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mutLBSgeneDB |
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| Gene summary for SOX2 |
 Gene summary |
| Basic gene Info. | Gene symbol | SOX2 |
| Gene name | SRY (sex determining region Y)-box 2 | |
| Synonyms | ANOP3|MCOPS3 | |
| Cytomap | UCSC genome browser: 3q26.3-q27 | |
| Type of gene | protein-coding | |
| RefGenes | NM_003106.3, | |
| Description | SRY-related HMG-box gene 2transcription factor SOX-2transcription factor SOX2 | |
| Modification date | 20141222 | |
| dbXrefs | MIM : 184429 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000181449 | ||
| HPRD : 08921 | ||
| Vega : OTTHUMG00000158222 | ||
| Protein | UniProt: P48431 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_SOX2 | |
| BioGPS: 6657 | ||
| Pathway | NCI Pathway Interaction Database: SOX2 | |
| KEGG: SOX2 | ||
| REACTOME: SOX2 | ||
| Pathway Commons: SOX2 | ||
| Context | iHOP: SOX2 | |
| ligand binding site mutation search in PubMed: SOX2 | ||
| UCL Cancer Institute: SOX2 | ||
| 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:0001649 | osteoblast differentiation | 18187129 | GO:0001714 | endodermal cell fate specification | 21245162 | GO:0006355 | regulation of transcription, DNA-templated | 16153702 | GO:0007050 | cell cycle arrest | 18268498 | GO:0035019 | somatic stem cell maintenance | 19409607 | GO:0043281 | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 18268498 | GO:0043410 | positive regulation of MAPK cascade | 18187129 | GO:0045893 | positive regulation of transcription, DNA-templated | 18407919 | GO:0045944 | positive regulation of transcription from RNA polymerase II promoter | 18027866 | GO:0050680 | negative regulation of epithelial cell proliferation | 18268498 | GO:0070848 | response to growth factor | 18187129 | GO:0090090 | negative regulation of canonical Wnt signaling pathway | 18285410 |
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| Ligand binding site mutations for SOX2 |
| 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 | H67 | H67Q | COAD | 1 | R56 | G54R | COAD | 1 | M45 | M45L | LUSC | 1 | R56 | G54R | SKCM | 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 SOX2 |
| 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 | R56 | G54R | 0.028750732 | M45 | M45L | -0.69735536 | H67 | H67Q | -0.67253429 |
| (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 SOX2 from PDB |
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| Differential gene expression and gene-gene network for SOX2 |
| 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 SOX2 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0003119 | Anophthalmos | 22 | Biomarker, GeneticVariation |
| umls:C0007137 | Carcinoma, Squamous Cell | 16 | Biomarker |
| umls:C0279626 | Esophageal Squamous Cell Carcinoma | 7 | Biomarker |
| umls:C0024121 | Lung Neoplasms | 5 | Biomarker |
| umls:C0149925 | Small Cell Lung Carcinoma | 4 | Biomarker |
| umls:C1859773 | Microphthalmia, Syndromic 3 | 3 | Biomarker, GeneticVariation |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for SOX2 |
| 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 SOX2 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 SOX2 |
| Multiple alignments for P48431 in multiple species |
| LBS | AA sequence | # species | Species | F48 | RPMNAFMVWSR | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | G76 | ISKRLGAEWKL | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | H67 | ENPKMHNSEIS | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | K10 | METELKPPGPQ | 2 | Homo sapiens, Mus musculus | K10 | METELKPPAPQ | 1 | Danio rerio | K10 | METDLKPPAPQ | 1 | Xenopus tropicalis | K42 | SPDRVKRPMNA | 3 | Homo sapiens, Xenopus tropicalis, Mus musculus | K42 | SPDRIKRPMNA | 1 | Danio rerio | K73 | NSEISKRLGAE | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | K80 | LGAEWKLLSET | 2 | Homo sapiens, Mus musculus | K80 | LGAEWKLLSES | 1 | Danio rerio | K80 | LGAEWKLLSEA | 1 | Xenopus tropicalis | M45 | RVKRPMNAFMV | 3 | Homo sapiens, Xenopus tropicalis, Mus musculus | M45 | RIKRPMNAFMV | 1 | Danio rerio | M49 | PMNAFMVWSRG | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | N46 | VKRPMNAFMVW | 3 | Homo sapiens, Xenopus tropicalis, Mus musculus | N46 | IKRPMNAFMVW | 1 | Danio rerio | N68 | NPKMHNSEISK | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | P112 | DYKYRPRRKTK | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | R43 | PDRVKRPMNAF | 3 | Homo sapiens, Xenopus tropicalis, Mus musculus | R43 | PDRIKRPMNAF | 1 | Danio rerio | R56 | WSRGQRRKMAQ | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | R57 | SRGQRRKMAQE | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | R98 | EAKRLRALHMK | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | S69 | PKMHNSEISKR | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | S72 | HNSEISKRLGA | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | W79 | RLGAEWKLLSE | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus | Y110 | HPDYKYRPRRK | 4 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus |
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