December 2009: GEMS Launcher Release 5.1.1

• GeneRanker:
  • Allows new identifier types as input (Accession Numbers, Gene Names/Symbols, Affymetrix Probe Set IDs).
  • Allows to use an example input set.
  • When using "Signal Transduction Pathways (canonical)" as annotation type, the user can go directly to the corresponding patthways in Genomatix Pathway System.
• FrameWorker now accepts up to 1000 input sequences.
• CoreSearch ("large scale" version):
  • Enhanced comparison of motifs defined from subsets.
  • Similarity of motifs defined from subsets is given in the output in order to assess the quality of the final motif.

July 2009: GEMS Launcher Release 5.1

• Extended matrix library of transcription factor binding sites (Matrix Family Library Version 8.1):
  • Includes 132 new matrices (101 fungi (yeast), 27 vertebrate, 2 plant, 1 insect, 1 general core promoter element).
  • Library contains now 1106 matrices in 364 families.
• Updated Restriction Site Library (based on REBASE version 907).
• Extended Promoter Module Library (Module Library Version 5.2):
  • Includes 50 new vertebrate modules and 7 new plant modules.
  • Library contains now 727 modules (657 vertebrate and 70 plant modules).
• CoreSearch:
  • Motifs defined from randomly selected subsets can be saved in "large-scale" CoreSearch version.
  • IUPAC conensus sequence of motifs is displayed in "Save Matrices" table in order to allow easier selection of motifs.
• MatDefine: sequence logos are added for better vizualization of matrix consensus sequences.
• GeneRanker: additional annotation type "Signal Transduction Pathways (canonical)" is introduced.

April 2009: GEMS Launcher Release 5.0

• New Task: GeneRanker, for characterizing sets of genes
• CoreSearch:
  • Unlimited number of input sequences (e.g. from ChIP-Seq experiments) are accepted.
  • The new "large-scale" CoreSearch algorithm is used when more than 250 sequences are entered. Definition of a binding motif from about 2000 ChIP-Seq regions usually takes less than 1 minute.
• MatInspector:
  • New lines of evidence to support MatInspector matches:
    • Known cocitation (only available on Genomatix server and GGA)
    • Known interaction (only available on Genomatix server and GGA)
    • Promoter Modules
  • Improved input features to select promoters from ElDorado/Genomatix Promoter Database to MatInspector.
    • Use combo box to select gene of interest
    • Map sequence(s) to any organism available in ElDorado
  • Interactive result tables that allow sorting and filtering.

December 2008: GEMS Launcher Release 4.8

New features and main changes from Release 4.7:

• Extended matrix library of transcription factor binding sites (Matrix Family Library Version 8.0):
  • Includes 178 new matrices (174 vertebrate, 3 plant, 1 fungi).
  • 155 of the new matrices describe homeodomain transcription factor binding sites.
  • 16 of the new vertebrate matrices are derived from ChIP-Chip or Chip-Seq experiments. These matrices describe binding sites for the following transcription factors: CMYC, CTCF, ESRRB, GKLF, HNF3B, HNF4A, NMYC, NRSF, OCT3/4, SOX2, STAT3, TCFCP2L1, USF1, ZFX.
  • Library contains now 974 matrices in 325 families.
• Updated Restriction Site Library (based on REBASE version 812).
• Extended Promoter Module Library (Module Library Version 5.1):
  • Includes 18 new vertebrate modules and 5 new plant modules.
  • Library contains now 670 modules (607 vertebrate and 63 plant modules).