title: ePIANNO: ePIgenomics ANNOtation tool.
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.
authors: Institute of Statistical Science, Academia Sinica, Nangang, Taipei, Taiwan.|Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Nangang, Taipei, Taiwan.|Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.
authors: Chia-Hsin
authors: CH
authors: Liu
authors: Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.|NTU Center for Genomic Medicine, National Taiwan University College of Medicine, Taipei, Taiwan.
authors: Bing-Ching
authors: BC
authors: Ho
authors: Institute of Statistical Science, Academia Sinica, Nangang, Taipei, Taiwan.
authors: Chun-Ling
authors: CL
authors: Chen
authors: Institute of Statistical Science, Academia Sinica, Nangang, Taipei, Taiwan.
authors: Ya-Hsuan
authors: YH
authors: Chang
authors: Institute of Statistical Science, Academia Sinica, Nangang, Taipei, Taiwan.
authors: Yi-Chiung
authors: YC
authors: Hsu
authors: Institute of Statistical Science, Academia Sinica, Nangang, Taipei, Taiwan.
authors: Yu-Cheng
authors: YC
authors: Li
authors: Institute of Statistical Science, Academia Sinica, Nangang, Taipei, Taiwan.
authors: Shin-Sheng
authors: SS
authors: Yuan
authors: Institute of Statistical Science, Academia Sinica, Nangang, Taipei, Taiwan.
authors: Yi-Huan
authors: YH
authors: Huang
authors: NTU Center for Genomic Medicine, National Taiwan University College of Medicine, Taipei, Taiwan.
authors: Chi-Sheng
authors: CS
authors: Chang
authors: Institute of Statistical Science, Academia Sinica, Nangang, Taipei, Taiwan.
authors: Ker-Chau
authors: KC
authors: Li
authors: Institute of Statistical Science, Academia Sinica, Nangang, Taipei, Taiwan.
authors: Hsuan-Yu
authors: HY
authors: Chen
mesh_terms: D057225:Data Mining; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020407:Internet; D058977:Molecular Sequence Annotation / Q000379:methods*; D016328:NF-kappa B / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D014157:Transcription Factors / Q000378:metabolism; D014584:User-Computer Interface
chemical_list: D016328:NF-kappa B; D014157:Transcription Factors