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mutLBSgeneDB |
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| Gene summary for TFAM |
 Gene summary |
| Basic gene Info. | Gene symbol | TFAM |
| Gene name | transcription factor A, mitochondrial | |
| Synonyms | MTTF1|MTTFA|TCF6|TCF6L1|TCF6L2|TCF6L3 | |
| Cytomap | UCSC genome browser: 10q21 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001270782.1, NM_003201.2,NR_073073.1,NM_012251.1, | |
| Description | mitochondrial transcription factor 1mitochondrial transcription factor Atranscription factor 6transcription factor 6-like 1transcription factor 6-like 2 (mitochondrial transcription factor)transcription factor 6-like 3 | |
| Modification date | 20141222 | |
| dbXrefs | MIM : 600438 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000108064 | ||
| HPRD : 02702 | ||
| Vega : OTTHUMG00000018270 | ||
| Protein | UniProt: Q00059 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_TFAM | |
| BioGPS: 7019 | ||
| Pathway | NCI Pathway Interaction Database: TFAM | |
| KEGG: TFAM | ||
| REACTOME: TFAM | ||
| Pathway Commons: TFAM | ||
| Context | iHOP: TFAM | |
| ligand binding site mutation search in PubMed: TFAM | ||
| UCL Cancer Institute: TFAM | ||
| Assigned class in mutLBSgeneDB | B: This gene belongs to targetable_mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID | GO:0006391 | transcription initiation from mitochondrial promoter | 20410300 | GO:0045893 | positive regulation of transcription, DNA-templated | 20410300 | GO:0045944 | positive regulation of transcription from RNA polymerase II promoter | 20410300 |
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| Ligand binding site mutations for TFAM |
| 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 | Y103,W107 | A105V | COAD | 1 | R140 | K141N | HNSC | 1 | P178 | P178Q | KIRC | 1 | R233 | R233H | LAML | 1 | M143 | M143I | PRAD | 1 | E208 | D207N | SKCM | 1 | K51 | K51N | UCEC | 1 | R232 | R232C | UCEC | 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 TFAM |
| 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 | Y103 | A105V | 0.1817326 | W107 | A105V | 0.1817326 | R232 | R232C | -1.1596273 | R233 | R233H | -1.1024295 | R140 | K141N | -0.89761734 | E208 | D207N | -0.8768129 | M143 | M143I | -0.85867888 | P178 | P178Q | -0.77264644 | K51 | K51N | -0.66222004 |
| (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 TFAM from PDB |
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| Differential gene expression and gene-gene network for TFAM |
| 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 TFAM |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0002395 | Alzheimer Disease | 8 | Biomarker, GeneticVariation |
| umls:C0006079 | Bowen's Disease | 1 | Biomarker |
| umls:C2931673 | Ceroid lipofuscinosis, neuronal 1, infantile | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for TFAM |
