Overview of Help-Pages

RegionMiner release notes

September 2011: RegionMiner Release 4.4

• Replicates for ChIPSeq-Workflow
  • allow merging clusters from different replicates (based on user parameters)
  • apply techniques for significance testing (DESeq or edgeR)
• Peak calling in the Clustering-Task and ChIPSeq-Workflow
  • included SICER as a third peak calling algorithm (recommended for histone modifications)
  • new MACS version 1.4.1
• Large Scale SNP Analysis
  • added nucleotide coverage to output files
  • added distance to nearest splice site to output files
• Upload of BED files from GGA/GMS
  • improved file chooser: now starts at the last location when used repeatedly
• NE-values (normalized enrichment/expression values)
  • all NE values are now based on nucleotides instead of read numbers (to be more precise when reads do not fall completely into a region/transcript)
• GenomeInspector:
  • added promoter ID / Symbol/ GeneID to the output of correlations with promoters
  • added the transcript quality to the output of correlations with transcripts
  • links to genomic positions now go directly to the Genomatix GenomeBrowser
• RNASeq Expression Analysis
  • added data plots (fold-change/volcano) for Audic-Claverie results
  • links to GePS now open a new window

April 2011: RegionMiner Release 4.3

• Replicate Analysis for RNASeq Expression Analysis (only available on GGA)
  • available methods: DESeq or edgeR for replicates, else Audic-Claverie
  • modeling count data (i.e. read counts in transcripts) using the negative binomial distribution
  • statistical testing for differential expression within transcripts
  • (adjusted) p-value and log2-fold-change thresholds can be set as parameters
  • data plots (fold change scatter plot, volcano plot) in output
  • start GePS with up-/down-regulated gene lists
• New module: Copy Number Variation analysis (only available on GGA with GMS)
  • Normalized expression values from two genomic mappings from the GMS are set in relation (locus per locus)
  • gene lists for variations can be exported
• Overrepresented transcription factor binding sites
  • added a "distance score" to overrepresentation of TF modules
  • allows sorting for interesting modules (with a preferred distance range of found matches, i.e. a peak in the distance profile)
• BED / bigBed format:
  • allowing bigBed files for input and for internal representation
  • bigBed files are compressed binary indexed files (developed at UCSC)
  • improved processing time and a smaller memory footprint
  • modified BED file upload functionality
  • allow upload of several files at once from local computer
• BED file toolbox:
  • conversion from Wiggle files to BED format
  • Pileup Removal
• Annotation and Statistics:
  • Details page is now built on the fly, allowing to scroll through large lists
• Large Scale SNP Analysis
  • SNP ids allow comparison of different results
  • better/more information about erroneous input data

December 2010: RegionMiner Release 4.2

• Large Scale SNP Analysis
  • Now also available in the Genomatix Software Suite.
  • Additional input formats are supported:
    • SNP data in VCF (variant call format)
    • dbSNP ids
• Expression Analysis for RNA-Seq (only available on GGA)
  • The Genomatix Pathway System (GePS) can be started directly from the output, using subsets of the up/down-regulated gene lists
• Annotation and Statistics:
  • added export of detail data in tab-separated format

August 2010: RegionMiner Release 4.1

• New Genomatix look & feel
• Projects (including all results & data) can now be archived and downloaded as a compressed file (see project management)
• New task: Large Scale SNP Analysis (only available on GGA)
  • genomic location of SNPs
  • their effects on the amino acid sequence of a transcript
  • their influence on transcription factor binding sites
• Expression Analysis for RNA-Seq (only available on GGA)
  • New option allows input of two files for differential analysis of expression between two samples
  • Re-worked output with direct display of the top 50 up/down-regulated genes
• Overrepresented transcription factor binding sites:
  • user-defined matrices can be used for overrepresentation analysis
  • user-defined background (sequences or BED file) can be used, additionally to genomic or promoter background
• BED file toolbox:
  • added conversion of Illumina _export.txt-file (from GERALD) to BED file
  • added extraction of subset from a BED file with the x highest/lowest scores

March 2010: RegionMiner Release 4.0

• Option to import BED files from a server mounted disk
• New task: Complete Workflow for the Analysis of ChipSeq Data (only available on GGA)
• Added optional read statistics and read annotation to the Expression Analysis and Clustering Tasks
• Removed the task "upload of ElDorado data" from RegionMiner (now available within ElDorado)
• Added CoreSearch to RegionMiner
• Annotation and Statistics:
  • General statistics of input regions (mininum, maximum, average region length) is included in the output
  • Quick classification of regions as exons, introns, promoters, intergenic regions
  • The time-consuming next neighbour analysis is now optional
• GenomeInspector:
  • Increased maximum number of regions for correlations to 5 million (only on GGA)
  • Allows download of graph values
  • Added extra info like BED file id and score in output tables
• BED file toolbox: subset selection by list of BED file IDs

