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Clustered protocadherins methylation alterations in cancer

Ana Florencia Vega-Benedetti, Eleonora Loi, Loredana Moi, Sylvain Blois, Antonio Fadda, Manila Antonelli, Antonella Arcella, Manuela Badiali, Felice Giangaspero, Isabella Morra, Amedeo Columbano, Angelo Restivo (+18 others)
2019 Clinical Epigenetics  
In cancer, clustered PCDHs undergo a mechanism of long-range epigenetic silencing by hypermethylation.  ...  Clustered protocadherins (PCDHs) map in tandem at human chromosome 5q31 and comprise three multi-genes clusters: α-, β- and γ-PCDH.  ...  Acknowledgements We gratefully acknowledge the CeSAR (Centro Servizi d'Ateneo per la Ricerca) of the University of Cagliari, Italy, for the use of the iScan platform (Illumina) for methylation assays.  ... 
doi:10.1186/s13148-019-0695-0 pmid:31288858 pmcid:PMC6617643 fatcat:oinu7kud7bfldknftwe3lfrup4

Semantic subgroup discovery: Using ontologies in microarray data analysis

N. Lavrac, P.K. Novak, I. Mozetic, V. Podpecan, H. Motaln, M. Petek, K. Gruden
2009 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society  
subgroup discovery, rules are constructed that allow the expert to recognize gene groups that are differentially expressed in different types of tissues.  ...  The paper presents also current directions in creative knowledge discovery through bisociative data analysis, illustrated on a systems biology case study.  ...  The work presented in this paper was supported by the Slovenian Research Agency grant Knowledge Technologies, and by the grant of the European Commission under the 7th Framework Programme FP7-ICT-2007-  ... 
doi:10.1109/iembs.2009.5333782 pmid:19964398 fatcat:4mc4f772r5gkjj2mmhkqtdrnze

Meta-analysis of the expression of the mitosis-related gene Fam83D

LOKMAN VARISLI
2012 Oncology Letters  
Furthermore, Fam83D is differentially expressed in various types of cancers.  ...  Pathway analysis results also showed that cell cycle-and mitosis-related pathways are enriched with Fam83D-coexpressed genes.  ...  This analysis provides a list of gene functions, which are overrepresented in a gene set.  ... 
doi:10.3892/ol.2012.925 pmid:23205133 pmcid:PMC3506721 fatcat:wdxro6xi5faxzkhyehhljh46xa

Relevance of Bioinformatics in the Era of Omics Driven Research

Dinesh Yadav
2015 Journal of Next Generation Sequencing & Applications  
in-silico tools.  ...  , quantifying pathogens, in drug therapy studies and also in cancer biology research.  ... 
doi:10.4172/2469-9853.1000e102 fatcat:4s4vkwbtzbfmlbvoqzjmmwqkmi

Bioinformatics and cancer target discovery

Brian Desany, Zemin Zhang
2004 Drug Discovery Today  
Identifying genes that have properties similar to known targets is conceptually straightforward. Additionally, genes can be linked to cancer via recurrent genomic or genetic abnormalities.  ...  Finally, by integrating large and disparate datasets, gene-level distinctions can be made between the different biological states that the data represents.  ...  Acknowledgements The authors would like to thank Colin Watanabe, Thomas Wu and Paul Polakis for critical review of the manuscript and Allison Bruce for assistance in preparing the figures.  ... 
doi:10.1016/s1359-6446(04)03224-6 pmid:15364067 fatcat:65t6cidoyvcj3nrruzd25kay5q

Polymorphisms in CARS are associated with gastric cancer risk: a two-stage case–control study in the Chinese population