| 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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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of TFAM go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | NUC | Nucleic Acids | 3tq6 | A | R140 E208 R232 R233 | NUC | Nucleic Acids | 3tq6 | B | R140 E208 R232 R233 | NUC | Nucleic Acids | 4nnu | A | R140 E208 R232 R233 | NUC | Nucleic Acids | 4nod | B | R140 M143 E208 | NUC | Nucleic Acids | 4nnu | B | R140 M143 E208 R232 R233 | NUC | Nucleic Acids | 4nnu | A | R140 M143 P178 | NUC | Nucleic Acids | 4nod | A | R140 M143 P178 E208 | NUC | Nucleic Acids | 4nod | G | R140 M143 P178 E208 | NUC | Nucleic Acids | 4nod | H | R140 M143 P178 E208 | NUC | Nucleic Acids | 4nnu | B | Y103 M143 P178 | NUC | Nucleic Acids | 3tq6 | A | Y103 R140 M143 P178 | NUC | Nucleic Acids | 3tq6 | B | Y103 R140 M143 P178 | NUC | Nucleic Acids | 4nnu | A | Y103 W107 | NUC | Nucleic Acids | 4nnu | B | Y103 W107 | NUC | Nucleic Acids | 4nod | B | Y103 W107 R140 M143 P178 | NUC | Nucleic Acids | 4nod | G | Y103 W107 R140 M143 P178 | NUC | Nucleic Acids | 4nod | H | Y103 W107 R140 M143 P178 | NUC | Nucleic Acids | 4nod | A | Y103 W107 R140 P178 |
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| Conservation information for LBS of TFAM |
| Multiple alignments for Q00059 in multiple species |
| LBS | AA sequence | # species | Species | A167 | YNIYVSESFQE | 2 | Mus musculus, Rattus norvegicus | A167 | YNVYVAERFQE | 1 | Homo sapiens | A167 | YNIFIAERFQE | 1 | Bos taurus | A85 | LIRRIAQRWRE | 1 | Homo sapiens | A85 | LVRKIAALWRE | 1 | Mus musculus | A85 | LIRKIAAMWRE | 1 | Rattus norvegicus | A85 | LIKKIAKLWRE | 1 | Bos taurus | E208 | LAKDDRIRYDN | 2 | Mus musculus, Rattus norvegicus | E208 | HAKEDETRYHN | 1 | Homo sapiens | E208 | LAKDDKIRYYN | 1 | Bos taurus | F170 | YVSESFQEAKD | 2 | Mus musculus, Rattus norvegicus | F170 | YVAERFQEAKG | 1 | Homo sapiens | F170 | FIAERFQEARD | 1 | Bos taurus | H137 | EIMDKHLKRKA | 1 | Homo sapiens | H137 | EARQRRLKKKA | 1 | Mus musculus | H137 | EARQKRLKKKA | 1 | Rattus norvegicus | H137 | EIMQKRLKKKA | 1 | Bos taurus | I235 | LLRRTIKKQRK | 1 | Homo sapiens | I235 | LIRRSVKR-SG | 1 | Mus musculus | I235 | LIRRSVKRPPG | 1 | Rattus norvegicus | I235 | LIRRSIKYPAK | 1 | Bos taurus | I81 | KTTELIRRIAQ | 1 | Homo sapiens | I81 | KLSELVRKIAA | 1 | Mus musculus | I81 | KVSELIRKIAA | 1 | Rattus norvegicus | I81 | KNSELIKKIAK | 1 | Bos taurus | K136 | KEIMDKHLKRK | 1 | Homo sapiens | K136 | KEARQRRLKKK | 1 | Mus musculus | K136 | KEARQKRLKKK | 1 | Rattus norvegicus | K136 | KEIMQKRLKKK | 1 | Bos taurus | K139 | MDKHLKRKAMT | 1 | Homo sapiens | K139 | RQRRLKKKALV | 1 | Mus musculus | K139 | RQKRLKKKAQI | 1 | Rattus norvegicus | K139 | MQKRLKKKALI | 1 | Bos taurus | K146 | KAMTKKKELTL | 1 | Homo sapiens | K146 | KALVKRRELIL | 1 | Mus musculus | K146 | KAQIKRRELIL | 1 | Rattus norvegicus | K146 | KALIKKRELTM | 1 | Bos taurus | K147 | AMTKKKELTLL | 1 | Homo sapiens | K147 | ALVKRRELILL | 1 | Mus musculus | K147 | AQIKRRELILL | 1 | Rattus norvegicus | K147 | ALIKKRELTML | 1 | Bos taurus | K156 | LLGKPKRPRSA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K156 | MLGKPKRPRSA | 1 | Bos taurus | K183 | PQEKLKTVKEN | 1 | Homo sapiens | K183 | AQGKLKLVNEA | 1 | Mus musculus | K183 | AQGKLKLVNQA | 1 | Rattus norvegicus | K183 | SQVKLKAINEN | 1 | Bos taurus | K186 | KLKTVKENWKN | 1 | Homo sapiens | K186 | KLKLVNEAWKN | 1 | Mus musculus | K186 | KLKLVNQAWKN | 1 | Rattus norvegicus | K186 | KLKAINENWKN | 1 | Bos taurus | K190 | VKENWKNLSDS | 1 | Homo sapiens | K190 | VNEAWKNLSPE | 1 | Mus musculus | K190 | VNQAWKNLSHD | 1 | Rattus norvegicus | K190 | INENWKNLSNS | 1 | Bos taurus | K51 | LASCPKKPVSS | 1 | Homo sapiens | K51 | MGSYPKKPMSS | 1 | Mus musculus | K51 | LGNYPKKPMSS | 1 | Rattus norvegicus | K51 | LSGYPKKPMTS | 1 | Bos taurus | K52 | ASCPKKPVSSY | 1 | Homo sapiens | K52 | GSYPKKPMSSY | 1 | Mus musculus | K52 | GNYPKKPMSSY | 1 | Rattus norvegicus | K52 | SGYPKKPMTSY | 1 | Bos taurus | K62 | YLRFSTEQLPK | 2 | Mus musculus, Rattus norvegicus | K62 | YLRFSKEQLPI | 1 | Homo sapiens | K62 | YVRFSKEQLPI | 1 | Bos taurus | K69 | QLPIFKAQNPD | 2 | Homo sapiens, Bos taurus | K69 | QLPKFKAKHPD | 2 | Mus musculus, Rattus norvegicus | L182 | SPQEKLKTVKE | 1 | Homo sapiens | L182 | SAQGKLKLVNE | 1 | Mus musculus | L182 | SAQGKLKLVNQ | 1 | Rattus norvegicus | L182 | TSQVKLKAINE | 1 | Bos taurus | L58 | PMSSYLRFSTE | 2 | Mus musculus, Rattus norvegicus | L58 | PVSSYLRFSKE | 1 | Homo sapiens | L58 | PMTSYVRFSKE | 1 | Bos taurus | L65 | FSKEQLPIFKA | 2 | Homo sapiens, Bos taurus | L65 | FSTEQLPKFKA | 2 | Mus musculus, Rattus norvegicus | M143 | LKRKAMTKKKE | 1 | Homo sapiens | M143 | LKKKALVKRRE | 1 | Mus musculus | M143 | LKKKAQIKRRE | 1 | Rattus norvegicus | M143 | LKKKALIKKRE | 1 | Bos taurus | N163 | PRSAYNIYVSE | 2 | Mus musculus, Rattus norvegicus | N163 | PRSAYNVYVAE | 1 | Homo sapiens | N163 | PRSAYNIFIAE | 1 | Bos taurus | P158 | GKPKRPRSAYN | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus | P178 | AKGDSPQEKLK | 1 | Homo sapiens | P178 | AKDDSAQGKLK | 1 | Mus musculus | P178 | AKDESAQGKLK | 1 | Rattus norvegicus | P178 | ARDGTSQVKLK | 1 | Bos taurus | Q100 | EKKVYEADFKA | 2 | Mus musculus, Rattus norvegicus | Q100 | KKKIYQDAYRA | 1 | Homo sapiens | Q100 | EKKIYEDAYRA | 1 | Bos taurus | Q179 | KGDSPQEKLKT | 1 | Homo sapiens | Q179 | KDDSAQGKLKL | 1 | Mus musculus | Q179 | KDESAQGKLKL | 1 | Rattus norvegicus | Q179 | RDGTSQVKLKA | 1 | Bos taurus | R140 | DKHLKRKAMTK | 1 | Homo sapiens | R140 | QRRLKKKALVK | 1 | Mus musculus | R140 | QKRLKKKAQIK | 1 | Rattus norvegicus | R140 | QKRLKKKALIK | 1 | Bos taurus | R157 | LGKPKRPRSAY | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus | R159 | KPKRPRSAYNI | 3 | Mus musculus, Rattus norvegicus, Bos taurus | R159 | KPKRPRSAYNV | 1 | Homo sapiens | R232 | RSDLIRRSVKR | 2 | Mus musculus, Rattus norvegicus | R232 | RKDLLRRTIKK | 1 | Homo sapiens | R232 | REDLIRRSIKY | 1 | Bos taurus | R233 | KDLLRRTIKKQ | 1 | Homo sapiens | R233 | SDLIRRSVKR- | 1 | Mus musculus | R233 | SDLIRRSVKRP | 1 | Rattus norvegicus | R233 | EDLIRRSIKYP | 1 | Bos taurus | R5 | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus | R82 | TTELIRRIAQR | 1 | Homo sapiens | R82 | LSELVRKIAAL | 1 | Mus musculus | R82 | VSELIRKIAAM | 1 | Rattus norvegicus | R82 | NSELIKKIAKL | 1 | Bos taurus | R89 | IAQRWRELPDS | 1 | Homo sapiens | R89 | IAALWRELPEA | 1 | Mus musculus | R89 | IAAMWRELPEA | 1 | Rattus norvegicus | R89 | IAKLWRELPDS | 1 | Bos taurus | S160 | PKRPRSAYNIY | 2 | Mus musculus, Rattus norvegicus | S160 | PKRPRSAYNVY | 1 | Homo sapiens | S160 | PKRPRSAYNIF | 1 | Bos taurus | S55 | PKKPMSSYLRF | 2 | Mus musculus, Rattus norvegicus | S55 | PKKPVSSYLRF | 1 | Homo sapiens | S55 | PKKPMTSYVRF | 1 | Bos taurus | S56 | KKPMSSYLRFS | 2 | Mus musculus, Rattus norvegicus | S56 | KKPVSSYLRFS | 1 | Homo sapiens | S56 | KKPMTSYVRFS | 1 | Bos taurus | S61 | SYLRFSTEQLP | 2 | Mus musculus, Rattus norvegicus | S61 | SYLRFSKEQLP | 1 | Homo sapiens | S61 | SYVRFSKEQLP | 1 | Bos taurus | T144 | KRKAMTKKKEL | 1 | Homo sapiens | T144 | KKKALVKRREL | 1 | Mus musculus | T144 | KKKAQIKRREL | 1 | Rattus norvegicus | T144 | KKKALIKKREL | 1 | Bos taurus | T150 | KRRELILLGKP | 2 | Mus musculus, Rattus norvegicus | T150 | KKKELTLLGKP | 1 | Homo sapiens | T150 | KKRELTMLGKP | 1 | Bos taurus | T234 | DLLRRTIKKQR | 1 | Homo sapiens | T234 | DLIRRSVKR-S | 1 | Mus musculus | T234 | DLIRRSVKRPP | 1 | Rattus norvegicus | T234 | DLIRRSIKYPA | 1 | Bos taurus | T77 | NPDAKTTELIR | 1 | Homo sapiens | T77 | HPDAKLSELVR | 1 | Mus musculus | T77 | HPDAKVSELIR | 1 | Rattus norvegicus | T77 | NPDAKNSELIK | 1 | Bos taurus | T78 | PDAKTTELIRR | 1 | Homo sapiens | T78 | PDAKLSELVRK | 1 | Mus musculus | T78 | PDAKVSELIRK | 1 | Rattus norvegicus | T78 | PDAKNSELIKK | 1 | Bos taurus | V166 | AYNIYVSESFQ | 2 | Mus musculus, Rattus norvegicus | V166 | AYNVYVAERFQ | 1 | Homo sapiens | V166 | AYNIFIAERFQ | 1 | Bos taurus | V54 | YPKKPMSSYLR | 2 | Mus musculus, Rattus norvegicus | V54 | CPKKPVSSYLR | 1 | Homo sapiens | V54 | YPKKPMTSYVR | 1 | Bos taurus | W107 | AYRAEWQVYKE | 1 | Homo sapiens | W107 | DFKAEWKAYKE | 1 | Mus musculus | W107 | DFKAEWKVYKE | 1 | Rattus norvegicus | W107 | AYRADWQVYKE | 1 | Bos taurus | W189 | TVKENWKNLSD | 1 | Homo sapiens | W189 | LVNEAWKNLSP | 1 | Mus musculus | W189 | LVNQAWKNLSH | 1 | Rattus norvegicus | W189 | AINENWKNLSN | 1 | Bos taurus | W88 | RIAQRWRELPD | 1 | Homo sapiens | W88 | KIAALWRELPE | 1 | Mus musculus | W88 | KIAAMWRELPE | 1 | Rattus norvegicus | W88 | KIAKLWRELPD | 1 | Bos taurus | Y103 | VYEADFKAEWK | 2 | Mus musculus, Rattus norvegicus | Y103 | IYQDAYRAEWQ | 1 | Homo sapiens | Y103 | IYEDAYRADWQ | 1 | Bos taurus | Y162 | RPRSAYNIYVS | 2 | Mus musculus, Rattus norvegicus | Y162 | RPRSAYNVYVA | 1 | Homo sapiens | Y162 | RPRSAYNIFIA | 1 | Bos taurus | Y211 | DDRIRYDNEMK | 2 | Mus musculus, Rattus norvegicus | Y211 | EDETRYHNEMK | 1 | Homo sapiens | Y211 | DDKIRYYNEMK | 1 | Bos taurus | Y57 | KPMSSYLRFST | 2 | Mus musculus, Rattus norvegicus | Y57 | KPVSSYLRFSK | 1 | Homo sapiens | Y57 | KPMTSYVRFSK | 1 | Bos taurus |
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