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TrSDB Analyses
TrSDB analyses for nine non-redundant eukaryotic proteomes are performed with TranScout and ProtLoc programs.
Different entries subgroups are generated according to prediction probabilty of TranScout matches, nuclear score of ProtLoc, and existing annotation references linked to InterPro (via InterPro2GO) and/or Gene Ontology Annotation.
Entries which have one of the following selected GO entries are considered to be formerly annotated as transcription factors.
All positive TranScout entries may be classified into:
Entries without any kind of InterPro or GOA reference. They might be entries that could be first annotated as putative transcription factors from TranScout prediction.
Entries with an InterPro or GOA reference not in selected GO entries.
Former annotation might have a somewhat ambigous reference, such as just referring to nuclear localization or zinc finger (some nuclear or zinc-finger proteins are not transcription factors); or references initially unrelated to transcription factors. So, TranScout might reinforce the considered entry as a transcription factor, or suggest a new functionality to be regarded apart from the previously annotated one/s (moonlighting).
Entries with an InterPro or GOA reference present in selected GO entries. They are very likely transcription factors since TranScout and InterPro/GOA coincide in their assignment.
As well, those entries with words such as hypothetical, putative or unknown in annotation description text, or even with no annotation at all, are also included in 'Incognito' group.
Additionally, detailed statistics of TRS motifs are provided for each organism.
Transcription Factors per Organism Analysis
Arabidopsis thaliana Drosophila melanogaster Homo sapiens Mus musculus Rattus norvegicus Schizosaccharomyces pombe Guillardia theta Caenorhadbitis elegans Saccharomyces cerevisiae
TRS motifs numbers in different Eukaryote Proteomes
Predicted TranScout putative Transcription Factors supported by Homology within TrSDB proteomes.
List of proteome entries detected as positive by TranScout, which have high similarity (BLAST with default parameters and threshold up to e-20) to other protein entries detected by TranScout. (listed up to 5 putative homologues and paralogues per organism). In right column, analyses are restricted to entries wich have at least 1 DNA-binding predicted contribution.
Arabidopsis thaliana 6084 Download 5448 Download Drosophila melanogaster 4195 Download 3806 Download Homo sapiens 11621 Download 10713 Download Mus musculus 10249 Download 9516 Download Rattus norvegicus 7509 Download 6933 Download Schizosaccharomyces pombe 958 Download 856 Download Guillardia theta 38 Download 36 Download Caenorhadbitis elegans 4675 Download 4289 Download Saccharomyces cerevisiae 1005 Download 864 Download
TrSDB version: 1.1
Sequence Sources: Proteome@EBI April 2003
InterPro: InterPro@EBI April 2003
GOA: GOA@EBI June 2003