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mutLBSgeneDB |
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| Gene summary for PADI4 |
 Gene summary |
| Basic gene Info. | Gene symbol | PADI4 |
| Gene name | peptidyl arginine deiminase, type IV | |
| Synonyms | PAD|PAD4|PADI5|PDI4|PDI5 | |
| Cytomap | UCSC genome browser: 1p36.13 | |
| Type of gene | protein-coding | |
| RefGenes | NM_012387.2, | |
| Description | HL-60 PADPADI-H proteinpeptidyl arginine deiminase, type Vprotein-arginine deiminase type IVprotein-arginine deiminase type-4 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 605347 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000159339 | ||
| HPRD : 05635 | ||
| Vega : OTTHUMG00000002371 | ||
| Protein | UniProt: Q9UM07 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PADI4 | |
| BioGPS: 23569 | ||
| Pathway | NCI Pathway Interaction Database: PADI4 | |
| KEGG: PADI4 | ||
| REACTOME: PADI4 | ||
| Pathway Commons: PADI4 | ||
| Context | iHOP: PADI4 | |
| ligand binding site mutation search in PubMed: PADI4 | ||
| UCL Cancer Institute: PADI4 | ||
| 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:0018101 | protein citrullination | 21584310 | GO:0036413 | histone H3-R26 citrullination | 15339660 | GO:0036414 | histone citrullination | 15339660 |
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| Ligand binding site mutations for PADI4 |
| 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 | E474 | E474K | BLCA | 1 | D388 | P387T | LUAD | 1 | Q397 | G399E | SKCM | 1 | P584 | P584L | SKCM | 1 | D165 | A163S | SKCM | 1 | F634 | F633L | STAD | 1 | R639 | R639K | 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 PADI4 |
| 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 | Q397 | G399E | 0.11387808 | D388 | P387T | -1.5588275 | R639 | R639K | -1.4883414 | D165 | A163S | -1.0171284 | F634 | F633L | -0.94503981 | E474 | E474K | -0.73238623 | P584 | P584L | -0.41963936 |
| (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 PADI4 from PDB |
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| Differential gene expression and gene-gene network for PADI4 |
| 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 PADI4 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0003873 | Arthritis, Rheumatoid | 72 | AlteredExpression, Biomarker, GeneticVariation |
| umls:C0007097 | Carcinoma | 2 | Biomarker |
| umls:C0024667 | Mammary Neoplasms, Animal | 1 | Biomarker |
| umls:C0024668 | Mammary Neoplasms, Experimental | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for PADI4 |
| 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 | DB00155 | L-Citrulline | Small molecule |  |
| Approved | DB00207 | Azithromycin | Small molecule |  |
| Approved|investigational|vet_approved | DB00254 | Doxycycline | Small molecule |  |
| Approved|vet_approved | DB00759 | Tetracycline | Small molecule |  |
| Approved|vet_approved | DB01082 | Streptomycin | Small molecule |  |
