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Extraction of human kinase mutations from literature, databases and genotyping studies

Martin Krallinger, Jose MG Izarzugaza, Carlos Rodriguez-Penagos, Alfonso Valencia
2009 BMC Bioinformatics  
When compared to state-of-the-art annotation databases and high throughput genotyping studies, the mutation mentions extracted from the literature overlap to a good extent with the existing from ECCB 2008  ...  Systematic integration and comparison of kinase mutation information from multiple sources, covering literature, manual annotation databases and large-scale experiments can result in a more comprehensive  ...  Acknowledgements The work of the two groups in this area is funded by the ENFIN (LSHG-CT-2005-  ... 
doi:10.1186/1471-2105-10-s8-s1 pmid:19758464 pmcid:PMC2745582 fatcat:qglkz5xiore5nlsadi2jomkaeq

wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases

Jose MG Izarzugaza, Miguel Vazquez, Angela del Pozo, Alfonso Valencia
2013 BMC Bioinformatics  
This research was supported by OpenPhacts European project (115191-2) and Spanish Ministry of Science and Innovation project BIO2007-6685  ...  Acknowledgements The authors thank the members of the Structural Biology and Biocomputing Programme (CNIO), especially A. Rausell, D. Juan, I. Ezkurdia and T.  ...  Furthermore, kinase mutations are analyzed in their structural context and mentions in dedicated databases, genotyping studies and the literature that suggest an implication in disease are also presented  ... 
doi:10.1186/1471-2105-14-345 pmid:24289158 pmcid:PMC3879071 fatcat:wblb72yq5nelnlseujbysgukgy

High-throughput genotyping in osteosarcoma identifies multiple mutations in phosphoinositide-3-kinase and other oncogenes

Edwin Choy, Francis Hornicek, Laura MacConaill, David Harmon, Zeeshan Tariq, Levi Garraway, Zhenfeng Duan
2011 Cancer  
Methods-We identified somatic non-synonymous coding mutations in oncogenes associated with human cancers and hotspot mutations from tumor suppressor genes that were either welldescribed in literature or  ...  list of malignancies with PI3 kinase mutations.  ...  and financial contributions from Harvard University and its affiliated academic health care centers).  ... 
doi:10.1002/cncr.26617 pmid:22006429 pmcid:PMC3272156 fatcat:gpzq3w6xw5egnhs53bpx4dtgri

cmvdrg - An R package for Human Cytomegalovirus antiviral Drug Resistance Genotyping [article]

Oscar J Charles, Cristina Venturini, Judith Breuer
2020 bioRxiv   pre-print
Here we present Cytomegalovirus Drug Resistance Genotyping (cmvdrg), a freely available database contained within an easily accessible R package, which provides a succinct extraction of literature material  ...  We identified the need for an open source and comprehensive HCMV resistance mutations database, to support the research community in this area.  ...  Acknowledgements We would like to thank Steven A Kemp and Salvatore Camiolo for their testing and informative suggestions.  ... 
doi:10.1101/2020.05.15.097907 fatcat:kqu6pjfs65a5bigzb4r2bnochi

Characterization of JAK2 V617F (1849 G > T) Mutation in Cervical Cancer Related to Human Papillomavirus and Sexually Transmitted Infections

Masoumeh Abdolmaleki, Amir Sohrabi
2018 Journal of Cancer Prevention  
The Janus kinase 2 is a non-receptor tyrosine kinase in cell signaling process of tumor genesis.  ...  Analysis of JAK2 V617F (1849 G > T) showed that prevalence of mutation was GG (65.1%), GA (34.9%), and TT (0%), respectively.  ...  ACKNOWLEDGMENTS We are grateful and indebted to reference health laboratory staffs and Dr.  ... 
doi:10.15430/jcp.2018.23.2.82 pmid:30003068 pmcid:PMC6037210 fatcat:if3lca4fvvdvnl5ws2nwsi2tme

mutLBSgeneDB: mutated ligand binding site gene DataBase

Pora Kim, Junfei Zhao, Pinyi Lu, Zhongming Zhao
2016 Nucleic Acids Research  
kinases, transcription factors, pharmacological genes, and cancer driver genes.  ...  Here, we built mutLBSgeneDB (mutated Ligand Binding Site gene DataBase) available at http://zhaobioinfo. org/mutLBSgeneDB.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.1093/nar/gkw905 pmid:27907895 pmcid:PMC5210621 fatcat:c3kebup7zbgencadkrsuuhkmka

