SlideBase

Selection of cell or tissue specific genomic elements using sliders.

Human Promoters

Promoter activity across the majority of cell types and tissues

Human Enhancers

Enhancer activity across the majority of cell types and tissues

Human miRNA

miRNA activity across cell types

The Human miRNA selector will be available as soon as FANTOM5 publishes their miRNA resource (deHoon, in review).

BioGPS GeneAtlas U133A

Gene selection based on microarray expression data across a wide range of human tissues

Protein Atlas

Combined mRNA (RNA-Seq) and protein (immunostaining) expression across cell types and tissues

GTEx V6

Gene selection based on RNA-Seq expression data across a wide range of human tissues


SlideBase slider demo

What is SlideBase?

Large consortia such as FANTOM , ENCODE , The Human Protein Atlas and GTEx are producing comprehensive datasets for as a result of measurements of molecular states of cells and tisses on different functional levels.

These atlases are uselful for understanding biology and diseases and describe expression of a multitude of genomic features such as gene promoters, miRNAs, proteins and enhancer regions.

Even so, it can be difficult to navigate such complex data sets if the user is not accustomed with the detailed aspects behind the research process. In addition, the lack of intuitive methods for selection of expressed genomic features of interest can limit the usage of such data sets by the community. Pre-defining and exploring the data sets can also become a challenge especially because expression thresholds are typically best defined by users, according to individual needs.

To this extent we present SlideBase ( http://slidebase.binf.ku.dk ), a tool for selection of expressed features from a given dataset by user-customized expression thresholds through the use of interacting sliders.


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