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mutLBSgeneDB |
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| Gene summary for PADI2 |
 Gene summary |
| Basic gene Info. | Gene symbol | PADI2 |
| Gene name | peptidyl arginine deiminase, type II | |
| Synonyms | PAD-H19|PAD2|PDI2 | |
| Cytomap | UCSC genome browser: 1p36.13 | |
| Type of gene | protein-coding | |
| RefGenes | NM_007365.2, | |
| Description | protein-arginine deiminase type IIprotein-arginine deiminase type-2 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 607935 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000117115 | ||
| HPRD : 06396 | ||
| Vega : OTTHUMG00000002295 | ||
| Protein | UniProt: Q9Y2J8 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PADI2 | |
| BioGPS: 11240 | ||
| Pathway | NCI Pathway Interaction Database: PADI2 | |
| KEGG: PADI2 | ||
| REACTOME: PADI2 | ||
| Pathway Commons: PADI2 | ||
| Context | iHOP: PADI2 | |
| ligand binding site mutation search in PubMed: PADI2 | ||
| UCL Cancer Institute: PADI2 | ||
| 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:0010848 | regulation of chromatin disassembly | 22853951 | GO:0018101 | protein citrullination | 12392711 | GO:0036413 | histone H3-R26 citrullination | 22853951 | GO:0070100 | negative regulation of chemokine-mediated signaling pathway | 18645041 | GO:1901624 | negative regulation of lymphocyte chemotaxis | 18645041 |
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| Ligand binding site mutations for PADI2 |
| 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 | D177 | L178V | BRCA | 1 | K363 | G364C | COAD | 1 | D125,D127 | R126P | HNSC | 1 | D123 | V122L | LUSC | 1 | E131 | N133K | LUSC | 1 | D125,D127 | R126W | OV | 1 | D127 | D127N | SKCM | 1 | K378 | F380L | 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 PADI2 |
| 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 | D177 | L178V | -1.2365836 | D123 | V122L | -1.184453 | K378 | F380L | -1.095134 | D127 | R126P | -1.0632854 | D125 | R126P | -1.0632854 | D125 | R126W | -0.96389424 | D127 | R126W | -0.96389424 | D127 | D127N | -0.90666798 | K363 | G364C | -0.70060691 | E131 | N133K | -0.64060985 |
| (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 PADI2 from PDB |
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| Differential gene expression and gene-gene network for PADI2 |
| 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 PADI2 |
| 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 PADI2 |
| 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 |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of PADI2 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | CA | CALCIUM(2+) | 4n20 | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n22 | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n24 | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n25 | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n26 | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n28 | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n2a | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n2b | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n2c | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n2f | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n2g | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n2h | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n2i | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n2k | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n2l | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n2m | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n2n | A | D123 D125 D127 E131 | CA | CALCIUM(2+) | 4n2d | A | D125 D127 E131 | CA | CALCIUM(2+) | 4n2e | A | D125 D127 E131 | CA | CALCIUM(2+) | 4n25 | A | D177 | CA | CALCIUM(2+) | 4n26 | A | D177 | CA | CALCIUM(2+) | 4n28 | A | D177 | CA | CALCIUM(2+) | 4n2a | A | D177 | CA | CALCIUM(2+) | 4n2b | A | D177 | CA | CALCIUM(2+) | 4n2c | A | D177 | CA | CALCIUM(2+) | 4n2e | A | D177 | CA | CALCIUM(2+) | 4n2g | A | D177 | CA | CALCIUM(2+) | 4n2l | A | D177 | CA | CALCIUM(2+) | 4n2n | A | D177 | CA | CALCIUM(2+) | 4n26 | A | K363 | CA | CALCIUM(2+) | 4n28 | A | K363 | CA | CALCIUM(2+) | 4n2a | A | K363 | CA | CALCIUM(2+) | 4n2b | A | K363 | CA | CALCIUM(2+) | 4n2e | A | K363 | CA | CALCIUM(2+) | 4n2g | A | K363 | CA | CALCIUM(2+) | 4n2l | A | K363 | CA | CALCIUM(2+) | 4n2n | A | K363 | CA | CALCIUM(2+) | 4n2c | A | K378 |
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| Conservation information for LBS of PADI2 |
| Multiple alignments for Q9Y2J8 in multiple species |
| LBS | AA sequence | # species | Species | D123 | ISLDVDADRDG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | D125 | LDVDADRDGEV | 2 | Mus musculus, Rattus norvegicus | D125 | LDVDADRDGVV | 1 | Homo sapiens | D127 | VDADRDGEVEK | 2 | Mus musculus, Rattus norvegicus | D127 | VDADRDGVVEK | 1 | Homo sapiens | D156 | LLVNCDRDTPW | 2 | Mus musculus, Rattus norvegicus | D156 | LLVNCDRETPW | 1 | Homo sapiens | D166 | WLPKEDCSDEK | 2 | Mus musculus, Rattus norvegicus | D166 | WLPKEDCRDEK | 1 | Homo sapiens | D169 | KEDCSDEKVYS | 2 | Mus musculus, Rattus norvegicus | D169 | KEDCRDEKVYS | 1 | Homo sapiens | D177 | VYSKQDLQDMS | 2 | Mus musculus, Rattus norvegicus | D177 | VYSKEDLKDMS | 1 | Homo sapiens | D180 | KQDLQDMSQMI | 2 | Mus musculus, Rattus norvegicus | D180 | KEDLKDMSQMI | 1 | Homo sapiens | D370 | FPVVLDSPRDG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | D374 | LDSPRDGNLKD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | D389 | QLLGPDFGYVT | 2 | Mus musculus, Rattus norvegicus | D389 | ELLGPDFGYVT | 1 | Homo sapiens | E131 | RDGEVEKNNPK | 2 | Mus musculus, Rattus norvegicus | E131 | RDGVVEKNNPK | 1 | Homo sapiens | E158 | VNCDRDTPWLP | 2 | Mus musculus, Rattus norvegicus | E158 | VNCDRETPWLP | 1 | Homo sapiens | E352 | RWIQDEIEFGY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E354 | IQDEIEFGYIE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E412 | SFGNLEVSPPV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | F408 | TSLDSFGNLEV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G409 | SLDSFGNLEVS | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K171 | DCSDEKVYSKQ | 2 | Mus musculus, Rattus norvegicus | K171 | DCRDEKVYSKE | 1 | Homo sapiens | K363 | IEAPHKGFPVV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K378 | RDGNLKDFPIK | 2 | Mus musculus, Rattus norvegicus | K378 | RDGNLKDFPVK | 1 | Homo sapiens | L411 | DSFGNLEVSPP | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | M299 | IAPWIMTPNIL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N154 | AILLVNCDRDT | 2 | Mus musculus, Rattus norvegicus | N154 | AILLVNCDRET | 1 | Homo sapiens | Q350 | GDRWIQDEIEF | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S371 | PVVLDSPRDGN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | V129 | ADRDGEVEKNN | 2 | Mus musculus, Rattus norvegicus | V129 | ADRDGVVEKNN | 1 | Homo sapiens | V172 | CSDEKVYSKQD | 2 | Mus musculus, Rattus norvegicus | V172 | CRDEKVYSKED | 1 | Homo sapiens |
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