TranSeqAnnotator: large-scale analysis of transcriptomic data

Preprocessing of Public RNA-Sequencing Datasets to Facilitate Downstream Analyses of Human Diseases

Publicly available RNA-sequencing (RNA-seq) data are a rich resource for elucidating the mechanisms of human disease; however, preprocessing these data requires considerable bioinformatic expertise and computational infrastructure. Analyzing multiple datasets with a consistent computational workflow increases the accuracy of downstream meta-analyses. This collection of datasets represents the human intracellular transcriptional response to disorders and diseases such as acute lymphoblastic leukemia (ALL), B-cell lymphomas, chronic obstructive pulmonary disease (COPD), colorectal cancer, lupus erythematosus; as well as infection with pathogens including Borrelia burgdorferi, hantavirus, influenza A virus, Middle East respiratory syndrome coronavirus (MERS-CoV), Streptococcus pneumoniae, respiratory syncytial virus (RSV), severe acute respiratory syndrome coronavirus (SARS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We calculated the statistically significant differentially expressed genes and Gene Ontology terms for all datasets. In addition, a subset of the datasets also includes results from splice variant analyses, intracellular signaling pathway enrichments as well as read mapping and quantification. All analyses were performed using well-established algorithms and are provided to facilitate future data mining activities, wet lab studies, and to accelerate collaboration and discovery.

Zinc Supplementation in a Randomized Controlled Trial Decreased ZIP4 and ZIP8 mRNA Abundance in Peripheral Blood Mononuclear Cells of Adult Women

Zinc plays an integral role in numerous cellular processes including regulation of gene expression. This randomized placebo-controlled trial in adult women evaluated the effects of 20 mg Zn for 23 days. The mRNA abundance of zinc transporters (ZnT1/ZIP3/ZIP4/ZIP8) and metallothionein (MT1) from peripheral blood mononuclear cells was determined by real-time quantitative polymerase chain reaction. In paired samples (n = 6-9), the ZIP4 (P = 0.036) and ZIP8 (P = 0.038) mRNA abundance decreased following zinc supplementation. ZnT1, ZIP3, and MT1 mRNA abundance did not change significantly. The mean ± standard deviation plasma zinc concentration (by inductively coupled plasma mass spectrometry) at baseline was 680 ± 110 μg/L for the zinc group (n = 24) and 741 ± 92 μg/L for the placebo group (n = 23). At endpoint, plasma zinc in the zinc group increased to 735 ± 80 μg/L (P < 0.01) while in the placebo group (717 ± 100 μg/L) it did not change significantly from baseline. The change in mRNA abundance highlights the importance of further investigating ZIP4 and ZIP8 mRNA abundance as potential zinc status biomarkers.

InCoB2012 Conference: from biological data to knowledge to technological breakthroughs

Ten years ago when Asia-Pacific Bioinformatics Network held the first International Conference on Bioinformatics (InCoB) in Bangkok its theme was North-South Networking. At that time InCoB aimed to provide biologists and bioinformatics researchers in the Asia-Pacific region a forum to meet, interact with, and disseminate knowledge about the burgeoning field of bioinformatics. Meanwhile InCoB has evolved into a major regional bioinformatics conference that attracts not only talented and established scientists from the region but increasingly also from East Asia, North America and Europe. Since 2006 InCoB yielded 114 articles in BMC Bioinformatics supplement issues that have been cited nearly 1,000 times to date. In part, these developments reflect the success of bioinformatics education and continuous efforts to integrate and utilize bioinformatics in biotechnology and biosciences in the Asia-Pacific region. A cross-section of research leading from biological data to knowledge and to technological applications, the InCoB2012 theme, is introduced in this editorial. Other highlights included sessions organized by the Pan-Asian Pacific Genome Initiative and a Machine Learning in Immunology competition. InCoB2013 is scheduled for September 18-21, 2013 at Suzhou, China.