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Gene: PDP1 |
Gene summary for PDP1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PDP1 | Gene ID | 54704 |
| Gene name | pyruvate dehydrogenase phosphatase catalytic subunit 1 | |
| Gene Alias | PDH | |
| Cytomap | 8q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | Q9P0J1 |
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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 |
| 54704 | PDP1 | HCC2_Meng | Human | Liver | HCC | 1.13e-20 | 1.42e-01 | 0.0107 |
| 54704 | PDP1 | S014 | Human | Liver | HCC | 1.80e-13 | 7.25e-01 | 0.2254 |
| 54704 | PDP1 | S015 | Human | Liver | HCC | 8.92e-15 | 7.71e-01 | 0.2375 |
| 54704 | PDP1 | S016 | Human | Liver | HCC | 1.30e-22 | 9.57e-01 | 0.2243 |
| 54704 | PDP1 | C04 | Human | Oral cavity | OSCC | 4.60e-25 | 8.78e-01 | 0.2633 |
| 54704 | PDP1 | C21 | Human | Oral cavity | OSCC | 4.63e-18 | 5.55e-01 | 0.2678 |
| 54704 | PDP1 | C30 | Human | Oral cavity | OSCC | 2.00e-31 | 1.36e+00 | 0.3055 |
| 54704 | PDP1 | C38 | Human | Oral cavity | OSCC | 1.20e-04 | 5.07e-01 | 0.172 |
| 54704 | PDP1 | C46 | Human | Oral cavity | OSCC | 1.39e-13 | 3.79e-01 | 0.1673 |
| 54704 | PDP1 | C51 | Human | Oral cavity | OSCC | 1.83e-16 | 8.95e-01 | 0.2674 |
| 54704 | PDP1 | C57 | Human | Oral cavity | OSCC | 2.90e-33 | 1.01e+00 | 0.1679 |
| 54704 | PDP1 | C08 | Human | Oral cavity | OSCC | 5.50e-14 | 4.95e-01 | 0.1919 |
| 54704 | PDP1 | C09 | Human | Oral cavity | OSCC | 2.47e-05 | 2.32e-01 | 0.1431 |
| 54704 | PDP1 | LN22 | Human | Oral cavity | OSCC | 4.31e-07 | 6.42e-01 | 0.1733 |
| 54704 | PDP1 | LN46 | Human | Oral cavity | OSCC | 1.52e-12 | 5.64e-01 | 0.1666 |
| 54704 | PDP1 | LP15 | Human | Oral cavity | LP | 9.12e-03 | 6.01e-01 | 0.2174 |
| 54704 | PDP1 | SYSMH1 | Human | Oral cavity | OSCC | 2.72e-10 | 3.68e-01 | 0.1127 |
| 54704 | PDP1 | SYSMH2 | Human | Oral cavity | OSCC | 4.24e-13 | 6.86e-01 | 0.2326 |
| 54704 | PDP1 | SYSMH3 | Human | Oral cavity | OSCC | 1.95e-42 | 1.05e+00 | 0.2442 |
| 54704 | PDP1 | SYSMH5 | Human | Oral cavity | OSCC | 7.67e-06 | 2.89e-01 | 0.0647 |
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| 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 | ||
| 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:001631110 | Esophagus | ESCC | dephosphorylation | 251/8552 | 417/18723 | 1.26e-09 | 2.99e-08 | 251 |
| GO:000647018 | Esophagus | ESCC | protein dephosphorylation | 177/8552 | 281/18723 | 3.13e-09 | 6.72e-08 | 177 |
| GO:00359703 | Esophagus | ESCC | peptidyl-threonine dephosphorylation | 13/8552 | 16/18723 | 4.05e-03 | 1.62e-02 | 13 |
| GO:00513534 | Esophagus | ESCC | positive regulation of oxidoreductase activity | 37/8552 | 59/18723 | 6.23e-03 | 2.29e-02 | 37 |
| GO:001631121 | Liver | HCC | dephosphorylation | 230/7958 | 417/18723 | 1.00e-07 | 1.96e-06 | 230 |
| GO:000647021 | Liver | HCC | protein dephosphorylation | 162/7958 | 281/18723 | 1.91e-07 | 3.46e-06 | 162 |
| GO:00359701 | Liver | HCC | peptidyl-threonine dephosphorylation | 13/7958 | 16/18723 | 1.84e-03 | 9.42e-03 | 13 |
| GO:000647015 | Oral cavity | OSCC | protein dephosphorylation | 162/7305 | 281/18723 | 1.56e-10 | 4.56e-09 | 162 |
| GO:00163119 | Oral cavity | OSCC | dephosphorylation | 220/7305 | 417/18723 | 6.33e-09 | 1.34e-07 | 220 |
