RegionMiner
RegionMiner details
RegionMiner consists of 6 subtasks:
- Clustering and Analysis of Tags from ChIP-Seq/DGE experiments (NGS Analyser) - only available on GGA
NGS-Analyser is a programme to analyse and cluster short sequence reads from next generation sequencing experiments. - General annotation and statistics for genomic regions
Here, the proximal genes for each region are calculated along with information about known annotations of the region such as overlap with promoters, exons, or introns. The data is statistically evaluated for the complete input set. Optionally, a MatInspector search can be started on the set of input regions. - Overrepresented TFBS or modules
This subtask generates statistics on transcription factor binding sites (TFBS) and pairs of TFBS (i.e. modules) within the set of input regions. Overrepresentation values and Z-scores are calculated against either the whole genome or all annotated promoter regions of the genome. - Search for orthologous regions in other species
This subtask identifies regions in genomes of different species, which are orthologous to the input regions, thus finding functional evidence by phylogenetic conservation. Optionally, a FrameWorker analysis can be started to identify phylogenetically conserved regulatory structures. - Comparison of two sets of genomic elements (GenomeInspector)
Here, distance correlations are calculated between elements, which either come from two input files or from one input file and annotated genomic elements such as promoters. A correlation graph is displayed as output. - Upload data into ElDorado
Finally, a set of chromosomal regions can be uploaded into Genomatix' annotation database ElDorado to be viewed as "user-defined data".