Overview of Help-Pages

RegionMiner - analysis of genomic regions

RegionMiner analyzes genomic regions e.g. from high-throughput Next Generation Sequencing Experiments. RegionMiner can also work with data from ChIP-on-chip or any positional data where a genomic position of a feature is known.

The program consists of several subtasks:

• Complete Workflow for ChIP-Seq Analysis (only available on GGA)
  Complete Workflow for the Analysis of ChIP-Seq data down to the description of new TF binding sites.
• Expression Analysis for RNA-Seq Data (only available on GGA)
  Analyze tags from Digital Gene Expression experiment and calculate expression profiles, optionally also differential expression if two data sets are submitted. This task alos handles replicate data.
• Clustering NGS Data (only available on GGA)
  Analyze tags from ChIP-Seq/RNA-Seq experiments, find significant regions, and optionally evaluate clusters with a control file.
• 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 transcription factor binding sites 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.
• Large Scale SNP Analysis
  This subtask analyzes SNP data for their genomic location, their effects on the amino acid sequence of a transcript and their influence on transcription factor binding site motifs. SNP data in various formats can be supplied, e.g. SNP data generated on the Genomatix Mining Station (GMS), SNP data in VCF format and dbSNP ids.
• Copy Number Variation Analysis (only available on GGA)
  This subtask analyzes CNV data generated on the Genomatix Mining Station (GMS).
• 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.
• Search for orthologous GeneIds
  This subtask identifies GeneIds in genomes of different species, which are orthologous to the input GeneIds.
• Correlations between 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.
• CoreSearch
  Definition of de-novo binding sites in ChIP-Seq regions.
• BED file toolbox
  Little helpers for handling BED files, like converting regions to sequences, subset extraction by various criteria and sorting.