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Gene: TPK1 |
Gene summary for TPK1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TPK1 | Gene ID | 27010 |
| Gene name | thiamin pyrophosphokinase 1 | |
| Gene Alias | HTPK1 | |
| Cytomap | 7q35 | |
| Gene Type | protein-coding | GO ID | GO:0006066 | UniProtAcc | F5GZG6 |
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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 |
| 27010 | TPK1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.58e-09 | -4.48e-01 | 0.0155 |
| 27010 | TPK1 | HTA11_10711_2000001011 | Human | Colorectum | AD | 4.55e-03 | -4.19e-01 | 0.0338 |
| 27010 | TPK1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 7.15e-12 | -3.98e-01 | 0.0674 |
| 27010 | TPK1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 3.07e-03 | -3.08e-01 | 0.294 |
| 27010 | TPK1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.44e-13 | -4.49e-01 | 0.3005 |
| 27010 | TPK1 | F007 | Human | Colorectum | FAP | 4.49e-03 | -3.42e-01 | 0.1176 |
| 27010 | TPK1 | A001-C-207 | Human | Colorectum | FAP | 3.99e-03 | -2.94e-01 | 0.1278 |
| 27010 | TPK1 | A015-C-203 | Human | Colorectum | FAP | 4.62e-17 | -4.30e-01 | -0.1294 |
| 27010 | TPK1 | A015-C-204 | Human | Colorectum | FAP | 3.13e-03 | -2.84e-01 | -0.0228 |
| 27010 | TPK1 | A002-C-201 | Human | Colorectum | FAP | 1.74e-09 | -3.64e-01 | 0.0324 |
| 27010 | TPK1 | A001-C-119 | Human | Colorectum | FAP | 7.47e-08 | -4.70e-01 | -0.1557 |
| 27010 | TPK1 | A001-C-108 | Human | Colorectum | FAP | 1.77e-09 | -3.43e-01 | -0.0272 |
| 27010 | TPK1 | A002-C-205 | Human | Colorectum | FAP | 3.18e-13 | -4.20e-01 | -0.1236 |
| 27010 | TPK1 | A001-C-104 | Human | Colorectum | FAP | 6.93e-07 | -3.08e-01 | 0.0184 |
| 27010 | TPK1 | A015-C-006 | Human | Colorectum | FAP | 7.62e-11 | -4.82e-01 | -0.0994 |
| 27010 | TPK1 | A015-C-106 | Human | Colorectum | FAP | 1.03e-06 | -2.59e-01 | -0.0511 |
| 27010 | TPK1 | A002-C-114 | Human | Colorectum | FAP | 7.28e-13 | -4.78e-01 | -0.1561 |
| 27010 | TPK1 | A015-C-104 | Human | Colorectum | FAP | 1.60e-18 | -4.23e-01 | -0.1899 |
| 27010 | TPK1 | A001-C-014 | Human | Colorectum | FAP | 7.67e-06 | -3.07e-01 | 0.0135 |
| 27010 | TPK1 | A002-C-016 | Human | Colorectum | FAP | 6.84e-09 | -2.98e-01 | 0.0521 |
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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 |
| ∗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:0042060 | Colorectum | AD | wound healing | 128/3918 | 422/18723 | 2.73e-06 | 7.89e-05 | 128 |
| GO:0006066 | Colorectum | AD | alcohol metabolic process | 106/3918 | 353/18723 | 3.02e-05 | 5.57e-04 | 106 |
| GO:0044262 | Colorectum | AD | cellular carbohydrate metabolic process | 87/3918 | 283/18723 | 6.00e-05 | 1.01e-03 | 87 |
| GO:0006790 | Colorectum | AD | sulfur compound metabolic process | 101/3918 | 339/18723 | 6.46e-05 | 1.07e-03 | 101 |
| GO:0050878 | Colorectum | AD | regulation of body fluid levels | 108/3918 | 379/18723 | 2.54e-04 | 3.20e-03 | 108 |
| GO:0034308 | Colorectum | AD | primary alcohol metabolic process | 35/3918 | 102/18723 | 1.16e-03 | 1.05e-02 | 35 |
| GO:0021915 | Colorectum | AD | neural tube development | 45/3918 | 152/18723 | 7.05e-03 | 4.31e-02 | 45 |
| GO:00420601 | Colorectum | SER | wound healing | 97/2897 | 422/18723 | 2.69e-05 | 7.30e-04 | 97 |
| GO:00060661 | Colorectum | SER | alcohol metabolic process | 79/2897 | 353/18723 | 3.50e-04 | 5.50e-03 | 79 |
| GO:00508781 | Colorectum | SER | regulation of body fluid levels | 81/2897 | 379/18723 | 1.28e-03 | 1.43e-02 | 81 |