February 2010: RegionMiner Release 3.3

• Overrepresented transcription factor binding sites or modules are now based on Matrix Family Library Version 8.2
• BED file toolbox:
  • Convert Sequences to BED file via mapping: added option to include only one region or to allow several mappings in the output file
  • Subset selection: when selecting region subsets based on length or score of the regions, the lower or upper limit can be arbitrary, by setting the parameter to "-"

December 2009: RegionMiner Release 3.2

• RegionMiner Peak-Finding (only available on GGA)
  • Separate tasks for
    • Clustering NGS Data (help page)
    • Expression Analysis for RNASeq Data (help page)
    replacing the previous "NGSAnalyzer" and "MACS" tasks, while retaining all options.
  • Optional evaluation of ChIPSeq data with a control data set by
    • Audic-Claverie algorithm
    • Subtraction of regions (overlap is a parameter)
    • Original MACS algorithm
  • MACS version 1.3.7
    • automatic detection of tag size
    • added mfold as parameter
  • NGS Analyzer version 2.4.3
    • improved output
• New task: Search for Orthologous GeneIds
• Search for Orthologous Regions
  • Improved algorithm to find orthologous regions in cases that were previously not found
  • Output regions can be extracted in GenBank or FASTA format as well as in BED file format (BED file format is supported only for input species).
• GenomeInspector now allows for user-selected colors of the correlation graphs in the output
• Added a number of features to the BED file toolbox:
  • Convert Sequences to BED file (limited number of input sequences)
  • Convert GFF to BED format
  • Extraction of first x regions from a BED file
• Option to upload zipped BED files (for large files)

July 2009: RegionMiner Release 3.1

• BED file upload within the project management
  • BED files can be uploaded to the webserver/GGA and can be re-used for other tasks
  • Uploaded BED files appear in the project management and can be viewed, renamed or deleted from there
  • BED files are automatically deleted from a project after 30 days, but can be protected (not for trial users)
• MACS was added as alternative clustering algorithm to NGSAnalyzer (only available on GGA)
• Added a number of features to the BED file toolbox:
  • Comparison of two BED files (to find unique and overlapping regions)
  • Create subsets by strand
  • Extend all regions by a given number of basepairs up- or downstream
  • Concatenate two or more BED files
• Enhanced extraction of subsets of regions or corresponding GeneIDs in the Annotation and Statistics subtask
• GenomeInspector now allows several correlations in one output graph

April 2009: RegionMiner Release 3.0

• Major speed-up of NGSAnalyzer (only available on GGA)
• Added a BED file toolbox: little helpers for handling BED files, e.g. for converting regions to sequences, sorting or subset extraction
• Easier extraction of Excel™ files in the "Annotation and Statistics" subtask
• Enhanced extraction of sequences in the "Orthologous Sequences" subtask
• Enhanced option for extraction of correlations in GenomeInspector, especially for gene correlation

January 2009: RegionMiner Release 2.02

General:

• Improved BED file parsing

RegionMiner subtask "Annotation and Statistics":

• Added export of number of TF binding sites for each region into Excel Sheet

December 2008: RegionMiner Release 2.01

RegionMiner subtask "GenomeInspector":

• Enhanced speed
• Progress of calculation is displayed on screen
• Slightly changed output graphics: vertical line at zero for better orientation

November 2008: RegionMiner Release 2.0

General:

• Added email option for all RegionMiner tasks
• New look and feel of all parameter pages

RegionMiner subtask "Annotation and Statistics":

• Major speed-up, by factor 10-20, depending on input
• Output of "Statistics"-table and "Details"-table on different pages,

RegionMiner subtask "Upload data into ElDorado":

• Added option to ignore duplicate entries for data upload

July 2008: RegionMiner Release 1.1

RegionMiner subtask "Overrepresented transcription factor binding sites or modules":

• Additional input option: sequence files in addition to regions in form of BED-files
• Additional Matrix Library selection

RegionMiner subtask "Annotation and Statistics":

• Option to extract input regions with flanking sequences

June 2008: RegionMiner Release 1.0

First release of RegionMiner