Tian Tian, Ling Xiao, Jiangbo Du, Xun Zhu, Yayun Gu, Na Qin, Caiwang Yan, Li Liu, Hongxia Ma, Yue Jiang, Jiaping Chen, Hao Yu (+1 others)
2017 Gastric Cancer  
Conclusions The potential functional SNPs in CARS might influence the biological functions of CARS or CARS-related genes and ultimately modify the occurrence and development of gastric cancer in Chinese  ...  Additionally, expression quantitative trait loci analysis showed rs384490 and rs729662 might alter expression of CARS-related genes.  ...  Human rights statement All procedures followed were in accordance with the ethical standards of the responsible committee on human experimentation (institutional and national) and with the Helsinki Declaration  ... 
doi:10.1007/s10120-017-0717-6 pmid:28409418 fatcat:udwkmfuqrfdppkf4lpmldog55m

Pancreatic Cancer and a Novel MSH2 Germline Alteration

Noralane M. Lindor, Gloria M. Petersen, Amanda B. Spurdle, Bryony Thompson, David E. Goldgar, Stephen N. Thibodeau
2011 Pancreas  
Lynch syndrome-related tumors from individuals carrying this alteration consistently showed loss of immunohistochemical expression of MSH2 and in-silico analyses support interpretation of this DNA alteration  ...  Conclusions-The MSH2 P349L may increase the risk for pancreatic cancer beyond the usual mutations in DNA mismatch repair genes; however studies of additional families with the identical missense alteration  ...  relative risks for colorectal cancer, endometrial cancer, and other Lynch Syndrome-related cancers (including pancreatic cancer) as estimated in Quehenberger et al. (2005) . 20 This analysis also provided  ... 
doi:10.1097/mpa.0b013e318220c217 pmid:21926548 pmcid:PMC3425611 fatcat:fckbbxlc7nfefcbvm4tgyjjnve

In silico saturation mutagenesis of cancer genes [article]

Ferran Muinos, Francisco Martinez-Jimenez, Oriol Pich, Abel Gonzalez-Perez, Nuria Lopez-Bigas
2020 bioRxiv   pre-print
Here, we present an in silico saturation mutagenesis approach to identify all drivermutations in 568 cancer genes across 66 tumor types.  ...  Extensive bioinformatics analysis of these datasets of tumor somatic mutations data have revealed the presence of some 500-600 cancer driver genes.  ...  Acknowledgements We acknowledge important technical contributions to the development of the in silico saturation mutagenesis approach and to the manuscript by Loris Mularoni, Iker Reyes-Salazar, EIectra  ... 
doi:10.1101/2020.06.03.130211 fatcat:y3wnbdks3vbhlahkdsrvtpizjy

In-silico Identification of lncRNA Functionality in Cancers Related to Obesity

Shalini Das, Nushrat Jahan, Chittabrata Mal
2020 Zenodo  
In-silico Identification of lncRNA Functionality in Cancers Related to Obesity Shalini Das, Nushrat Jahan and Chittabrata Mal Amity Institute of Biotechnology, Amity University Kolkata, Rajarhat, Newtown  ...  Here we emphasize their aberrant expression and performance in cancers. We found that Chromosome 11 consists of the highest number of lncRNA specific to different 14 cancers related to obesity.  ...  CONFLLICT OF INTEREST The authors declare no potential conflict of interest.  ... 
doi:10.5281/zenodo.4275605 fatcat:foffobpai5b6dbgk3nnxoj6foa

Data Mining Methods for OMICs Applications in Anticancer Drug Design and Discovery

Soroush Sardari
2012 Drug Designing: Open Access  
biologic activity in the domain of  ...  Gene expression altered in response to a drug or a toxin is usually measures by microarrays.  ...  It would be obvious that the in silico drug discovery based on data mining approaches play great roles in cancer treatment and are gaining increased applications in drug discovery and development with  ... 
doi:10.4172/2169-0138.1000e102 fatcat:i3a6t2cm75eqnmjcxeraol6spi

Development of drugs for Epstein–Barr virus using high-throughputin silicovirtual screening

