EPIANNO: EPIgenomics ANNOtation tool

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Title:	EPIANNO: EPIgenomics ANNOtation tool
Authors:	許藝瓊;Liu, Chia-Hsin;Ho, Bing-Ching;Chen, Chun-Ling;Chang, Ya-Hsuan;Hsu, Yi-Chiung;Li, Yu-Cheng;Yuan, Shin-Sheng;Huang, Yi-Huan;Chang, Chi-Sheng;Li, Ker-Chau;Chen, Hsuan-Yu
Contributors:	生醫理工學院生醫科學與工程學系
Keywords:	Analysis;Annotations;Binding sites;Biology and Life Sciences;Chromatin;Chromosomes;Consortia;Data Mining;Data structures;Databases, Genetic;Datasets;DNA sequencing;Experiments;Gene expression;Gene frequency;Genomes;Genomics;Genomics - methods;High-Throughput Nucleotide Sequencing;Humans;Hypotheses;Immunoprecipitation;Inflammatory bowel disease;Internet;Lung cancer;Medical research;Medicine;Molecular Sequence Annotation - methods;NF-kappa B - genetics;Polymorphism, Single Nucleotide;Population;Population genetics;Populations;Public domain;Research and Analysis Methods;Researchers;Science;Servers;Single-nucleotide polymorphism;Studies;Transcription factors;Transcription Factors - metabolism;User-Computer Interface;Variation
Date:	2016-02-01
Issue Date:	2026-04-23 11:15:56 (UTC+8)
Publisher:	Public Library of Science;United States: Public Library of Science
Abstract:	摘要： Recently, with the development of next generation sequencing (NGS), the combination of chromatin immunoprecipitation (ChIP) and NGS, namely ChIP-seq, has become a powerful technique to capture potential genomic binding sites of regulatory factors, histone modifications and chromatin accessible regions. For most researchers, additional information including genomic variations on the TF binding site, allele frequency of variation between different populations, variation associated disease, and other neighbour TF binding sites are essential to generate a proper hypothesis or a meaningful conclusion. Many ChIP-seq datasets had been deposited on the public domain to help researchers make new discoveries. However, researches are often intimidated by the complexity of data structure and largeness of data volume. Such information would be more useful if they could be combined or downloaded with ChIP-seq data. To meet such demands, we built a webtool: ePIgenomic ANNOtation tool (ePIANNO, http://epianno.stat.sinica.edu.tw/index.html). ePIANNO is a web server that combines SNP information of populations (1000 Genomes Project) and gene-disease association information of GWAS (NHGRI) with ChIP-seq (hmChIP, ENCODE, and ROADMAP epigenomics) data. ePIANNO has a user-friendly website interface allowing researchers to explore, navigate, and extract data quickly. We use two examples to demonstrate how users could use functions of ePIANNO webserver to explore useful information about TF related genomic variants. Users could use our query functions to search target regions, transcription factors, or annotations. ePIANNO may help users to generate hypothesis or explore potential biological functions for their studies. 其他題名： PLoS One 出版者： United States: Public Library of Science 出版日期： 2016-02-09 出處： PloS one, 2016-02, Vol.11 (2), p.e0148321 資源來源： Agricultural & Environmental Science Collection 版權： COPYRIGHT 2016 Public Library of Science 版權： 2016 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 版權： 2016 Liu et al 2016 Liu et al 識別號： ISSN: 1932-6203 識別號： EISSN: 1932-6203 識別號： DOI: 10.1371/journal.pone.0148321 識別號： PMID: 26859295
Appears in Collections:	[Department of Biomedical Sciences and Engineering ] journal & Dissertation

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