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Overview of Help-Pages

Overview of Release Notes



December 2017: new

  1. Data background:

  2. General Features:

  3. NGS Analysis:

  4. Genes & Genomes:

  5. Gene Regulation:

  6. Literature & Pathways:



  7. June 2017:

    1. General Features:

    2. NGS Analysis:

      • Task "CNV analysis" has been removed as only whole genome DNA-Seq data could be analyzed. Old CNV analysis results can still be viewed. Starting with the next release, viewing of old results will not be supported anymore. If you still need some of those results, please consider exporting them. For this purpose you can either use the "Archive Project" functionality on the "Projects & Results" page or the export options on the result page itself.
    3. Genes & Genomes:

      • GenomeBrowser:
        • Allow loading of BAM/BED files from all projects available to the user (previously only BAM/BED files from the current default project could be loaded)
        • Genomic positions of annotation track elements can be exported in BED format
      • ElDorado / Gene2Promoter: genes search can be restricted to certain keywords (e.g. gene IDs, gene symbols, transcript accession numbers)
      • Comparative Genomics view: replaced Java applet with HTML5 in order to get better support with newer browsers
      • Gene2Promoter / Alternative Transcripts / Comparative Genomics: improved promoter selection
        • Promoters can be selected according to several filter criteria (filters are combined with AND).
        • Human promoters can be filtered for overlap with public annotation data, e.g. histone modifications or ChIP-Seq data from ENCODE.
    4. Gene Regulation:

      • MatInspector: genomic positions of matches included if Genomatix promoter sequences are analyzed
        • Genomic position of matches are shown in result table and graphical view as tooltip. Furthermore, they are included as additional columns in the Excel and TSV export of the matches.
        • If the promoter sequences have been selected by input of a gene name, genomic positions of matches can be exported in BED format.
    5. Literature & Pathways:

      • GePS (Genomatix Pathway System): the "Signal Transduction Pathways (canonical)" category has been replaced by "Pathway Based Networks (Public Sources)".
        • The generation and display of these networks has been adapted to our proprietary literature data mining algorithm which uses scientific literature as well as public and in-house curated databases.
        • Underlying literature and background data can now be updated at regular intervals.
        • Previously unclear display of large networks can now be improved by reducing the number of input genes.
      • GeneRanker: the "Signal Transduction Pathways (canonical)" category has been replaced by "Pathway Based Networks (Public Sources)".


    December 2016:

    1. Data background:

      • ElDorado 12-2016: 7 updated genomes and new transcript annotation for all 33 organisms:
        for details see the genome statistics page and the public data sources
      • Literature data update, now based on PubMed, 11-2016
      • Extended matrix library of transcription factor binding sites (MatBase Version 10.0):
        • Includes 78 new matrices (8 vertebrate, 70 plant)
        • Library now contains 1679 matrices in 456 families
      • Updated Restriction Site Library (based on REBASE version 612)
      • Extended Promoter Module Library (Module Library Version 6.1):
        • Includes 18 new vertebrate modules
        • Library now contains 988 modules (883 vertebrate and 105 plant modules)
    2. General Features:

      • The standard length of promoters in all Genomatix programs is now 1000 bp upstream and 100 bp downstream of a transcription start site
        (used to be 500 bp upstream and 100 bp downstream), see the definition and source of elements in the database.
      • New VCF file toolbox to upload and work with VCF files (see below)
    3. NGS Analysis:

      • Latest version of DESeq (1.26.0)
      • Latest version of DESeq2 (1.14.1)
      • Latest version of edgeR (3.16.5)
    4. Genes & Genomes:

      • New task in the Genes & Genomes menu: quick overview of all available information for a gene, including links for details
        • DNA Sequence Based: transcripts, SNPs, orthologous genes, microRNAs, etc.
        • Biological Knowledge Mining: literature, pathways, associated GO and MeSH terms
        • Transcription Factor Facts: bindings sites, TF-modules, target genes
      • Number of CAGE tags found in transcripts is displayed in the output of Gene2Promoter and Comparative Genomics (for human and mouse).
    5. Gene Regulation:

      • MatInspector Release 8.3: Search for transcription factor binding sites
        • Improved additional lines of evidences:
          • Evidence 'Known cocitation' is more specific now:
            a co-citation additionally requires a function word (like activates, affects, regulates) between the two genes within a sentence of the literature
          • Evidence 'Known interaction' is more specific now:
            only evidence for "gene of interest is regulated by TF" are shown (not vice versa)
          • Lines of evidences are grouped into the categories
            • experimental evidence
            • literature evidence
            • Promoter Module evidence
            In order to speed up the analysis, the time-consuming "Promoter Module evidence" is not computed by default.
        • Improved output for a large number of short input sequences.
        • Export functionality moved from bottom of result to a new "Export" tab.
        • Enhanced performance of match export (Excel, TSV), especially if additional lines of evidences are included.
      • Overrepresented TFBS task now features an intuitive coloring of over- or under-represented transcription factor binding sites
    6. Literature & Pathways:

      • Gene-TF Analysis task now features an email option and the results are kept in the result management.
      • LitInspector Release 1.9: Additional annotation type: Significant pathways that are associated with search terms in the literature can be identified.
    7. Genomatix Tools:

      • New VCF file toolbox allowing to
        • filter VCF files by genes or positions
        • merge or concatenate VCF files
        • convert VCF files to BED/bigBED files


    July 2016:

    1. Data background:

    2. General Features:

    3. NGS Analysis:

      • Small Variant Detection
        • uses latest samtools version (1.3)
        • speed up by parallel computation of variants for each chromosome
    4. Literature & Pathways:



    April 2016:

    1. Data background:

      • Zea mays genome updated, new transcript annotation for all 33 organisms:
        for details see the genome statistics page and the public data sources
      • Extended matrix library of transcription factor binding sites (MatBase Version 9.4):
        • Includes 23 new matrices (15 vertebrate, 6 plant, 2 fungi)
        • Library now contains 1601 matrices in 447 families
      • Updated Restriction Site Library (based on REBASE version 603)
      • Extended Promoter Module Library (Module Library Version 6.0):
        • Includes 13 new vertebrate and 7 new plant modules
        • Library now contains 970 modules (865 vertebrate and 105 plant modules)
      • More than 60 new mouse transcription factor binding site tracks in GenomeBrowser
      • Literature data update, now based on PubMed, 02-2016
    2. General Features:

      • Better file chooser display (adjustable size) for selection of BED, BAM and sequence files.
    3. New module: NGS Mapping

    4. Genes & Genomes:

      • Orthologous Regions: new input option: single genomic region (e.g. chr1, 1650000 - 1655000)
      • GenomeBrowser:
        • Visualization of VCF files
        • Non-coding transcripts are now visually distinguishable from coding transcripts
      • Gene2Promoter: option to select promoters of coding transcripts
    5. Gene Regulation

      • MatBase: Search for target genes of modules. Enter a gene symbol and get a list of modules targeting that gene.
    6. Literature & Pathways:

      • LitInspector and GePS are now based on the latest Literature (02-2016) (details)
    7. Genomatix Tools:

      • New task in BAM file toolbox: pileup removal
      • BED file comparison: new option for extraction of intersected overlapping regions
      • All BED file tools can now be started with email option
    8. Microarray Analysis (ChipInspector):



    October 2015:

    1. Data background:

    2. General Features:

      • The user's organism selection (reference genome) will persist across sessions
      • ElDorado query results will not be saved in the project management anymore
      • GGA only: Submitted jobs of all users are shown in "Projects & Results"
    3. Genes & Genomes:

      • GenomeInspector can now be started with email option
      • Orthologous Regions: output includes links to GenomeBrowser to quickly evaluate orthologous regions
      • GenomeBrowser: transcript start regions are colored according to number of CAGE tags and a link to the corresponding tissue profile is available for each transcript start region
    4. Gene Regulation:

      • MatInspector: Search for transcription factor binding sites
        • new look & feel for output table with match details
    5. Literature & Pathways:

      • GePS (Genomatix Pathway System) now provides a link to the corresponding locus in GenomeBrowser (in the gene info panel)
    6. Genomatix Tools:



    July 2015:

    1. Data background:

      • 8 updated genomes, including human (GRCh38), and new transcript annotation for all 33 organisms:
        for details see the genome statistics page and the public data sources
      • Extended matrix library of transcription factor binding sites (MatBase Version 9.3):
        • Includes 4 new vertebrate matrices
        • Library now contains 1578 matrices in 444 families
      • Updated Restriction Site Library (based on REBASE version 506)
      • Extended Promoter Module Library (Module Library Version 5.9):
        • Includes 16 new vertebrate modules
        • Library now contains 950 modules (852 vertebrate and 98 plant modules)
      • More than 200 new transcription factor binding site tracks in GenomeBrowser
      • Literature data update, now based on PubMed, 05-2015
      • Homo sapiens NCBI build 36 / hg18 will no longer be supported. Discontinued ElDorado versions are
        • ElDorado 07-2009 (including Homo sapiens NCBI build 36 / hg18)
        • ElDorado 02-2010
        • ElDorado 12-2010
    2. General Features:

    3. NGS Analysis:

    4. Genes & Genomes:

      • ElDorado: improved sequence search in genomes based on Blast
    5. Gene Regulation:

      • Matrix definition: Sequence logos can be downloaded in various formats (e.g. for publication)
    6. Literature & Pathways:

      • LitInspector and GePS are now based on the latest Literature (05-2015) (details)
      • LitInspector, Release 1.8: Tagging of Diseases, Tissues, and Small Molecules now based on the UMLS database
      • Gene-TF-Analysis:
        • Added direct links to co-citations
        • Added input options (input can be various keywords like GeneIds, accession numbers, symbols)
      • GePS (Genomatix Pathway System)
        • new arrow for regulations:
        • Export: added support for 'TIFF' and 'EPS'
      • GeneRanker:
        • new annotation type Clinical Diseases, based on ClinVar
        • annotation type "Small Molecules (Genomatix Literature Mining)" replaced by "Pharmacological Substances (Genomatix Literature Mining)"
        • annotation types "Associated Cancer Tissues (COSMIC)" and "Chemical Entities of Biological Interest (ChEBI)" are discontinued
    7. Genomatix Tools:

      • BAM file tools: extended BAM file statistics with
        • more information on reads in BAM file (flags like paired, unpaired, mapped etc are shown)
        • graphics for chromosome distribution
        • optional classification of input reads on exons, introns, promoters or intergenic
    8. Microarray Analysis (ChipInspector):


    January 2015:

    1. Data background:

      • Updated Transcription Factor Database: MatBase Version 9.2
        • Matrix Family Library Version 9.2
          • Includes 149 new matrices (among them 139 vertebrate matrices and 8 plants)
          • Library now contains 1574 matrices in 440 families
        • Module Library Version 5.8
          • Includes 18 new vertebrate modules and 1 new plant module
          • Library now contains 934 modules (836 vertebrate modules and 98 plant modules)
      • Updated Restriction Site Library (based on REBASE version 412)
    2. General:

    3. NGS Analysis:

      • RNA-Seq Expression Analysis
        • "locus-based" expression analysis (in addition to "transcript-based" option), where all exons of all alternative transcripts of a locus are taken together and this "gene body" is used for counting reads
      • ChIP-Seq Workflow
        • MACS2 added for peak calling (in addition to NGSanalyzer, MACS1.4 and SICER)
    4. Genes & Genomes:

    5. Genomatix Tools:


    July 2014:

    1. NGS Analysis:

      • RNA-Seq Expression Analysis
        • additional option: DESeq2, (version 1.4.5) including selection of 'fitting type' parameter and two alternative methods for testing for differential expression
        • latest version of DESeq (1.16.0), including selection of 'fitting type' parameter
        • latest version of edgeR (3.6.2)
        • two additional plots in the output:
        • added number of transcripts, mean NE, mean RPKM for each differentially expressed gene in the expression profile table
        • bug fix: sometimes redundant transcripts were included in the expression analysis (only when using ALL transcripts from ElDorado)
      • Small Variant Detection
      • CNV Analysis
        • latest version of cn.MOPS (1.10.0)
        • latest version of Control-FREEC (7.0)
    2. Genes & Genomes:

      • Transcriptome Viewer
        • the transcripts to be displayed can be filtered by their source (NCBI RefSeq, Ensembl, ...)
      • GenomeInspector:
        • correlation lists now link to GenomeBrowser, where the corresponding tracks from the correlation are pre-selected and shown
    3. Gene Regulation:

    4. Literature & Pathways:

      • New task: Gene-TF-Analysis
        • new sub-task to determine for a list of input genes and transcription factors if the TF has a validated or predicted binding site on the gene's promoter or not
      • GePS (Genomatix Pathway System)
        • new network extension method: extension by microRNAs
        • changed default: validated regulatory evidences will be excluded from the evidence filter by default (see settings)
        • user-defined colors can be saved across sessions
        • added so-called gene families as nodes (generic terms for genes, based on proprietary Genomatix algorithms, e.g. "metallothionein" for genes like MT1A, MT1B, MT1E, etc.) to include co-citations with imprecise notations in the literature/abstracts
      • GeneRanker
        • recognises Ensembl gene IDs (e.g. ENSG00000115041) and microRNA IDs (e.g. hsa-mir-181a)
      • Genomatix Tools:

        • BAM file tools: new task for BAM file statistics with graphics for
          • Pileup Distribution
          • Mapping Quality
          • Paired End: Insert Size
          • Paired End: Strand Orientation
        • GeneID Toolbox
          • the information retrieval tools now also allow Ensembl GeneIds, transcript accession numbers and Affymetrix probeset ids as input
        • List comparison
          • improved algorithm to handle key-value pairs with the same key

    January 2014: 

    1. Data background:

      • Three updated genomes and new transcript annotation for all 33 organisms:
        for details see the genome statistics page and the public data sources
      • Extended matrix library of transcription factor binding sites (MatBase Version 9.1):
        • Includes 44 new matrices (26 vertebrate, 18 plant).
        • Library now contains 1424 matrices in 418 families.
      • Updated Restriction Site Library (based on REBASE version 311)
      • Extended Promoter Module Library (Module Library Version 5.7):
        • Includes 43 new vertebrate modules and 7 new plant modules
        • Library now contains 915 modules (818 vertebrate and 97 plant modules)
    2. General Features:

    3. NGS Analysis:

      • New Task: Small Variant Detection new
        • Variant calling (SNPs and small InDels) via samtools using BAM files as input, resulting in VCF files
      • MicroRNA Analysis:
        • Tab delimited input files containing microRNA ID and read counts can now be used as input
    4. Genes & Genomes:

      • Annotation and Statistics:
        • The transcript source can now be selected (e.g. Refseq or Ensembl transcripts only)
      • GenomeInspector:
        • Here, the transcript source can also be selected (e.g. Refseq or Ensembl transcripts only), if one of the correlation partner sets is exons/transcripts
        • Updated public data for correlations:
          • ENCODE TF data: 35 new human transcription factors
          • Genomatix ChIP-Seq data: 40 human transcription factors
      • GenomeBrowser:
        • The orientation of paired reads can be highlighted to easily detect structural variants like inversions, duplications or translocations.
        • Reads in the alignment track can be sorted or filtered to show the highlighted reads on top.
        • Public data: New transcription factor binding site tracks (35 new human transcription factors from ENCODE, 40 human and 31 mouse transcription factors from various sources compiled by Genomatix).
      • Variant Analysis:
        • VCF files previously uploaded to the Genomatix Project Management can be used as input files for the Variant Analysis task. New VCF input files are automatically added to the user's Project Management.
    5. Gene Regulation:

      • MatInspector
        • Updated ChIP-Seq data for correlation with experimental data: 35 new human transcription factors from ENCODE, 40 human transcription factors compiled by Genomatix
    6. Literature & Pathways:

      • GePS (Pathway System):
        • Literature can be filtered by publication date. E.g. networks can be generated and extended with literature published between 1995/01/01 and 2013/11/19.
        • Terms like small molecules can be extended by genes.
    7. Genomatix Tools:

      • The GeneID ↔ Symbols tasks in the GeneID Tools now allow saving the gene body positions in BED file format,
        allowing further analysis with tasks that take genomic positions as input, like GenomeInspector.
    8. Microarray Analysis (ChipInspector):