| Experimental | DB07449 | N-[(1S)-1-(AMINOCARBONYL)-4-(ETHANIMIDOYLAMINO)BUTYL]BENZAMIDE | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of PADI4 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | CA | CALCIUM(2+) | 1wd9 | A | D165 | CA | CALCIUM(2+) | 1wd9 | A | D165 | CA | CALCIUM(2+) | 1wda | A | D165 | CA | CALCIUM(2+) | 1wda | A | D165 | CA | CALCIUM(2+) | 2dew | X | D165 | CA | CALCIUM(2+) | 2dew | X | D165 | CA | CALCIUM(2+) | 2dex | X | D165 | CA | CALCIUM(2+) | 2dex | X | D165 | CA | CALCIUM(2+) | 2dey | X | D165 | CA | CALCIUM(2+) | 2dey | X | D165 | CA | CALCIUM(2+) | 2dw5 | A | D165 | CA | CALCIUM(2+) | 2dw5 | A | D165 | CA | CALCIUM(2+) | 3b1t | A | D165 | CA | CALCIUM(2+) | 3b1t | A | D165 | CA | CALCIUM(2+) | 3b1u | A | D165 | CA | CALCIUM(2+) | 3b1u | A | D165 | CA | CALCIUM(2+) | 4dkt | A | D165 | CA | CALCIUM(2+) | 4dkt | A | D165 | CA | CALCIUM(2+) | 4x8g | A | D165 | CA | CALCIUM(2+) | 4x8g | A | D165 | CA | CALCIUM(2+) | 1wd9 | A | D388 | CA | CALCIUM(2+) | 1wda | A | D388 | CA | CALCIUM(2+) | 2dew | X | D388 | CA | CALCIUM(2+) | 2dex | X | D388 | CA | CALCIUM(2+) | 2dey | X | D388 | CA | CALCIUM(2+) | 2dw5 | A | D388 | CA | CALCIUM(2+) | 3b1t | A | D388 | CA | CALCIUM(2+) | 3b1u | A | D388 | CA | CALCIUM(2+) | 4dkt | A | D388 | CA | CALCIUM(2+) | 4x8g | A | D388 | 3YZ | [(3S,4R)-3-AMINO-4-HYDROXYPIPERIDIN-1-YL]{2-[1- (CYCLOPROPYLMETHYL)-1H-PYRROLO[2,3-B]PYRIDIN-2-YL]-7- METHOXY-1-METHYL-1H-BENZIMIDAZOL-5-YL}METHANONE | 4x8c | A | E474 P584 F634 | 3Z0 | [(3R)-3-AMINOPIPERIDIN-1-YL][2-(1-ETHYL-1H-PYRROLO[2,3- B]PYRIDIN-2-YL)-7-METHOXY-1-METHYL-1H-BENZIMIDAZOL-5- YL]METHANONE | 4x8g | A | E474 P584 F634 | CA | CALCIUM(2+) | 4dkt | A | Q397 | BAG | N-[(E)-1-AMINO-5-(DIAMINOMETHYLIDENEAMINO)-1-HYDROXYPENT-1-EN-2-YL]BENZAMIDE | 1wda | A | R639 | III | Peptide ligand (THR,ALA,ARG,LYS,SER) | 2dew | X | R639 | III | Peptide ligand (ALA,PRO,ARG,LYS,GLN) | 2dex | X | R639 | III | Peptide ligand (ACE,SER,GLY,ARG,GLY,LYS) | 2dey | X | R639 | BFB | (S)-N-ALPHA-BENZOYL-N5-(2-FLUORO-1-IMINOETHYL)-L-ORNITHINE AMIDE | 2dw5 | A | R639 | YCL | O-CL-AMIDINE | 3b1t | A | R639 | YFF | O-F-AMIDINE | 3b1u | A | R639 | III | Peptide ligand (ASP,ARG,NH2) | 4dkt | A | R639 |
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| Conservation information for LBS of PADI4 |
| Multiple alignments for Q9UM07 in multiple species |
| LBS | AA sequence | # species | Species | A581 | FSKAEAFFPNM | 1 | Homo sapiens | A581 | NSKAQAFFPNM | 1 | Mus musculus | A581 | NPKAEAFFPNM | 1 | Rattus norvegicus | C645 | HGEVHCGTNVR | 2 | Homo sapiens, Rattus norvegicus | C645 | NGEVHCGTNVR | 1 | Mus musculus | D155 | LLVNCDRDNLE | 1 | Homo sapiens | D155 | LLVNCDKEDPQ | 1 | Mus musculus | D155 | LLVNCDKEDPK | 1 | Rattus norvegicus | D157 | VNCDRDNLESS | 1 | Homo sapiens | D157 | VNCDKEDPQAS | 1 | Mus musculus | D157 | VNCDKEDPKSS | 1 | Rattus norvegicus | D165 | ESSAMDCEDDE | 1 | Homo sapiens | D165 | QASGMDFEDDK | 1 | Mus musculus | D165 | KSSGMDFEDDK | 1 | Rattus norvegicus | D168 | AMDCEDDEVLD | 1 | Homo sapiens | D168 | GMDFEDDKILD | 1 | Mus musculus | D168 | GMDFEDDKVLD | 1 | Rattus norvegicus | D176 | VLDSEDLQDMS | 1 | Homo sapiens | D176 | ILDNKDLQDMS | 1 | Mus musculus | D176 | VLDNKDLQDMS | 1 | Rattus norvegicus | D179 | NKDLQDMSPMT | 2 | Mus musculus, Rattus norvegicus | D179 | SEDLQDMSLMT | 1 | Homo sapiens | D344 | EEENMDDQWMQ | 1 | Homo sapiens | D344 | EEENIDDQWMQ | 1 | Mus musculus | D344 | EEENQDDQWMQ | 1 | Rattus norvegicus | D350 | DQWMQDEMEIG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | D369 | LPVVFDSPRDR | 2 | Mus musculus, Rattus norvegicus | D369 | LPVVFDSPRNR | 1 | Homo sapiens | D388 | RVMGPNFGYVT | 2 | Mus musculus, Rattus norvegicus | D388 | RVMGPDFGYVT | 1 | Homo sapiens | D473 | FVGHVDEFLSF | 2 | Mus musculus, Rattus norvegicus | D473 | SVGHVDEFLSF | 1 | Homo sapiens | E170 | DCEDDEVLDSE | 1 | Homo sapiens | E170 | DFEDDKILDNK | 1 | Mus musculus | E170 | DFEDDKVLDNK | 1 | Rattus norvegicus | E175 | EVLDSEDLQDM | 1 | Homo sapiens | E175 | KILDNKDLQDM | 1 | Mus musculus | E175 | KVLDNKDLQDM | 1 | Rattus norvegicus | E252 | TDFYVEGLAFP | 2 | Mus musculus, Rattus norvegicus | E252 | MDFYVEALAFP | 1 | Homo sapiens | E351 | QWMQDEMEIGY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E353 | MQDEMEIGYIQ | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E411 | AFGNLEVSPPV | 2 | Mus musculus, Rattus norvegicus | E411 | SFGNLEVSPPV | 1 | Homo sapiens | E474 | VGHVDEFLSFV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E580 | EFSKAEAFFPN | 1 | Homo sapiens | E580 | GNSKAQAFFPN | 1 | Mus musculus | E580 | GNPKAEAFFPN | 1 | Rattus norvegicus | F407 | TGLDAFGNLEV | 2 | Mus musculus, Rattus norvegicus | F407 | SGLDSFGNLEV | 1 | Homo sapiens | F582 | SKAEAFFPNMV | 1 | Homo sapiens | F582 | SKAQAFFPNMV | 1 | Mus musculus | F582 | PKAEAFFPNMV | 1 | Rattus norvegicus | F583 | KAEAFFPNMVN | 2 | Homo sapiens, Rattus norvegicus | F583 | KAQAFFPNMVN | 1 | Mus musculus | F634 | FINDFFTYHIR | 1 | Homo sapiens | F634 | FINDFYTYHVY | 1 | Mus musculus | F634 | FINDFYSYHMY | 1 | Rattus norvegicus | G408 | GLDAFGNLEVS | 2 | Mus musculus, Rattus norvegicus | G408 | GLDSFGNLEVS | 1 | Homo sapiens | H471 | WLFVGHVDEFL | 2 | Mus musculus, Rattus norvegicus | H471 | WLSVGHVDEFL | 1 | Homo sapiens | H640 | TYHIRHGEVHC | 1 | Homo sapiens | H640 | TYHVYNGEVHC | 1 | Mus musculus | H640 | SYHMYHGEVHC | 1 | Rattus norvegicus | K362 | IQAPHKTLPVV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K377 | RDRGLKDFPVK | 2 | Mus musculus, Rattus norvegicus | K377 | RNRGLKEFPIK | 1 | Homo sapiens | L410 | DAFGNLEVSPP | 2 | Mus musculus, Rattus norvegicus | L410 | DSFGNLEVSPP | 1 | Homo sapiens | M180 | KDLQDMSPMTL | 2 | Mus musculus, Rattus norvegicus | M180 | EDLQDMSLMTL | 1 | Homo sapiens | N153 | AILLVNCDKED | 2 | Mus musculus, Rattus norvegicus | N153 | AILLVNCDRDN | 1 | Homo sapiens | N373 | FDSPRDRGLKD | 2 | Mus musculus, Rattus norvegicus | N373 | FDSPRNRGLKE | 1 | Homo sapiens | N585 | EAFFPNMVNML | 2 | Homo sapiens, Rattus norvegicus | N585 | QAFFPNMVNML | 1 | Mus musculus | N588 | FPNMVNMLVLG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | P371 | VVFDSPRDRGL | 2 | Mus musculus, Rattus norvegicus | P371 | VVFDSPRNRGL | 1 | Homo sapiens | P584 | AEAFFPNMVNM | 2 | Homo sapiens, Rattus norvegicus | P584 | AQAFFPNMVNM | 1 | Mus musculus | Q346 | ENMDDQWMQDE | 1 | Homo sapiens | Q346 | ENIDDQWMQDE | 1 | Mus musculus | Q346 | ENQDDQWMQDE | 1 | Rattus norvegicus | Q349 | DDQWMQDEMEI | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | Q397 | VTRGPQTGGIS | 1 | Homo sapiens | Q397 | VTRKLYMSELT | 1 | Mus musculus | Q397 | VTRGLYRAEVT | 1 | Rattus norvegicus | R372 | VFDSPRDRGLK | 2 | Mus musculus, Rattus norvegicus | R372 | VFDSPRNRGLK | 1 | Homo sapiens | R374 | DSPRDRGLKDF | 2 | Mus musculus, Rattus norvegicus | R374 | DSPRNRGLKEF | 1 | Homo sapiens | R639 | FTYHIRHGEVH | 1 | Homo sapiens | R639 | YTYHVYNGEVH | 1 | Mus musculus | R639 | YSYHMYHGEVH | 1 | Rattus norvegicus | S370 | PVVFDSPRDRG | 2 | Mus musculus, Rattus norvegicus | S370 | PVVFDSPRNRG | 1 | Homo sapiens | S468 | FSDWLFVGHVD | 2 | Mus musculus, Rattus norvegicus | S468 | YSDWLSVGHVD | 1 | Homo sapiens | V469 | SDWLFVGHVDE | 2 | Mus musculus, Rattus norvegicus | V469 | SDWLSVGHVDE | 1 | Homo sapiens | W347 | NMDDQWMQDEM | 1 | Homo sapiens | W347 | NIDDQWMQDEM | 1 | Mus musculus | W347 | NQDDQWMQDEM | 1 | Rattus norvegicus |
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