Open Access Published by De Gruyter

Volume 13 Issue 4 - Special Issue: 12th International Symposium on Integrative Bioinformatics, Bielefeld, Germany, 2016 / Guest Editors: Ralf Hofestädt, Jens Allmer

Issue of Journal of Integrative Bioinformatics

Contents
Journal Overview

Open Access April 20, 2017

Analysis of differential gene expression by RNA-seq data in brain areas of laboratory animals

Vladimir N. Babenko, Anatoly O. Bragin, Anastasia M. Spitsina, Irina V. Chadaeva, Elvira R. Galieva, Galina V. Orlova, Irina V. Medvedeva, Yuriy L. Orlov

Page range: 1-15

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Abstract

Computer analysis of gene expression in the nervous system plays a fundamental role in biology, genetics, and neurosciences. We studied molecular and genetic mechanisms of enhanced aggressiveness in comparison with tolerant behaviour using experimental animal models developed at the Institute of Cytology and Genetics SB RAS. Grey rats (Rattus norvegicus) have been subjected to selection during several generations in two directions - friendly, tolerant behaviour towards man (tame grey rats) and increased aggressive behaviour. We used samples from hypothalamus, mesencephalic tegmentum and periaqueductum grey matter from brain areas of grey rats genetically selected by behaviour in many generations. The set of computer tools and data processing pipelines helped to find genes and gene regulation patterns related to behaviour patterns. RNAprofiling experiments revealed the lists of differentially expressed genes in the contrast samples as well as differentially spliced isoforms. The gene ontology categories of protein transport, phosphoproteins, and nucleotide binding are presented together with categories of transmission of nerve impulses and neuron development were identified. Differential alternative splicing events found in the brain areas studied are statistically significant. We discuss role of alternative splicing events for neurospecific genes in behaviour patterns as well as extension of brain transcriptomics profiling.

Open Access April 20, 2017

PGMiner reloaded, fully automated proteogenomic annotation tool linking genomes to proteomes

Canan Has, Sergey A. Lashin, Alexey Kochetov, Jens Allmer

Page range: 16-23

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Abstract

Improvements in genome sequencing technology increased the availability of full genomes and transcriptomes of many organisms. However, the major benefit of massive parallel sequencing is to better understand the organization and function of genes which then lead to understanding of phenotypes. In order to interpret genomic data with automated gene annotation studies, several tools are currently available. Even though the accuracy of computational gene annotation is increasing, a combination of multiple lines of experimental evidences should be gathered. Mass spectrometry allows the identification and sequencing of proteins as major gene products; and it is only these proteins that conclusively show whether a part of a genome is a coding region or not to result in phenotypes. Therefore, in the field of proteogenomics, the validation of computational methods is done by exploiting mass spectrometric data. As a result, identification of novel protein coding regions, validation of current gene models, and determination of upstream and downstream regions of genes can be achieved. In this paper, we present new functionality for our proteogenomic tool, PGMiner which performs all proteogenomic steps like acquisition of mass spectrometric data, peptide identification against preprocessed sequence databases, assignment of statistical confidence to identified peptides, mapping confident peptides to gene models, and result visualization. The extensions cover determining proteotypic peptides and thus unambiguous protein identification. Furthermore, peptides conflicting with gene models can now automatically assessed within the context of predicted alternative open reading frames.

Open Access April 20, 2017

Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processing

Diogo Almeida, Ida Skov, Jesper Lund, Afsaneh Mohammadnejad, Artur Silva, Fabio Vandin, Qihua Tan, Jan Baumbach, Richard Röttger

Page range: 24-32

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Abstract

Measuring differential methylation of the DNA is the nowadays most common approach to linking epigenetic modifications to diseases (called epigenome-wide association studies, EWAS). For its low cost, its efficiency and easy handling, the Illumina HumanMethylation450 BeadChip and its successor, the Infinium MethylationEPIC BeadChip, is the by far most popular techniques for conduction EWAS in large patient cohorts. Despite the popularity of this chip technology, raw data processing and statistical analysis of the array data remains far from trivial and still lacks dedicated software libraries enabling high quality and statistically sound downstream analyses. As of yet, only R-based solutions are freely available for low-level processing of the Illumina chip data. However, the lack of alternative libraries poses a hurdle for the development of new bioinformatic tools, in particular when it comes to web services or applications where run time and memory consumption matter, or EWAS data analysis is an integrative part of a bigger framework or data analysis pipeline. We have therefore developed and implemented Jllumina, an open-source Java library for raw data manipulation of Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data, supporting the developer with Java functions covering reading and preprocessing the raw data, down to statistical assessment, permutation tests, and identification of differentially methylated loci. Jllumina is fully parallelizable and publicly available at http://dimmer.compbio.sdu.dk/download.html

Open Access April 20, 2017

New insights into genotype–phenotype correlation in individuals with different level of general non-specific reactivity of an organism

Alexander Mulik, Valery Novochadov, Alexander Bondarev, Sofya Lipnitskaya, Irina Ulesikova, Yulia Shatyr