      • Probe annotation is based on ElDorado 12-2013.
      • The following new chips are supported:
        • Affymetrix Human Gene 2.0 ST
        • Affymetrix Mouse Gene 2.0 ST
        • Affymetrix Human Gene 2.1 ST
        • Affymetrix Mouse Gene 2.1 ST

    August 2013:

    Complete new package and menu structure of the Genomatix Suite (please also see the general introduction).
    The following packages are now available:

    1. NGS Analysis:

      • Selection of the current genome via organism, build or ElDorado annotation date
        • BED and BAM files in parameter pages are pre-selected to match the currently selected genome
      • RNA-Seq Expression Analysis
        • You can now select the transcript source to use (e.g. Refseq or Ensembl transcripts only)
        • RPKM values are listed in output, in addition to NE values
        • Direct download of gene lists from result table
      • New graphics for region classification
        • Visualization of read enrichment in exons, introns, intergenic regions and promoters compared to the genomic distribution.
      See the complete release notes for the "NGS Analysis" package.
    2. Genes & Genomes:

      • Selection of the current genome via Organism, Build, and ElDorado Annotation date
      • GenomeBrowser
        • Display of score from BED file in the coverage track (e.g. for ChIP-Seq peaks)
        • Additional public data from the ENCODE project can selected as tracks for the human genome:
          • ENCODE transcription factor and Polymerase binding data combined into supertrack, by cell line or by transcription factor
          • ENCODE Histone modification data combined into supertracks or by cell line
          • ENCODE DNase hypersensitivity site data combined into supertracks or by cell line
      • GenomeInspector
        • Redesigned interface for selection of the partner sets for correlation
        • Added public data for correlation
          • ENCODE transcription factor and Polymerase binding data, in supertrack or by transcription factor
          • Evolutionary constrained elements according to Kerstin Lindblad-Toh et al., Nature 478: 476-482 (2011)
          • Chromatin state data combined into supertracks according to Jason Ernst et al., Nature 473: 43-49 (2011)
          • ENCODE Histone modification data combined into supertracks
          • ENCODE DNase hypersensitivity site data combined into supertracks
      See the complete release notes for the "Genes & Genomes" package.
    3. Gene Regulation:

      • MatInspector
        • Completely new graphics based on HTML5, allowing better display of large results. (Java is no longer needed for HTML5 compatible browsers, but the applet is still available for downward compatibility with older browsers.)
        • Additional lines of evidence for a TF binding site:
          • Correlation with ENCODE Chip-Seq data, i.e. a peak from a ChIP-Seq experiment is overlapping the found TFBS
          • Overlap with evolutionary constrained elements according to Kerstin Lindblad-Toh et al., Nature 478: 476-482 (2011); here human constrained elements were filtered for position within promoter but not within exon.
        • Newly structured output: Tabs with Graphical View, Match Details and Match Summary Table
      • FrameWorker
        • Completely new graphics based on HTML5, allowing better display of large results, up to 100 sequences can be displayed graphically. (Java is no longer needed for HTML5 compatible browsers, but the applet is still available for downward compatibility with older browsers.)
        • Newly structured output: Tabs with Graphical View, Model Overview, Model Details and Common Elements
      • Transcription Factor Database: MatBase Release 9.0
      See the complete release notes for the "Gene Regulation" package.
    4. Literature & Pathways:

      • GePS (Pathway System):
        • Improved network generation and extension:
          • A minimum evidence level can be selected
          • Interactions are selected based on all evidence levels above minimum level
        • New evidence level: Validated regulatory level with ENCODE ChIP-Seq data
          • Gene-TF correlations
          • Gene/TF-miRNA correlations
        • Interaction export:
          • All network interactions: Count data for all network interactions
          • Single interaction: Most recent abstracts where both elements are co-cited and other interaction details
        • Networks with terms: Small molecules and diseases
        • Search panel for genes and terms
        • Create filters from selected network genes
      See the complete release notes for the "Literature & Pathways" package.
    5. Genomatix Tools:

      See the complete release notes for "Genomatix Tools".
    6. Microarray Analysis:

      ChipInspector