FinaleDB: a browser and database of cell-free DNA fragmentation patterns
| Autor: | Haizi Zheng, Yaping Liu, Michelle S Zhu |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
Statistics and Probability
AcademicSubjects/SCI01060 Computer science Databases and Ontologies DNA Fragmentation Genome browser computer.software_genre Biochemistry Genome Market fragmentation 03 medical and health sciences chemistry.chemical_compound Gene expression DNA database Epigenetics Molecular Biology 030304 developmental biology Whole genome sequencing 0303 health sciences Whole Genome Sequencing Database 030302 biochemistry & molecular biology Applications Notes Computer Science Applications Biomarker (cell) Computational Mathematics Computational Theory and Mathematics Cell-free fetal DNA chemistry DNA fragmentation Cell-Free Nucleic Acids computer Software DNA |
| Zdroj: | Bioinformatics |
| DOI: | 10.1101/2020.08.18.255885 |
| Popis: | SummaryCirculating cell-free DNA (cfDNA) is a promising biomarker for the diagnosis and prognosis of many diseases, including cancer. The genome-wide non-random fragmentation patterns of cfDNA are associated with the nucleosomal protection, epigenetic environment, and gene expression in the cell types that contributed to cfDNA. However, current progress on the development of computational methods and understanding of molecular mechanisms behind cfDNA fragmentation patterns is significantly limited by the controlled-access of cfDNA whole-genome sequencing (WGS) dataset. Here, we present FinaleDB (FragmentatIoN AnaLysis of cEll-free DNA DataBase), a comprehensive database to host thousands of uniformly processed and curated de-identified cfDNA WGS datasets across different pathological conditions. Furthermore, FinaleDB comes with a fragmentation genome browser, from which users can seamlessly integrate thousands of other omics data in different cell types to experience a comprehensive view of both gene-regulatory landscape and cfDNA fragmentation patterns.Availability and implementationFinaleDB service: http://finaledb.research.cchmc.org/ FinaleDB source code: https://github.com/epifluidlab/finaledb_portal and https://github.com/epifluidlab/finaledb_workflow.Contactlyping1986@gmail.com |
| Databáze: | OpenAIRE |
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