Page range: 33-42

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Abstract

The objective of the study was to investigate the genetic basis of general non-specific reactivity of an organism. Systematic search in PubMedCentral, PDB, KEGG and SNP databases identified a set of genes and their polymorphisms that can determine pain sensitivity and therefore the level of general non-specific reactivity of the human organism. Six SNPs were selected for genotyping kit design; 230 healthy volunteers were enrolled in the study. It was revealed that very high pain threshold was associated with allele A in rs1851048 and allele C in rs6777055. High level of general non-specific reactivity of an organism was associated with allele G in rs2562456 (OR=1.804, CI=1.139-2.857, p=0.011) and allele C in rs6923492 (OR=1.582, CI=1.071-2.335, p=0.021). Low level of general non-specific reactivity of an organism was associated with allele T in rs6923492 (OR=0.351, CI=0.154-0.799, p=0.010). A set of genes and single-nucleotide polymorphisms associated with the pain sensitivity and indirectly with the level of general non-specific reactivity of human organism were determined. The identified correlations reveal some molecular mechanisms of general non-specific reactivity of an organism variability and can guide further research in this area.

Open Access April 20, 2017

Omics Fusion – A Platform for Integrative Analysis of Omics Data

Benedikt G. Brink, Annica Seidel, Nils Kleinbölting, Tim W. Nattkemper, Stefan P. Albaum

Page range: 43-46

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Abstract

We present Omics Fusion, a new web-based platform for integrative analysis of omics data. Omics Fusion provides a collection of new and established tools and visualization methods to support researchers in exploring omics data, validating results or understanding how to adjust experiments in order to make new discoveries. It is easily extendible and new visualization methods are added continuously. It is available for free under: https://fusion.cebitec.uni-bielefeld.de/

Open Access April 20, 2017

DaTo: an atlas of biological databases and tools

Qilin Li, Yincong Zhou, Yingmin Jiao, Zhao Zhang, Lin Bai, Li Tong, Xiong Yang, Björn Sommer, Ralf Hofestädt, Ming Chen

Page range: 30-38

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Abstract

This work presents DaTo, a semi-automatically generated world atlas of biological databases and tools. It extracts raw information from all PubMed articles which contain exact URLs in their abstract section, followed by a manual curation of the abstract and the URL accessibility. DaTo features a user-friendly query interface, providing extensible URL-related annotations, such as the status, the location and the country of the URL. A graphical interaction network browser has also been integrated into the DaTo web interface to facilitate exploration of the relationship between different tools and databases with respect to their ontology-based semantic similarity. Using DaTo, the geographical locations, the health statuses, as well as the journal associations were evaluated with respect to the historical development of bioinformatics tools and databases over the last 20 years. We hope it will inspire the biological community to gain a systematic insight into bioinformatics resources. DaTo is accessible via http://bis.zju.edu.cn/DaTo/.

Open Access April 20, 2017

Web-based hybrid-dimensional Visualization and Exploration of Cytological Localization Scenarios

Gökhan Kovanci, Mehmood Ghaffar, Björn Sommer

Page range: 47-58

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Abstract

The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybriddimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3.js. In this way it is possible to visualize and explore CmPI-generated localization scenarios including networks mapped to 3D cell components by just providing a URL to a collaboration partner. This publication describes the integration of the different technologies - Three.js, D3.js and PHP - as well as an application case: a localization scenario of the citrate cycle. The CmPI web viewer is available at: http://CmPIweb.CELLmicrocosmos.org.

About this journal

Objective
Journal of Integrative Bioinformatics (JIB) is an international open access journal publishing original peer-reviewed research articles in all aspects of integrative bioinformatics.

Molecular biology produces huge amounts of data in the post-genomic era. This includes data describing metabolic mechanisms and pathways, structural genomic organization, patterns of regulatory regions; proteomics, transcriptomics, and metabolomics. On the one hand, analysis of this data uses essentially the methods and concepts of computer science; on the other hand, the range of biological tasks solved by researchers determines the range and scope of the data. Currently, there are about 1,000 database systems and various analytical tools available via the Internet which are directed at solving various biological tasks.

The challenge we have is to integrate these list-parts and relationships from genomics and proteomics at novel levels of understanding. Integrative Bioinformatics is a new area of research using the tools of computer science and electronic infrastructure applied to Biotechnology. These tools will also represent the backbone of the concept of a virtual cell.

Topics

Software applications/tools and databases covering the following topics:

Molecular Databases, Information Systems and Data Warehouses
Integration of Data, Methods and Tools
Metabolic and Regulatory Network Modeling and Simulation
Signal Pathways and Cell Control
Network Analysis
Medical Informatics, Biomedicine and Biotechnology
Integrative Approaches for Drug Design
Integrative Data and Text Mining Approaches
Integrative, whole cell and molecular modeling
Visualization and animation

Review papers are also welcome with regard to JIB.tools.

Article formats
Research articles, Review papers, Workshop contributions (if peer-reviewed)

Article processing charges (APCs)
Each unsolicited article, which is accepted for publication in the Journal of Integrative Bioinformatics is subject to an Article Processing Charge of 1,000€.
The Open Access publication of invited articles for Special Issues is sponsored by the editors.

Inquiries concerning APCs should be addressed to the Editorial Office at De Gruyter (see contact details below).