| GO:00359702 | Oral cavity | OSCC | peptidyl-threonine dephosphorylation | 13/7305 | 16/18723 | 7.05e-04 | 3.89e-03 | 13 |
| GO:00513533 | Oral cavity | OSCC | positive regulation of oxidoreductase activity | 35/7305 | 59/18723 | 1.24e-03 | 6.23e-03 | 35 |
| GO:000647016 | Oral cavity | LP | protein dephosphorylation | 89/4623 | 281/18723 | 4.60e-03 | 2.93e-02 | 89 |
| GO:000647024 | Skin | cSCC | protein dephosphorylation | 111/4864 | 281/18723 | 4.10e-07 | 7.96e-06 | 111 |
| GO:001631115 | Skin | cSCC | dephosphorylation | 134/4864 | 417/18723 | 2.65e-03 | 1.50e-02 | 134 |
| GO:001631116 | Thyroid | PTC | dephosphorylation | 174/5968 | 417/18723 | 1.20e-05 | 1.31e-04 | 174 |
| GO:000647020 | Thyroid | PTC | protein dephosphorylation | 123/5968 | 281/18723 | 1.69e-05 | 1.77e-04 | 123 |
| GO:0006470111 | Thyroid | ATC | protein dephosphorylation | 129/6293 | 281/18723 | 1.11e-05 | 1.09e-04 | 129 |
| GO:001631117 | Thyroid | ATC | dephosphorylation | 179/6293 | 417/18723 | 3.88e-05 | 3.15e-04 | 179 |
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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 |
| PDP1 | SNV | Missense_Mutation | c.1655N>A | p.Ser552Tyr | p.S552Y | Q9P0J1 | protein_coding | deleterious(0.02) | benign(0.139) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PDP1 | SNV | Missense_Mutation | c.916N>A | p.Gly306Ser | p.G306S | Q9P0J1 | protein_coding | tolerated(0.06) | possibly_damaging(0.479) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| PDP1 | SNV | Missense_Mutation | c.700N>C | p.Phe234Leu | p.F234L | Q9P0J1 | protein_coding | tolerated(0.66) | benign(0.115) | TCGA-D8-A142-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cyclophosphamid | SD | |
| PDP1 | SNV | Missense_Mutation | c.878C>A | p.Ala293Glu | p.A293E | Q9P0J1 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-D8-A1JK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PDP1 | SNV | Missense_Mutation | c.880T>A | p.Phe294Ile | p.F294I | Q9P0J1 | protein_coding | deleterious(0.04) | probably_damaging(0.959) | TCGA-D8-A1JK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PDP1 | insertion | Frame_Shift_Ins | novel | c.468_469insCAGGCACATTTTCATTGTTTTTT | p.Cys157GlnfsTer51 | p.C157Qfs*51 | Q9P0J1 | protein_coding | TCGA-A8-A09D-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR | ||
| PDP1 | insertion | Frame_Shift_Ins | novel | c.1183_1184insTTTTCCTTATAGCTGCTAAGCAGGGAACACTGTTAGTAGGT | p.Glu395ValfsTer21 | p.E395Vfs*21 | Q9P0J1 | protein_coding | TCGA-AN-A0FV-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| PDP1 | insertion | Frame_Shift_Ins | novel | c.1255_1256insCATCTCCTCAGCTTTCCCCAGCCAA | p.Tyr419SerfsTer13 | p.Y419Sfs*13 | Q9P0J1 | protein_coding | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
| PDP1 | SNV | Missense_Mutation | novel | c.711N>C | p.Leu237Phe | p.L237F | Q9P0J1 | protein_coding | tolerated(0.36) | probably_damaging(1) | TCGA-C5-A2LZ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Unknown | Unknown | PD |
| PDP1 | SNV | Missense_Mutation | c.1173N>C | p.Lys391Asn | p.K391N | Q9P0J1 | protein_coding | tolerated(0.2) | benign(0.043) | TCGA-EK-A2RJ-01 | Cervix | cervical & endocervical cancer | 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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