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mutLBSgeneDB |
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| Gene summary for PHF2 |
 Gene summary |
| Basic gene Info. | Gene symbol | PHF2 |
| Gene name | PHD finger protein 2 | |
| Synonyms | CENP-35|GRC5|JHDM1E | |
| Cytomap | UCSC genome browser: 9q22.31 | |
| Type of gene | protein-coding | |
| RefGenes | NM_005392.3, NM_024517.1, | |
| Description | centromere protein 35jumonji C domain-containing histone demethylase 1Elysine-specific demethylase PHF2 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 604351 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000197724 | ||
| HPRD : 05071 | ||
| Vega : OTTHUMG00000020253 | ||
| Protein | UniProt: O75151 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PHF2 | |
| BioGPS: 5253 | ||
| Pathway | NCI Pathway Interaction Database: PHF2 | |
| KEGG: PHF2 | ||
| REACTOME: PHF2 | ||
| Pathway Commons: PHF2 | ||
| Context | iHOP: PHF2 | |
| ligand binding site mutation search in PubMed: PHF2 | ||
| UCL Cancer Institute: PHF2 | ||
| 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 | GO:0006482 | protein demethylation | 21532585 |
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| Ligand binding site mutations for PHF2 |
| 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 | E39 | E38Q | 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 PHF2 |
| 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 | E39 | E38Q | -0.2082789 |
| (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 PHF2 from PDB |
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| Differential gene expression and gene-gene network for PHF2 |
| 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 PHF2 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for PHF2 |
| 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 PHF2 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | III | Peptide ligand (ALA,ARG,THR,LYS,GLN,THR) | 3kqi | A | E39 |
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| Conservation information for LBS of PHF2 |
| Multiple alignments for O75151 in multiple species |
| LBS | AA sequence | # species | Species | C10 | PVYCVCRLPYD | 2 | Homo sapiens, Mus musculus | C10 | PVYCICRLPYD | 1 | Danio rerio | C23 | RFMIECDACKD | 2 | Homo sapiens, Mus musculus | C23 | QFMIECDACKD | 1 | Danio rerio | C240 | KYCLICVKDSY | 3 | Homo sapiens, Danio rerio, Mus musculus | C26 | IECDACKDWFH | 3 | Homo sapiens, Danio rerio, Mus musculus | C34 | WFHGSCVGVEE | 2 | Homo sapiens, Mus musculus | C34 | WFHGSCVGVDE | 1 | Danio rerio | C50 | IDIYHCPNCEK | 3 | Homo sapiens, Danio rerio, Mus musculus | C53 | YHCPNCEKTHG | 3 | Homo sapiens, Danio rerio, Mus musculus | C8 | TVPVYCVCRLP | 2 | Homo sapiens, Mus musculus | C8 | TVPVYCICRLP | 1 | Danio rerio | D251 | TDFHIDSGGAS | 2 | Homo sapiens, Mus musculus | D251 | TDFHIECGGAS | 1 | Danio rerio | D46 | EAPDIDIYHCP | 3 | Homo sapiens, Danio rerio, Mus musculus | E22 | TRFMIECDACK | 2 | Homo sapiens, Mus musculus | E22 | TQFMIECDACK | 1 | Danio rerio | E39 | CVGVEEEEAPD | 2 | Homo sapiens, Mus musculus | E39 | CVGVDEDEAPD | 1 | Danio rerio | F19 | YDVTRFMIECD | 2 | Homo sapiens, Mus musculus | F19 | YDVTQFMIECD | 1 | Danio rerio | H249 | SYTDFHIDSGG | 2 | Homo sapiens, Mus musculus | H249 | SYTDFHIECGG | 1 | Danio rerio | H31 | CKDWFHGSCVG | 3 | Homo sapiens, Danio rerio, Mus musculus | H335 | LAFAGHFLHSL | 2 | Homo sapiens, Mus musculus | H335 | LAFSGHFVHSL | 1 | Danio rerio | I21 | VTRFMIECDAC | 2 | Homo sapiens, Mus musculus | I21 | VTQFMIECDAC | 1 | Danio rerio | I45 | EEAPDIDIYHC | 2 | Homo sapiens, Mus musculus | I45 | DEAPDIDIYHC | 1 | Danio rerio | K266 | VLKGEKTFYLI | 1 | Homo sapiens | K266 | VLKGEKIFFLI | 1 | Danio rerio | K266 | VLKGEKIFYLI | 1 | Mus musculus | L238 | VTKYCLICVKD | 2 | Homo sapiens, Mus musculus | L238 | VSKYCLICVKD | 1 | Danio rerio | M20 | DVTRFMIECDA | 2 | Homo sapiens, Mus musculus | M20 | DVTQFMIECDA | 1 | Danio rerio | R18 | PYDVTRFMIEC | 2 | Homo sapiens, Mus musculus | R18 | PYDVTQFMIEC | 1 | Danio rerio | T17 | LPYDVTRFMIE | 2 | Homo sapiens, Mus musculus | T17 | LPYDVTQFMIE | 1 | Danio rerio | T193 | RVLNVTNLEFS | 2 | Homo sapiens, Mus musculus | T193 | KVLNVINLEFS | 1 | Danio rerio | T246 | VKDSYTDFHID | 2 | Homo sapiens, Mus musculus | T246 | VKDSYTDFHIE | 1 | Danio rerio | T323 | GWIYATLTPVD | 2 | Homo sapiens, Mus musculus | T323 | GWINAILTPVD | 1 | Danio rerio | W29 | DACKDWFHGSC | 3 | Homo sapiens, Danio rerio, Mus musculus | Y14 | VCRLPYDVTRF | 2 | Homo sapiens, Mus musculus | Y14 | ICRLPYDVTQF | 1 | Danio rerio | Y259 | GASAWYHVLKG | 2 | Homo sapiens, Mus musculus | Y259 | GASVWYHVLKG | 1 | Danio rerio | Y321 | PSGWIYATLTP | 2 | Homo sapiens, Mus musculus | Y321 | PSGWINAILTP | 1 | Danio rerio | Y7 | ATVPVYCVCRL | 2 | Homo sapiens, Mus musculus | Y7 | ATVPVYCICRL | 1 | Danio rerio |
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