An examination of the OMIM database for associating mutation to a consensus reference sequence

Zuofeng Li, Beili Ying, Xingnan Liu, Xiaoyan Zhang, Hong Yu
2012 Protein & Cell  
In the current study, we examined the quality of protein single-point mutations in the OMIM and identified whether the corresponding reference sequences align with the mutation positions.  ...  Gene mutation (e.g. substitution, insertion and deletion) and related phenotype information are important biomedical knowledge. Many biomedical databases (e.g. OMIM) incorporate such data.  ...  All of the mutation data are extracted from this section.  ... 
doi:10.1007/s13238-012-2037-2 pmid:22477700 pmcid:PMC4875428 fatcat:karxjzgb4ren5k6t6rqzwb4enu

High-Throughput Genotyping in Metastatic Esophageal Squamous Cell Carcinoma Identifies Phosphoinositide-3-Kinase and BRAF Mutations

Chi Hoon Maeng, Jeeyun Lee, Paul van Hummelen, Se Hoon Park, Emanuele Palescandolo, Jiryeon Jang, Ha Young Park, So Young Kang, Laura MacConaill, Kyoung-Mee Kim, Young-Mog Shim, Javier S. Castresana
2012 PLoS ONE  
Our study led to the detection of potentially druggable mutations in esophageal SCC which may guide novel therapies in small subsets of esophageal cancer patients.  ...  Tumor specimens were prepared from primary cancer sites in 70 patients and from metastatic sites in 17 patients.  ...  We selected the candidate somatic mutations in OncoMap v4 based on literature reviews and frequently detected mutations reported in the COSMIC Database.  ... 
doi:10.1371/journal.pone.0041655 pmid:22870241 pmcid:PMC3411721 fatcat:brxpe3dp3bga7lbaq33iwbwf2q

A novel PAK3 pathogenic variant identified in two siblings from a Japanese family with X-linked intellectual disability: case report and review of the literature

Aritoshi Iida, Kyoko Takano, Eri Takeshita, Chihiro Abe Hatano, Shinichi Hirabayashi, Yuji Inaba, Shunichi Kosugi, Yoichiro Kamatani, Yukihide Momozawa, Michiaki Kubo, Eiji Nakagawa, Ken Inoue (+1 others)
2019 Molecular Case Studies  
In addition, this variant has not been reported in public databases (as of the middle of December 2018) or in the data from 3275 individuals of the Japanese general population analyzed using high-depth  ...  , which is associated with X-linked ID. p.W428R is located within the highly conserved kinase domain and was predicted to induce loss of enzymatic function by three mutation prediction tools (SIFT, PolyPhen  ...  from the National Center of Neurology and Psychiatry, Japan.  ... 
doi:10.1101/mcs.a003988 pmid:31444167 pmcid:PMC6913141 fatcat:rmpv7brqlbfrxho5cbkz2tafji

Close and regular surveillance is key to prevent severe complications for Peutz-Jeghers syndrome patients without gastrointestinal polyps: case report of a novel STK11 mutation (c.471_472delCT) in a Chinese girl

Zi-Ye Zhao, Yu-Liang Jiang, Bai-Rong Li, Jing Li, Xiao-Wei Jin, En-Da Yu, Shou-Bin Ning
2018 BMC Surgery  
Conclusion: The mutation we reported here is a novel one and a de-novo one, so our results enlarge the spectrum of STK11.  ...  Case presentation: We report here a girl without a positive family history, who grew oral and fingertip MP at her age of 2 and got abdomen dull pain from 7 years old.  ...  Availability of data and materials The datasets used and analysed during the current study available from the corresponding author on reasonable request.  ... 
doi:10.1186/s12893-018-0357-8 pmid:29685139 pmcid:PMC5914036 fatcat:32qj2ls2enf6dkt2j7dcp3cizm

