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mutLBSgeneDB |
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| Gene summary for LIN28A |
 Gene summary |
| Basic gene Info. | Gene symbol | LIN28A |
| Gene name | lin-28 homolog A (C. elegans) | |
| Synonyms | CSDD1|LIN-28|LIN28|ZCCHC1|lin-28A | |
| Cytomap | UCSC genome browser: 1p36.11 | |
| Type of gene | protein-coding | |
| RefGenes | NM_024674.4, | |
| Description | RNA-binding protein LIN-28protein lin-28 homolog Azinc finger CCHC domain-containing protein 1zinc finger, CCHC domain containing 1 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 611043 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000131914 | ||
| HPRD : 17278 | ||
| Vega : OTTHUMG00000003550 | ||
| Protein | UniProt: Q9H9Z2 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_LIN28A | |
| BioGPS: 79727 | ||
| Pathway | NCI Pathway Interaction Database: LIN28A | |
| KEGG: LIN28A | ||
| REACTOME: LIN28A | ||
| Pathway Commons: LIN28A | ||
| Context | iHOP: LIN28A | |
| ligand binding site mutation search in PubMed: LIN28A | ||
| UCL Cancer Institute: LIN28A | ||
| 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 |
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| Ligand binding site mutations for LIN28A |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | H148 | H148Y | BLCA | 1 | C139 | C139S | COAD | 1 | M129 | M129I | 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 LIN28A |
| 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 | C139 | C139S | -1.5853623 | M129 | M129I | -0.60657022 | H148 | H148Y | -0.60237789 |
| (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 LIN28A from PDB |
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| Differential gene expression and gene-gene network for LIN28A |
| 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 LIN28A |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0007621 | Cell Transformation, Neoplastic | 1 | Biomarker |
| umls:C0027651 | Neoplasms | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for LIN28A |
| 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 LIN28A go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ZN | ZINC(2+) | 2cqf | A | C139 | ZN | ZINC(2+) | 2li8 | A | C139 | NUC | Nucleic Acids | 2li8 | A | M129 C139 H148 |
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| Conservation information for LBS of LIN28A |
| Multiple alignments for Q9H9Z2 in multiple species |
| LBS | AA sequence | # species | Species | A149 | GLDHHAKECKL | 4 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Mus musculus | A149 | GPNHHAKECQL | 1 | Danio rerio | A172 | ISHMVASCPLK | 1 | Homo sapiens | A172 | ISHMVANCPIK | 1 | Danio rerio | A172 | PNHMVAQCPAK | 1 | Xenopus tropicalis | A172 | ISHMVANCPAK | 1 | Gallus gallus | A172 | INHMVASCPLK | 1 | Mus musculus | C139 | SKGDRCYNCGG | 3 | Homo sapiens, Gallus gallus, Mus musculus | C139 | SKGDRCFNCGG | 1 | Danio rerio | C139 | QKGDRCYNCGG | 1 | Xenopus tropicalis | C142 | DRCYNCGGLDH | 4 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Mus musculus | C142 | DRCFNCGGPNH | 1 | Danio rerio | C152 | HHAKECKLPPQ | 4 