miRNA is known to regulate up to several hundreds coding genes, thus the integrated analysis of miRNA and mRNA expression data is an important problem. Unfortunately, the integrated analysis is challenging since it needs to consider expression data of two different types, miRNA and mRNA, and target relationship between miRNA and mRNA is not clear,

In eukaryotic cells, alternative cleavage of 3' untranslated regions (UTRs) can affect transcript stability, transport and translation. For polyadenylated (poly(A)) transcripts, cleavage sites can be characterized with short-read sequencing using specialized library construction methods. However, for large-scale cohort studies as well as for clinical sequencing applications, it is desirable to characterize such events using RNA-seq

SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the

Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently, non-templated addition of nucleotides

Oscillatory gene expression is fundamental to development, but technologies for monitoring expression oscillations are limited. Researchers at the University of Wisconsin-Madison have developed a statistical approach called Oscope to identify and characterize the transcriptional dynamics of oscillating genes in single-cell RNA-seq data from an unsynchronized cell population. (a) An oscillating gene group with two

Flowering plants, also known as angiosperms, add an allure to the world that is unlike anything else in nature, but more importantly, they sustain us. Most of the fruits, vegetables, grains, beans, nuts, and even herbs and spices that we consume are produced by flowering plants. They all belong to the green plant branch of

Functional Analysis of Your RNAseq Data - Fiona McCarthy, University of Arizona The broad applicability and availability of RNASeq data has accelerated the generation of functional genomics data sets across a wide range of species. However, the end point of RNASeq analyses is to generate a list of differentially expressed genes; this list contributes little

Global gene expression analysis using microarrays and, more recently, RNA-seq, has allowed investigators to understand biological processes at a system level. However, the identification of differentially expressed genes in experiments with small sample size, high dimensionality, and high variance remains challenging, limiting the usability of these tens of thousands of publicly available, and possibly many

ANIS4 RNAome meeting 2014 Marc Friedländer Xavier Estivill lab Bioinformatics and Genomics Centre for Genomic Regulation, Barcel

High resolution version - https://youtu.be/Wfxh9_fsRfo

If NASA is going to send astronauts on years-long missions, the agency will need new and better tools to monitor whether the men and women are healthy along

The fundamental task in RNA-Seq-based transcriptome analysis is alignment of millions of short reads to the reference genome or transcriptome. Choosing the right tool for the dataset in hand from many existent RNA-Seq alignment packages remains a critical challenge for downstream analysis. To facilitate this choice, researchers from Miami University designed a novel tool for

Researchers at the Francis Crick Institute provide fundamental insights into early human development by single-cell RNA-sequencing of human and mouse preimplantation embryos. They elucidate conserved transcriptional programs along with those that are human-specific and validate their RNA-sequencing findings at the protein level. They identified several genes exclusively expressed in the human pluripotent epiblast including the

Recent transcriptome annotation using deep sequencing approaches have annotated a large number of long non-coding RNAs in zebrafish, a popular model organism for human diseases. These studies characterized lncRNAs in critical developmental stages as well as adult tissues. Each of the studies has uncovered a distinct set of lncRNAs, with minor overlaps. The availability of

Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most alternative isoforms vary in expression between human tissues (Pan et al. 2008; Wang et al. 2012). As RNA-Seq datasets grow in size, it remains challenging to

Analysis of large-scale omics data has become more and more challenging due to high dimensionality. More complex analysis methods and tools are required to handle such data. While many methods already exist, those methods often produce different results. To help users obtain more appropriate results (i.e. candidate genes), researchers from Seoul National University, have developed

Scientists at the University of Maryland have developed a new, web-based tool that enables researchers to quickly and easily visualize and compare large amounts of genomic information resulting from high-throughput sequencing experiments. The free tool, called Epiviz, was described in a paper published online on Aug. 3, 2014 in the journal Nature Methods. Next-generation sequencing

Fast algorithms and well-arranged visualizations are required for the comprehensive analysis of the ever-growing size of genomic and transcriptomic next generation sequencing (NGS) data. ReadXplorer is a software offering straightforward visualization and extensive analysis functions for genomic and transcriptomic DNA sequences mapped on a reference. A unique specialty of ReadXplorer is the quality classification of

Differential expression analysis on the basis of RNA-Seq count data has become a standard tool in transcriptomics. Several studies have shown that prior normalization of the data is crucial for a reliable detection of transcriptional differences. Until now it has not been clear whether and how the transcriptomic approach can be used for differential expression