Ning Li, Scott Thompson, Hualiang Jiang, Paul M Lieberman, Cheng Luo
2010 Expert Opinion on Drug Discovery  
Since the atomic structure of the EBNA1 DNA binding domain has been described, it is an attractive target for in silico methods of drug design and small molecule screening.  ...  High throughput in silico screening can accelerate the process of drug discovery for novel and selective agents that inhibit EBV latent infection and associated disease.  ...  in silico drug discovery targeting EBNA1.  ... 
doi:10.1517/17460441.2010.524640 pmid:22822721 pmcid:PMC3816986 fatcat:2eybhvt4yfaxjgvuoa7f5sm5km

In silico frameworks for systematic pre-clinical screening of potential anti-leukemia therapeutics

Matthew H. Ung, Frederick S. Varn, Chao Cheng
2016 Expert Opinion on Drug Discovery  
Therefore, integration of in silico screens prior to experimental validation can improve the efficiency of pre-clinical drug development.  ...  In particular, three approaches are discussed including molecular docking, transcriptomic integration, and network analysis.  ...  Acknowledgments Funding: This work was supported by American Cancer Society Research grant #IRG-82-003-30, the National Center for Advancing Translational Sciences of the National Institutes of Health  ... 
doi:10.1080/17460441.2016.1243524 pmid:27689915 pmcid:PMC5180445 fatcat:hkb5o4zforhd7kr4ywxc7lbum4

In silico pathway analysis in cervical carcinoma reveals potential new targets for treatment

Pieter-Jan H. H. van Dam, Christian Rolfo, Marco Giallombardo, Christophe van Berckelaer, Xuan Bich Trinh, Sevilay Altintas, Manon Huizing, Kostas Papadimitriou, Wiebren A. A. Tjalma, Steven van Laere
2015 OncoTarget  
An in silico pathway analysis was performed in order to improve current knowledge on the molecular drivers of cervical cancer and detect potential targets for treatment.  ...  Predication analysis of microarrays was performed in the Affymetrix sets to identify cervical cancer biomarkers. To select cancer cell-specific genes the CCSs were compared to the CCCLs.  ...  In their analysis important other upregulated pathways were those of calcium signaling and MAPK signaling, as well as cell cycle-related genes.  ... 
doi:10.18632/oncotarget.6667 pmid:26701206 pmcid:PMC4823071 fatcat:vgybodeukjbufa7vgjrxfdd5vu

Cellular Stress-Modulating Drugs Can Potentially Be Identified by in Silico Screening with Connectivity Map (CMap)

Yurong Gao, Sungwoo Kim, Yun-Il Lee, Jaemin Lee
2019 International Journal of Molecular Sciences  
Moreover, by querying through CMap, researchers may screen registered chemicals in silico and obtain the likelihood of drugs showing a similar gene expression profile with desired and chemopreventive conditions  ...  Accompanied by increased life span, aging-associated diseases, such as metabolic diseases and cancers, have become serious health threats.  ...  Furthermore, (4) recent advances in machine learning could empower future genome-based in silico drug discovery tools by potentially providing the information about probable modes of action and target  ... 
doi:10.3390/ijms20225601 pmid:31717493 pmcid:PMC6888006 fatcat:zszmlmnnanafrjn5v3ha7ix76i

Molecular modelling and docking of Mus musculus HMGB1 inflammatory protein with CGA

Alok Tripathi, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi-221005, India, Kriti Shrinet, Vinay Kumar Singh, Arvind Kumar
2019 Bioinformation  
Cancer atlas of HMGB1 protein showed up-regulated expression of HMGB1 gene in different cancer, proved by CAB (CAB005873) and HPA-antibody (HPA003506) in silico.  ...  Ramachandran plot analysis showed 98.2% and 92.3% residues lies in favoured region, verified by RAMPAGE and PDBsum server respectively.  ...  The corresponding author is thankful to DST-PURSE, UGC-SAP and DBT-DIC for the research grant support to the School of Biotechnology, Institute of Science, BHU, India.  ... 
doi:10.6026/97320630015467 pmid:31485132 pmcid:PMC6704330 fatcat:vgvrgewaxbdhxh2oqvyvu67djq
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