SlideBase
Selection of cell or tissue specific genomic elements using sliders.
Selection of cell or tissue specific genomic elements using sliders.
Promoter activity across the majority of cell types and tissues
Enhancer activity across the majority of cell types and tissues
miRNA activity across cell types
Gene selection based on microarray expression data across a wide range of human tissues
Combined mRNA (RNA-Seq) and protein (immunostaining) expression across cell types and tissues
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 ( https://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.
If you want to acknowledge SlideBase in your research please cite:
Ienasescu, H., et al. (2016). On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase, Database 2016, doi: 10.1093/database/baw144
