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mutLBSgeneDB |
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| Gene summary for TPK1 |
 Gene summary |
| Basic gene Info. | Gene symbol | TPK1 |
| Gene name | thiamin pyrophosphokinase 1 | |
| Synonyms | HTPK1|PP20|THMD5 | |
| Cytomap | UCSC genome browser: 7q34-q35 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001042482.1, NM_022445.3, | |
| Description | placental protein 20thiamine diphosphokinasethiamine kinase | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 606370 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000196511 | ||
| HPRD : 06967 | ||
| Vega : OTTHUMG00000152774 | ||
| Protein | UniProt: Q9H3S4 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_TPK1 | |
| BioGPS: 27010 | ||
| Pathway | NCI Pathway Interaction Database: TPK1 | |
| KEGG: TPK1 | ||
| REACTOME: TPK1 | ||
| Pathway Commons: TPK1 | ||
| Context | iHOP: TPK1 | |
| ligand binding site mutation search in PubMed: TPK1 | ||
| UCL Cancer Institute: TPK1 | ||
| Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID |
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| Ligand binding site mutations for TPK1 |
| Lollipop-style diagram of mutations at LBS in amino-acid sequence. We represented ligand binding site mutations only. (You can see big image via clicking.)  : non-synonymous mutation on LBS, Circle size denotes number of samples. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | D100 | D100N | BRCA | 1 | Q134 | D133N | HNSC | 1 | Q134 | D133H | LUAD | 1 | R131 | G130W | SKCM | 1 | S216 | V215A | STAD | 1 |
| cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma. |
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| Protein structure related information for TPK1 |
| Relative protein structure stability change (ΔΔE) using Mupro 1.1 Mupro score denotes assessment of the effect of mutations on thermodynamic stability. (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability) |
 : nsSNV at non-LBS : nsSNV at LBS |
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| nsSNVs sorted by the relative stability change of protein structure by each mutation Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene. |
| LBS | AAchange of nsSNV | Relative stability change | S216 | V215A | -1.203919 | D100 | D100N | -0.78237958 | R131 | G130W | -0.78186866 | Q134 | D133N | -0.68686473 | Q134 | D133H | -0.56059104 |
| (MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132) |
| Structure image for TPK1 from PDB |
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| Differential gene expression and gene-gene network for TPK1 |
| Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types |
| Differential co-expressed gene network based on protein-protein interaction data (CePIN) |
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| Phenotype information for TPK1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C3280866 | THIAMINE METABOLISM DYSFUNCTION SYNDROME 5 (EPISODIC ENCEPHALOPATHY TYPE) | 1 | GeneticVariation |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for TPK1 |
| Gene expression profile of anticancer drug treated cell-lines (CCLE) Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient. |
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| Gene-centered drug-gene interaction network |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Approved|nutraceutical|vet_approved | DB00152 | Thiamine | Small molecule |  |
