPDA2 | SNV | Missense_Mutation | c.718G>A | p.Asp240Asn | p.D240N | Q8TDQ7 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.898) | TCGA-A5-A0GP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| GNPDA2 | SNV | Missense_Mutation | rs761357281 | c.292G>A | p.Asp98Asn | p.D98N | Q8TDQ7 | protein_coding | tolerated_low_confidence(0.11) | possibly_damaging(0.722) | TCGA-A5-A0GP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| GNPDA2 | SNV | Missense_Mutation | rs755743137 | c.682G>A | p.Ala228Thr | p.A228T | Q8TDQ7 | protein_coding | deleterious_low_confidence(0.01) | benign(0.367) | TCGA-AP-A051-01 | 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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