| GO:00060662 | Colorectum | MSS | alcohol metabolic process | 92/3467 | 353/18723 | 2.57e-04 | 3.46e-03 | 92 |
| GO:00067902 | Colorectum | MSS | sulfur compound metabolic process | 85/3467 | 339/18723 | 1.52e-03 | 1.39e-02 | 85 |
| GO:00420604 | Colorectum | FAP | wound healing | 99/2622 | 422/18723 | 9.50e-08 | 6.33e-06 | 99 |
| GO:00442621 | Colorectum | FAP | cellular carbohydrate metabolic process | 66/2622 | 283/18723 | 1.53e-05 | 4.01e-04 | 66 |
| GO:00508784 | Colorectum | FAP | regulation of body fluid levels | 79/2622 | 379/18723 | 1.52e-04 | 2.35e-03 | 79 |
| GO:00219152 | Colorectum | FAP | neural tube development | 36/2622 | 152/18723 | 9.05e-04 | 9.17e-03 | 36 |
| GO:00060663 | Colorectum | FAP | alcohol metabolic process | 69/2622 | 353/18723 | 2.29e-03 | 1.85e-02 | 69 |
| GO:00420605 | Colorectum | CRC | wound healing | 80/2078 | 422/18723 | 1.06e-06 | 6.54e-05 | 80 |
| GO:00508785 | Colorectum | CRC | regulation of body fluid levels | 65/2078 | 379/18723 | 2.38e-04 | 3.96e-03 | 65 |
| GO:00442622 | Colorectum | CRC | cellular carbohydrate metabolic process | 49/2078 | 283/18723 | 1.06e-03 | 1.24e-02 | 49 |
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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. |
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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 |
| TPK1 | SNV | Missense_Mutation | c.298N>A | p.Asp100Asn | p.D100N | Q9H3S4 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-E2-A10C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| TPK1 | SNV | Missense_Mutation | novel | c.653C>A | p.Ser218Tyr | p.S218Y | Q9H3S4 | protein_coding | deleterious(0) | probably_damaging(0.975) | TCGA-AA-A01K-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | folinic | CR |
| TPK1 | SNV | Missense_Mutation | rs775457916 | c.51N>C | p.Leu17Phe | p.L17F | Q9H3S4 | protein_coding | tolerated(0.4) | benign(0.375) | TCGA-AD-6901-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD |
| TPK1 | SNV | Missense_Mutation | novel | c.493C>A | p.Leu165Ile | p.L165I | Q9H3S4 | protein_coding | deleterious(0.04) | possibly_damaging(0.752) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TPK1 | SNV | Missense_Mutation | novel | c.343A>C | p.Lys115Gln | p.K115Q | Q9H3S4 | protein_coding | tolerated(0.28) | benign(0.005) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TPK1 | SNV | Missense_Mutation | rs200717734 | c.169G>A | p.Glu57Lys | p.E57K | Q9H3S4 | protein_coding | tolerated(0.58) | benign(0.035) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| TPK1 | SNV | Missense_Mutation | c.194N>T | p.Pro65Leu | p.P65L | Q9H3S4 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CI-6624-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TPK1 | SNV | Missense_Mutation | rs368467309 | c.97N>T | p.Arg33Cys | p.R33C | Q9H3S4 | protein_coding | tolerated(0.12) | possibly_damaging(0.704) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| TPK1 | SNV | Missense_Mutation | c.330N>T | p.Lys110Asn | p.K110N | Q9H3S4 | protein_coding | tolerated(0.19) | benign(0.038) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TPK1 | SNV | Missense_Mutation | c.718N>A | p.Ala240Thr | p.A240T | Q9H3S4 | protein_coding | deleterious(0.03) | benign(0.18) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | 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 |
| 27010 | TPK1 | KINASE, ENZYME | ANTIMETABOLITE | 228770 |
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