Projects can either be shared read-only or with write access.
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.
December 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)
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 catgories
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.
April 2016
Better file chooser display (adjustable size) for selection of BED, BAM and sequence files.
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)
Library now contains 950 modules (852 vertebrate and 98 plant modules)
Matrix definition: Sequence logos can be downloaded in various formats (e.g. for publication)
January 2015
Added a quick sequence upload option for all tasks that allow DNA sequence analysis
(e.g. MatInspector):
with this option, the DNA sequence is not saved into the result management
Updated ChIP-Seq data for correlation with experimental data: 35 new human transcription factors from ENCODE, 40 human transcription factors compiled by Genomatix
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
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
