https://scholars.lib.ntu.edu.tw/handle/123456789/146990
Title: | ePIANNO: ePIgenomics ANNOtation tool | Authors: | 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 Fujii, Hodaka |
Issue Date: | 2016 | Start page/Pages: | e0148321 | Source: | PLoS ONE | Abstract: | 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. |
URI: | http://ntur.lib.ntu.edu.tw//handle/246246/280928 | DOI: | 10.1371/journal.pone.0148321 | SDG/Keyword: | transcription factor; immunoglobulin enhancer binding protein; access to information; Article; biological functions; computer interface; epigenetics; ePIgenomics ANNOtation tool; genetic association; genetic database; genetic disorder; genetic variability; genome analysis; Internet; medical information system; single nucleotide polymorphism; data mining; genetic database; genetics; genomics; high throughput sequencing; human; Internet; metabolism; molecular genetics; procedures; Data Mining; Databases, Genetic; Genomics; High-Throughput Nucleotide Sequencing; Humans; Internet; Molecular Sequence Annotation; NF-kappa B; Polymorphism, Single Nucleotide; Transcription Factors; User-Computer Interface |
Appears in Collections: | 醫學檢驗暨生物技術學系 |
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