mutLBSgeneDB |
Gene summary for PHF8 |
Gene summary |
Basic gene Info. | Gene symbol | PHF8 |
Gene name | PHD finger protein 8 | |
Synonyms | JHDM1F|MRXSSD|ZNF422 | |
Cytomap | UCSC genome browser: Xp11.22 | |
Type of gene | protein-coding | |
RefGenes | NM_001184896.1, NM_001184897.1,NM_001184898.1,NM_015107.2, | |
Description | histone lysine demethylase PHF8jumonji C domain-containing histone demethylase 1F | |
Modification date | 20141222 | |
dbXrefs | MIM : 300560 | |
HGNC : HGNC | ||
Ensembl : ENSG00000172943 | ||
HPRD : 06599 | ||
Vega : OTTHUMG00000021622 | ||
Protein | UniProt: Q9UPP1 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PHF8 | |
BioGPS: 23133 | ||
Pathway | NCI Pathway Interaction Database: PHF8 | |
KEGG: PHF8 | ||
REACTOME: PHF8 | ||
Pathway Commons: PHF8 | ||
Context | iHOP: PHF8 | |
ligand binding site mutation search in PubMed: PHF8 | ||
UCL Cancer Institute: PHF8 | ||
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:0033169 | histone H3-K9 demethylation | 20023638 | GO:0035574 | histone H4-K20 demethylation | 20622853 | GO:0045893 | positive regulation of transcription, DNA-templated | 20622853 | GO:0045943 | positive regulation of transcription from RNA polymerase I promoter | 20208542 | GO:0061188 | negative regulation of chromatin silencing at rDNA | 20208542 | GO:0070544 | histone H3-K36 demethylation | 20208542 | GO:0071557 | histone H3-K27 demethylation | 20622853 |
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Ligand binding site mutations for PHF8 |
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. |
Cancer type specific mutLBS sorted by frequency |
LBS | AAchange of nsSNV | Cancer type | # samples | H355 | H355Y | LUAD | 1 | Q201 | R200H | 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 PHF8 |
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 |
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 | Q201 | R200H | -0.96741248 | H355 | H355Y | -0.17696098 |
(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 PHF8 from PDB |
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Differential gene expression and gene-gene network for PHF8 |
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 PHF8 |
Gene level disease information (DisGeNet) |
Disease ID | Disease name | # PubMed | Association type |
umls:C1846055 | Siderius X-linked mental retardation syndrome | 2 | Biomarker, GeneticVariation |
Mutation level pathogenic information (ClinVar annotation) |
Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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Pharmacological information for PHF8 |
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. |
Drug information targeting mutLBSgene (Approved drugs only) |
Drug status | DrugBank ID | Name | Type | Drug structure |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of PHF8 go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS |
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Conservation information for LBS of PHF8 |
Multiple alignments for Q9UPP1 in multiple species |
LBS | AA sequence | # species | Species | A202 | DVTRQADCKMK | 1 | Homo sapiens | A202 | DVSRQADLKMK | 1 | Danio rerio | A202 | DVARQADCKMK | 1 | Mus musculus | A392 | KRLSTADLFKF | 2 | Danio rerio, Mus musculus | A392 | KRLSTADLFRF | 1 | Homo sapiens | A78 | VEEEKAADIDL | 2 | Homo sapiens, Mus musculus | A78 | VEEDKAAEIDL | 1 | Danio rerio | C44 | SVPVYCLCRLP | 3 | Homo sapiens, Danio rerio, Mus musculus | C46 | PVYCLCRLPYD | 3 | Homo sapiens, Danio rerio, Mus musculus | C59 | RFMIECDMCQD | 2 | Homo sapiens, Mus musculus | C59 | RFMIECDVCQD | 1 | Danio rerio | C62 | IECDMCQDWFH | 2 | Homo sapiens, Mus musculus | C62 | IECDVCQDWFH | 1 | Danio rerio | C70 | WFHGSCVGVEE | 3 | Homo sapiens, Danio rerio, Mus musculus | C86 | IDLYHCPNCEV | 2 | Homo sapiens, Mus musculus | C86 | IDLYHCPNCQV | 1 | Danio rerio | C89 | YHCPNCEVLHG | 2 | Homo sapiens, Mus musculus | C89 | YHCPNCQVTHG | 1 | Danio rerio | D203 | VTRQADCKMKL | 1 | Homo sapiens | D203 | VSRQADLKMKL | 1 | Danio rerio | D203 | VARQADCKMKL | 1 | Mus musculus | D285 | TDFHIDFGGTS | 3 | Homo sapiens, Danio rerio, Mus musculus | D362 | VLTPVDCLAFG | 3 | Homo sapiens, Danio rerio, Mus musculus | D393 | RLSTADLFKFP | 2 | Danio rerio, Mus musculus | D393 | RLSTADLFRFP | 1 | Homo sapiens | E386 | KAYEIEKRLST | 2 | Homo sapiens, Mus musculus | E386 | RAYEIEKRLST | 1 | Danio rerio | E58 | TRFMIECDMCQ | 2 | Homo sapiens, Mus musculus | E58 | TRFMIECDVCQ | 1 | Danio rerio | F282 | DSYTDFHIDFG | 3 | Homo sapiens, Danio rerio, Mus musculus | F286 | DFHIDFGGTSV | 3 | Homo sapiens, Danio rerio, Mus musculus | F315 | ANLTLFECWSS | 2 | Homo sapiens, Mus musculus | F315 | ANLSLFERWSS | 1 | Danio rerio | F395 | STADLFKFPNF | 2 | Danio rerio, Mus musculus | F395 | STADLFRFPNF | 1 | Homo sapiens | F55 | YDVTRFMIECD | 3 | Homo sapiens, Danio rerio, Mus musculus | G218 | KYYYSGKREKV | 2 | Homo sapiens, Mus musculus | G218 | EYYNSPNRDRV | 1 | Danio rerio | H283 | SYTDFHIDFGG | 3 | Homo sapiens, Danio rerio, Mus musculus | H355 | PTGWIHAVLTP | 3 | Homo sapiens, Danio rerio, Mus musculus | H67 | CQDWFHGSCVG | 3 | Homo sapiens, Danio rerio, Mus musculus | I196 | KEIDVIDVTRQ | 1 | Homo sapiens | I196 | KEIDVIDVSRQ | 1 | Danio rerio | I196 | KEIDVIDVARQ | 1 | Mus musculus | I227 | KVLNVISLEFS | 2 | Homo sapiens, Mus musculus | I227 | RVLNVISLEFS | 1 | Danio rerio | I284 | YTDFHIDFGGT | 3 | Homo sapiens, Danio rerio, Mus musculus | I57 | VTRFMIECDMC | 2 | Homo sapiens, Mus musculus | I57 | VTRFMIECDVC | 1 | Danio rerio | I81 | EKAADIDLYHC | 2 | Homo sapiens, Mus musculus | I81 | DKAAEIDLYHC | 1 | Danio rerio | K300 | VLKGEKIFYLI | 2 | Homo sapiens, Mus musculus | K300 | VLRGEKIFYLI | 1 | Danio rerio | L272 | VQKYCLMSVRD | 2 | Homo sapiens, Mus musculus | L272 | VQKYCLMGVKD | 1 | Danio rerio | L389 | EIEKRLSTADL | 3 | Homo sapiens, Danio rerio, Mus musculus | L394 | LSTADLFKFPN | 2 | Danio rerio, Mus musculus | L394 | LSTADLFRFPN | 1 | Homo sapiens | M56 | DVTRFMIECDM | 2 | Homo sapiens, Mus musculus | M56 | DVTRFMIECDV | 1 | Danio rerio | N225 | REKVLNVISLE | 2 | Homo sapiens, Mus musculus | N225 | RDRVLNVISLE | 1 | Danio rerio | N325 | SSSNQNEMFFG | 2 | Homo sapiens, Mus musculus | N325 | SSSNQNELFFG | 1 | Danio rerio | N369 | LAFGGNFLHSL | 3 | Homo sapiens, Danio rerio, Mus musculus | Q201 | IDVTRQADCKM | 1 | Homo sapiens | Q201 | IDVSRQADLKM | 1 | Danio rerio | Q201 | IDVARQADCKM | 1 | Mus musculus | Q324 | SSSSNQNEMFF | 2 | Homo sapiens, Mus musculus | Q324 | SSSSNQNELFF | 1 | Danio rerio | R220 | YYSGKREKVLN | 2 | Homo sapiens, Mus musculus | R220 | YNSPNRDRVLN | 1 | Danio rerio | R396 | TADLFKFPNFE | 2 | Danio rerio, Mus musculus | R396 | TADLFRFPNFE | 1 | Homo sapiens | S228 | VLNVISLEFSD | 3 | Homo sapiens, Danio rerio, Mus musculus | S319 | LFECWSSSSNQ | 2 | Homo sapiens, Mus musculus | S319 | LFERWSSSSNQ | 1 | Danio rerio | S320 | FECWSSSSNQN | 2 | Homo sapiens, Mus musculus | S320 | FERWSSSSNQN | 1 | Danio rerio | S322 | CWSSSSNQNEM | 2 | Homo sapiens, Mus musculus | S322 | RWSSSSNQNEL | 1 | Danio rerio | S390 | IEKRLSTADLF | 3 | Homo sapiens, Danio rerio, Mus musculus | T280 | VRDSYTDFHID | 2 | Homo sapiens, Mus musculus | T280 | VKDSYTDFHID | 1 | Danio rerio | T391 | EKRLSTADLFK | 2 | Danio rerio, Mus musculus | T391 | EKRLSTADLFR | 1 | Homo sapiens | V357 | GWIHAVLTPVD | 3 | Homo sapiens, Danio rerio, Mus musculus | V52 | RLPYDVTRFMI | 3 | Homo sapiens, Danio rerio, Mus musculus | W65 | DMCQDWFHGSC | 2 | Homo sapiens, Mus musculus | W65 | DVCQDWFHGSC | 1 | Danio rerio | Y215 | DFVKYYYSGKR | 2 | Homo sapiens, Mus musculus | Y215 | EFVEYYNSPNR | 1 | Danio rerio | Y216 | FVKYYYSGKRE | 2 | Homo sapiens, Mus musculus | Y216 | FVEYYNSPNRD | 1 | Danio rerio | Y270 | PNVQKYCLMSV | 2 | Homo sapiens, Mus musculus | Y270 | PNVQKYCLMGV | 1 | Danio rerio | Y293 | GTSVWYHVLKG | 2 | Homo sapiens, Mus musculus | Y293 | GTSVWYHVLRG | 1 | Danio rerio | Y43 | ASVPVYCLCRL | 3 | Homo sapiens, Danio rerio, Mus musculus | Y50 | LCRLPYDVTRF | 3 | Homo sapiens, Danio rerio, Mus musculus |
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