Genomics data from The Cancer Genome Atlas (TCGA) project has led to the comprehensive molecular characterization of multiple cancer types. The large sample numbers in TCGA offer an excellent opportunity to address questions associated with tumo heterogeneity. Exploration of the ...
Read More »Gene expression should be analyzed on the isoform level
Alternative usage of transcript isoforms from the same gene has been hypothesized as an important feature in cancers. However, differential usage of gene transcripts between conditions – isoform switching – has not been comprehensively characterized in and across cancer types. ...
Read More »ASAP – a Web-based platform for the analysis and interactive visualization of single-cell RNA-seq data
Single-cell RNA-sequencing (scRNA-seq) allows whole transcriptome profiling of thousands of individual cells, enabling the molecular exploration of tissues at the cellular level. Such analytical capacity is of great interest to many research groups in the world, yet these groups often ...
Read More »CellView – Interactive Exploration Of High Dimensional Single Cell RNA-Seq Data
Advances in high-throughput single cell transcriptomics technologies have revolutionized the study of complex tissues. It is now possible to measure gene expression across thousands of individual cells to define cell types and states. While powerful computational and statistical frameworks are ...
Read More »SeqTU – A Web Server for Identification of Bacterial Transcription Units
A transcription unit (TU) consists of K ≥ 1consecutive genes on the same strand of a bacterial genome that are transcribed into a single mRNA molecule under certain conditions. Their identification is an essential step in elucidation of transcriptional regulatory networks. A ...
Read More »ATGC transcriptomics – a web-based application to integrate, explore and analyze de novo transcriptomic data
In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for ...
Read More »LocExpress – a web server for efficiently estimating expression of novel transcripts
The temporal and spatial-specific expression pattern of a transcript in multiple tissues and cell types can indicate key clues about its function. While several gene atlas available online as pre-computed databases for known gene models, it’s still challenging to obtain ...
Read More »DEIVA – a web application for interactive visual analysis of differential gene expression profiles
Differential gene expression (DGE) analysis is a technique to identify statistically significant differences in RNA abundance for genes or arbitrary features between different biological states. The result of a DGE test is typically further analyzed using statistical software, spreadsheets or ...
Read More »CATchUP – A web database for spatiotemporally regulated genes
For proper control of biological activity, some key genes are highly expressed in a particular spatiotemporal domain. Mining of such spatiotemporally expressed genes using large-scale gene expression data derived from a broad range of experimental sources facilitates our understanding of ...
Read More »JCVI launches a web portal for RNA-seq based gene expression analysis for agricultural animals
There is now a web portal that will provide the required tools and computing power for the research community to help drill down into the genetic make-up of horses. The portal was developed by scientists at the J. Craig Venter Institute, ...
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