CFEA: a cell-free epigenome atlas in human diseases
作者： Fulong Yu , Kai Li , Shuangquan Li , Jiaqi Liu , Yan Zhang
DOI: 10.1093/NAR/GKZ715
关键词:
摘要: Epigenetic alterations, including 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and nucleosome positioning (NP), in cell-free DNA (cfDNA) have been widely observed human diseases, many available cfDNA-based epigenome-wide profiles exhibit high sensitivity specificity disease detection classification. However, due to the lack of efficient collection, standardized quality control, analysis procedures, efficiently integrating reusing these data remain considerable challenges. Here, we introduce CFEA (http://www.bio-data.cn/CFEA), a epigenome database dedicated three types adopted epigenetic modifications (5mC, 5hmC NP) involved 27 diseases. We developed bioinformatic pipelines for control standard processing an easy-to-use web interface facilitate query, visualization download data. also manually curated related biological clinical information each profile, allowing users better browse compare cfDNA epigenomes at specific stage (such as early- or metastasis-stage) cancer development. provides comprehensive timely resource scientific community supports development liquid biopsy-based biomarkers various
oup.com
sci-hub.se 参考文章(25)
Luis A. Diaz, Alberto Bardelli, Liquid Biopsies: Genotyping Circulating Tumor DNA Journal of Clinical Oncology. ,vol. 32, pp. 579- 586 ,(2014) , 10.1200/JCO.2012.45.2011
Rasko Leinonen, Ruth Akhtar, Ewan Birney, James Bonfield, Lawrence Bower, Matt Corbett, Ying Cheng, Fehmi Demiralp, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Christopher Hunter, Mikyung Jang, Steven Leonard, Quan Lin, Rodrigo Lopez, Michael Maguire, Hamish McWilliam, Sheila Plaister, Rajesh Radhakrishnan, Siamak Sobhany, Guy Slater, Petra Ten Hoopen, Franck Valentin, Robert Vaughan, Vadim Zalunin, Daniel Zerbino, Guy Cochrane, Improvements to services at the European Nucleotide Archive Nucleic Acids Research. ,vol. 38, pp. 39- 45 ,(2010) , 10.1093/NAR/GKP998
Jianxing Feng, Tao Liu, Bo Qin, Yong Zhang, Xiaole Shirley Liu, Identifying ChIP-seq enrichment using MACS Nature Protocols. ,vol. 7, pp. 1728- 1740 ,(2012) , 10.1038/NPROT.2012.101
K. Chen, Y. Xi, X. Pan, Z. Li, K. Kaestner, J. Tyler, S. Dent, X. He, W. Li, DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Research. ,vol. 23, pp. 341- 351 ,(2013) , 10.1101/GR.142067.112
Martin J. Aryee, Andrew E. Jaffe, Hector Corrada-Bravo, Christine Ladd-Acosta, Andrew P. Feinberg, Kasper D. Hansen, Rafael A. Irizarry, Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays Bioinformatics. ,vol. 30, pp. 1363- 1369 ,(2014) , 10.1093/BIOINFORMATICS/BTU049
H. Li, R. Durbin, Fast and accurate short read alignment with Burrows–Wheeler transform Bioinformatics. ,vol. 25, pp. 1754- 1760 ,(2009) , 10.1093/BIOINFORMATICS/BTP324
Matthias Lienhard, Christina Grimm, Markus Morkel, Ralf Herwig, Lukas Chavez, MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments Bioinformatics. ,vol. 30, pp. 284- 286 ,(2014) , 10.1093/BIOINFORMATICS/BTT650
R. Leinonen, H. Sugawara, M. Shumway, , The sequence read archive. Nucleic Acids Research. ,vol. 39, pp. 19- 21 ,(2011) , 10.1093/NAR/GKQ1019
Tanya Barrett, Stephen E. Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F. Kim, Maxim Tomashevsky, Kimberly A. Marshall, Katherine H. Phillippy, Patti M. Sherman, Michelle Holko, Andrey Yefanov, Hyeseung Lee, Naigong Zhang, Cynthia L. Robertson, Nadezhda Serova, Sean Davis, Alexandra Soboleva, NCBI GEO: archive for functional genomics data sets—update Nucleic Acids Research. ,vol. 41, pp. 991- 995 ,(2012) , 10.1093/NAR/GKS1193
Felix Krueger, Simon R. Andrews, Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. ,vol. 27, pp. 1571- 1572 ,(2011) , 10.1093/BIOINFORMATICS/BTR167