CancerGenes: a gene selection resource for cancer genome projects

M. E. Higgins, M. Claremont, J. E. Major, C. Sander, A. E. Lash
2007 Nucleic Acids Research  
The genome sequence framework provided by the human genome project allows us to precisely map human genetic variations in order  ...  ACKNOWLEDGEMENTS We gratefully acknowledge the efforts of Marc Ladanyi and Doron Betel in the critical review of a preliminary implementation of CancerGenes and their helpful suggestions.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkl811 pmid:17088289 pmcid:PMC1781153 fatcat:e24xyjazizfc5prisj6zr2fd4m

Hyper-IgD and periodic fever syndrome: a new MVK mutation (p.R277G) associated with a severe phenotype

Joana A. Santos, Juan I. Aróstegui, Maria J. Brito, Conceição Neves, Marta Conde
2014 Gene  
Further studies are needed to evaluate a co-relation genotype, enzyme activity and phenotype, and to define the best therapeutic strategies.  ...  Hyperimmunoglobulinemia D and periodic fever syndrome (HIDS; MIM# 260920) is a rare recessively-inherited autoinflammatory condition caused by mutations in the MVK gene, which encodes for mevalonate kinase  ...  In this database are included samples from different ancestries and origins, including samples from the Iberian Peninsula.  ... 
doi:10.1016/j.gene.2014.03.031 pmid:24656624 fatcat:44eyjsyzu5eofobyzaj24u6nxu

PTMsnp: A Web Server for the Identification of Driver Mutations That Affect Protein Post-translational Modification

Di Peng, Huiqin Li, Bosu Hu, Hongwan Zhang, Li Chen, Shaofeng Lin, Zhixiang Zuo, Yu Xue, Jian Ren, Yubin Xie
2020 Frontiers in Cell and Developmental Biology  
A total of 4,11,574 modification sites from 33 different types of PTMs and 1,776,848 somatic mutations from TCGA across 33 different cancer types are integrated into the web server, enabling identification  ...  High-throughput sequencing technologies have identified millions of genetic mutations in multiple human diseases.  ...  Database for PTM Sites and Mutations PTM sites of human proteins were retrieved from the dbPTM (2019 update), iPTMnet (November 2019) database and manually collected from published literatures in PubMed  ... 
doi:10.3389/fcell.2020.593661 pmid:33240890 pmcid:PMC7683509 fatcat:qofib3nfdveflkb7zbdiuqsspi

Associations of Polymorphisms Localized in the 3′UTR Regions of the KRAS, NRAS, MAPK1 Genes with Laryngeal Squamous Cell Carcinoma

Ruta Insodaite, Alina Smalinskiene, Vykintas Liutkevicius, Virgilijus Ulozas, Roberta Poceviciute, Arunas Bielevicius, Laimutis Kucinskas
2021 Genes  
Genotyping of the SNPs was performed using TaqMan SNP genotyping assays. Five KRAS, NRAS, and MAPK1 polymorphisms were analyzed.  ...  Results: Significant associations of the studied SNPs with reduced LSCC risk were observed between NRAS rs14804 major genotype CC.  ...  Acknowledgments: We would like to thank the Lithuanian University of Health Sciences Science Foundation for funding this study. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/genes12111679 pmid:34828284 pmcid:PMC8625477 fatcat:3tlg4mzv2zh47hxkkt263fjosq

COSMIC 2005

S Forbes, J Clements, E Dawson, S Bamford, T Webb, A Dogan, A Flanagan, J Teague, R Wooster, P A Futreal, M R Stratton
2006 British Journal of Cancer  
In addition, there is data from the systematic sequencing of 518 protein kinase genes.  ...  The Catalogue Of Somatic Mutations In Cancer (COSMIC) database and web site was developed to preserve somatic mutation data and share it with the community.  ...  ACKNOWLEDGEMENTS We thank Francis Martin, Andrew King and Joan Green in the Sanger Institute library for their continued support and The Wellcome Trust for funding this work.  ... 
doi:10.1038/sj.bjc.6602928 pmid:16421597 pmcid:PMC2361125 fatcat:b357kb5mbbggfmi422oqtkw2gy
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