RegionMiner
Introduction
RegionMiner analyses genomic regions coming from high-throughput Chromatin Immunoprecipitation experiments such as ChIP-on-chip, ChIP-Seq (deep sequencing) or methylation studies. It determines the genomic context for the enriched regions and evaluates the transcription factor binding sites (TFBS).
Features
- Annotation, correlation, statistics and in depth analysis of genomic regions
- Visualisation in personalised ElDorado extended genome annotation database
- Cutting edge molecular biology high-throughput methods allow for genome wide experimental analysis of multiple genomic aspects
- Chromatin Immunoprecipitation of bound transcription factors
- ChIP-on-chip
- ChIP-Seq (deep sequencing)
- Epigenetic modifications
- Methylation studies
- Histone modification
- Open chromatin
- DNase-Seq
- Other methods which require application of high-throughput technologies, such as next generation sequencing (NGS)
All these techniques deliver large sets of short oligo-nucleotide sequences mapped to their respective genomes, resulting in large files with genomic positional information (regions).
RegionMiner provides fast, easy to use and comprehensive analysis of these genomic regions and integrates them easily into a customised ElDorado extended genome annotation database.
Annotation
Based on the largest, most complete, and most accurate genomic annotation database available - ElDorado - the regions are translated into genomic annotation knowledge. Each region is annotated for:
- overlaps with:
- transcripts
- exons
- introns
- promoters
- transcriptional start regions
- repeats
- microRNAs
- conserved regions
- next upstream/downstream transcript
Statistics
General statistics for the regions is given. Absolute numbers and percentage of overlaps with:
- locus
- intergenic region
- promoter region
- transcriptional start region
- exon 1, exon 2, exon 3…
- intron1, intron 2, intron 3…
- repeat
- conserved region
- microRNA
Correlations
Extremely fast and easy distance correlation calculations and graphical display for any regions and genomic annotation knowledge by GenomeInspector. Correlates:
- regions with regions
- regions with any annotated genomic elements, i.e.:
- primary transcripts
- promoter regions
- transcriptional start region
- conserved regions
- microRNAs
Deep Analysis
RegionMiner provides integrated and powerful deep analysis options for genomic regions.
- Annotation independent search for orthologous regions in different species
- phylogenetic conservation
- exploration of phylogenetically conserved regulatory patterns and structures by FrameWorker and DiAlign TF *
- Transcription Factor Binding Site analysis of single regions using MatInspector
- all transcription factors
- specific transcription factors
- Global over-representation of TFBS or TFBS combinations (modules) and statistical significance measure
- genomic regions versus genomic background
- genomic regions versus promoter region background
- promoter association
Visualisation
Genomic region data can be uploaded into the ElDorado extended genome annotation data base and visualised in combination with all other annotation **
- up to ten personal annotation sets can be uploaded (up to three of these can be viewed concurrently)
- up to 100,000 regions per personal annotation set
RegionMiner compatibility
- Web-based service that can be accessed via any modern web browser
- No installation procedures needed
- Accepts:
- ChipInspector region output for tiling arrays
- BED format files from analysis programs such as MAT
- Generic tab-delimited files with genomic region data
- Exports results to tab delimited files, which can be opened with Microsoft Excel and other spreadsheet software
Example output
