ePIANNO: ePIgenomics ANNOtation tool

Chia-Hsin Liu; Bing-Ching Ho; Chun-Ling Chen; Ya-Hsuan Chang; Yi-Chiung Hsu; Yu-Cheng Li; Shin-Sheng Yuan; Yi-Huan Huang; Chi-Sheng Chang; Ker-Chau Li; Hsuan-Yu Chen

doi:10.1371/journal.pone.0148321

ePIANNO: ePIgenomics ANNOtation tool

PLoS One. 2016 Feb 9;11(2):e0148321. doi: 10.1371/journal.pone.0148321. eCollection 2016.

Authors

Chia-Hsin Liu^{1

2

3}, Bing-Ching Ho^{4

5}, Chun-Ling Chen¹, Ya-Hsuan Chang¹, Yi-Chiung Hsu¹, Yu-Cheng Li¹, Shin-Sheng Yuan¹, Yi-Huan Huang¹, Chi-Sheng Chang⁵, Ker-Chau Li¹, Hsuan-Yu Chen¹

Affiliations

¹ Institute of Statistical Science, Academia Sinica, Nangang, Taipei, Taiwan.
² Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Nangang, Taipei, Taiwan.
³ Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.
⁴ Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.
⁵ NTU Center for Genomic Medicine, National Taiwan University College of Medicine, Taipei, Taiwan.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Data Mining
Databases, Genetic
Genomics / methods*
High-Throughput Nucleotide Sequencing
Humans
Internet
Molecular Sequence Annotation / methods*
NF-kappa B / genetics
Polymorphism, Single Nucleotide
Transcription Factors / metabolism
User-Computer Interface

Substances

NF-kappa B
Transcription Factors

Grants and funding

Supported by grants from Academia Sinica, Institute of Statistical Science AS, AS-100-TP-AB2, NSC 98-3112-B-001-034, NSC 99-2314-B-001-003-MY3, NSC 100-2325-B-001-027, NSC 101-2325-B-002-071, NSC 102-2325-B-002-078, NSC 101-2319-B-002-002, NSC 102-2319-B-002 -002, NSC 102-2911-I-002-303, NSC 101-2911-I-002-303, NSC 102-2911-I-002-303, DOH101-TD-B-111-001, 102R7557, NSC 102-2923-B-002-004, NSC 103-2923-B-002-003, MOST 104-2923-B-002-003, and Taiwan Biosignature Project of Lung Cancer. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.