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Mus musculus | C152 | HHAKECQLPPQ | 1 | Danio rerio | C161 | PQPKKCHFCQS | 5 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Mus musculus | D137 | RRSKGDRCYNC | 3 | Homo sapiens, Gallus gallus, Mus musculus | D137 | RRSKGDRCFNC | 1 | Danio rerio | D137 | RRQKGDRCYNC | 1 | Xenopus tropicalis | H147 | CGGLDHHAKEC | 4 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Mus musculus | H147 | CGGPNHHAKEC | 1 | Danio rerio | H148 | GGLDHHAKECK | 4 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Mus musculus | H148 | GGPNHHAKECQ | 1 | Danio rerio | H162 | QPKKCHFCQSI | 4 | Homo sapiens, Danio rerio, Gallus gallus, Mus musculus | H162 | QPKKCHFCQSP | 1 | Xenopus tropicalis | K131 | GKSMQKRRSKG | 1 | Homo sapiens | K131 | GT--QKRRSKG | 1 | Danio rerio | K131 | VKGQQKRRQKG | 1 | Xenopus tropicalis | K131 | SKSLQKRRSKG | 1 | Gallus gallus | K131 | GKNMQKRRSKG | 1 | Mus musculus | K150 | LDHHAKECKLP | 4 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Mus musculus | K150 | PNHHAKECQLP | 1 | Danio rerio | K159 | LPPQPKKCHFC | 5 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Mus musculus | K160 | PPQPKKCHFCQ | 5 | Homo sapiens, Danio rerio, Xenopus tropicalis, Gallus gallus, Mus musculus | K177 | ASCPLKAQQ-G | 2 | Homo sapiens, Mus musculus | K177 | ANCPIKAQQLS | 1 | Danio rerio | K177 | AQCPAKASQ-A | 1 | Xenopus tropicalis | K177 | ANCPAKAQQ-S | 1 | Gallus gallus | M129 | PKGKSMQKRRS | 1 | Homo sapiens | M129 | PKGT--QKRRS | 1 | Danio rerio | M129 | PKVKGQQKRRQ | 1 | Xenopus tropicalis | M129 | PKSKSLQKRRS | 1 | Gallus gallus | M129 | PKGKNMQKRRS | 1 | Mus musculus | M170 | QSISHMVANCP | 2 | Danio rerio, Gallus gallus | M170 | QSISHMVASCP | 1 | Homo sapiens | M170 | QSPNHMVAQCP | 1 | Xenopus tropicalis | M170 | QSINHMVASCP | 1 | Mus musculus | Q130 | KGKSMQKRRSK | 1 | Homo sapiens | Q130 | KGT--QKRRSK | 1 | Danio rerio | Q130 | KVKGQQKRRQK | 1 | Xenopus tropicalis | Q130 | KSKSLQKRRSK | 1 | Gallus gallus | Q130 | KGKNMQKRRSK | 1 | Mus musculus | R132 | KSMQKRRSKGD | 1 | Homo sapiens | R132 | T--QKRRSKGD | 1 | Danio rerio | R132 | KGQQKRRQKGD | 1 | Xenopus tropicalis | R132 | KSLQKRRSKGD | 1 | Gallus gallus | R132 | KNMQKRRSKGD | 1 | Mus musculus | R133 | SMQKRRSKGDR | 1 | Homo sapiens | R133 | --QKRRSKGDR | 1 | Danio rerio | R133 | GQQKRRQKGDR | 1 | Xenopus tropicalis | R133 | SLQKRRSKGDR | 1 | Gallus gallus | R133 | NMQKRRSKGDR | 1 | Mus musculus | R138 | RSKGDRCYNCG | 3 | Homo sapiens, Gallus gallus, Mus musculus | R138 | RSKGDRCFNCG | 1 | Danio rerio | R138 | RQKGDRCYNCG | 1 | Xenopus tropicalis | S134 | MQKRRSKGDRC | 2 | Homo sapiens, Mus musculus | S134 | -QKRRSKGDRC | 1 | Danio rerio | S134 | QQKRRQKGDRC | 1 | Xenopus tropicalis | S134 | LQKRRSKGDRC | 1 | Gallus gallus | V171 | SISHMVASCPL | 1 | Homo sapiens | V171 | SISHMVANCPI | 1 | Danio rerio | V171 | SPNHMVAQCPA | 1 | Xenopus tropicalis | V171 | SISHMVANCPA | 1 | Gallus gallus | V171 | SINHMVASCPL | 1 | Mus musculus | Y140 | KGDRCYNCGGL | 4 | Homo sapiens, Xenopus tropicalis, Gallus gallus, Mus musculus | Y140 | KGDRCFNCGGP | 1 | Danio rerio |
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