| Experimental | DB04768 | Pyrithiamine Pyrophosphate | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of TPK1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | CA | CALCIUM(2+) | 3s4y | A | D100 | CA | CALCIUM(2+) | 3s4y | B | D100 | TPP | THIAMINE(1+) DIPHOSPHATE(3-) | 3s4y | B | D100 Q134 | TPP | THIAMINE(1+) DIPHOSPHATE(3-) | 3s4y | A | D100 R131 Q134 | TPP | THIAMINE(1+) DIPHOSPHATE(3-) | 3s4y | A | S216 | TPP | THIAMINE(1+) DIPHOSPHATE(3-) | 3s4y | B | S216 |
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| Conservation information for LBS of TPK1 |
| Multiple alignments for Q9H3S4 in multiple species |
| LBS | AA sequence | # species | Species | D100 | DQDHTDFTKCL | 3 | Homo sapiens, Bos taurus, Mus musculus | D100 | DQDYTDLSKS- | 1 | Caenorhabditis elegans | D100 | NQETTDLHKCI | 1 | Oryza sativa subsp. japonica | D46 | LRACADGGANH | 2 | Bos taurus, Mus musculus | D46 | LRACADGGANR | 1 | Homo sapiens | D46 | YRVATDGAVNE | 1 | Caenorhabditis elegans | D46 | LRICADGGANR | 1 | Oryza sativa subsp. japonica | D71 | EFINGDFDSIR | 1 | Homo sapiens | D71 | HIICGDFDSIN | 1 | Caenorhabditis elegans | D71 | EIIEGDMDSIR | 1 | Oryza sativa subsp. japonica | D71 | EFISGDFDSIR | 1 | Bos taurus | D71 | EFVSGDFDSIR | 1 | Mus musculus | D73 | INGDFDSIRPE | 1 | Homo sapiens | D73 | ICGDFDSINKQ | 1 | Caenorhabditis elegans | D73 | IEGDMDSIRPE | 1 | Oryza sativa subsp. japonica | D73 | ISGDFDSIRPE | 1 | Bos taurus | D73 | VSGDFDSIRPE | 1 | Mus musculus | D97 | -TPDQDHTDFT | 3 | Homo sapiens, Bos taurus, Mus musculus | D97 | -LPDQDYTDLS | 1 | Caenorhabditis elegans | D97 | KSHNQETTDLH | 1 | Oryza sativa subsp. japonica | H98 | TPDQDHTDFTK | 3 | Homo sapiens, Bos taurus, Mus musculus | H98 | LPDQDYTDLSK | 1 | Caenorhabditis elegans | H98 | SHNQETTDLHK | 1 | Oryza sativa subsp. japonica | L204 | GLKWNLTNDVL | 2 | Homo sapiens, Mus musculus | L204 | GLKYEMENLAL | 1 | Caenorhabditis elegans | L204 | GLKWNLSEAKM | 1 | Oryza sativa subsp. japonica | L204 | GLKWNLTHQML | 1 | Bos taurus | N219 | LVSTSNTYDGS | 3 | Homo sapiens, Bos taurus, Mus musculus | N219 | LISTSNEVTTS | 1 | Caenorhabditis elegans | N219 | MISTSNIVHAE | 1 | Oryza sativa subsp. japonica | Q134 | AGRFDQIMASV | 2 | Homo sapiens, Bos taurus | Q134 | NGRFDHTMSTL | 1 | Caenorhabditis elegans | Q134 | GGRFDHEAANI | 1 | Oryza sativa subsp. japonica | Q134 | GGRFDQIMASV | 1 | Mus musculus | Q96 | S-TPDQDHTDF | 3 | Homo sapiens, Bos taurus, Mus musculus | Q96 | H-LPDQDYTDL | 1 | Caenorhabditis elegans | Q96 | DKSHNQETTDL | 1 | Oryza sativa subsp. japonica | R131 | GGLAGRFDQIM | 2 | Homo sapiens, Bos taurus | R131 | GGLNGRFDHTM | 1 | Caenorhabditis elegans | R131 | GALGGRFDHEA | 1 | Oryza sativa subsp. japonica | R131 | GGLGGRFDQIM | 1 | Mus musculus | S216 | FGTLVSTSNTY | 3 | Homo sapiens, Bos taurus, Mus musculus | S216 | FGKLISTSNEV | 1 | Caenorhabditis elegans | S216 | FGSMISTSNIV | 1 | Oryza sativa subsp. japonica | S218 | TLVSTSNTYDG | 3 | Homo sapiens, Bos taurus, Mus musculus | S218 | KLISTSNEVTT | 1 | Caenorhabditis elegans | S218 | SMISTSNIVHA | 1 | Oryza sativa subsp. japonica | T217 | GTLVSTSNTYD | 3 | Homo sapiens, Bos taurus, Mus musculus | T217 | GKLISTSNEVT | 1 | Caenorhabditis elegans | T217 | GSMISTSNIVH | 1 | Oryza sativa subsp. japonica | T99 | PDQDHTDFTKC | 3 | Homo sapiens, Bos taurus, Mus musculus | T99 | PDQDYTDLSKS | 1 | Caenorhabditis elegans | T99 | HNQETTDLHKC | 1 | Oryza sativa subsp. japonica | W202 | TTGLKWNLTND | 2 | Homo sapiens, Mus musculus | W202 | SIGLKYEMENL | 1 | Caenorhabditis elegans | W202 | TTGLKWNLSEA | 1 | Oryza sativa subsp. japonica | W202 | TTGLKWNLTHQ | 1 | Bos taurus |
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