Transcriptional regulation is carried out by transcription associated proteins (TAPs), comprising transcription factors
(TFs, binding in sequence-specific manner to cis-regulatory elements to enhance or repress transcription), transcriptional
regulators (TRs, acting as part of the transcription core complex, via unspecific binding, protein-protein interaction
or chromatin modification) and putative TAPs (PTs), the role of which needs to be determined.
Protein names (e.g. in download and phylogenetic trees) are extended by a (typically five) letter code abbreviating the species,
e.g. ORYSA = ORYza SAtiva. Please see this table for the alphabetically sorted codes.
Version history and citations
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TAPscan v1
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The TAPscan v1 tool was published 2010 ((Lang et al. in GBE).
It combined the rule sets of three previous resources,
PlanTAPDB
(Richardt et al. 2007, Plant Physiol),
PlantTFDB
(Guo et al. 2008, NAR) and
PlnTFDB
(Riano-Pachon et al. 2009, NAR).
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| TAPscan v2 |
The TAPscan v2 web interface makes the genome-wide annotation of TAPs available for the community.
TAPscan V2 was published in 2017 (
Wilhelmsson et al. 2017, GBE).
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TAPscan v3
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TAPscan v3 includes the improvement of selected TAP families to annotate TAPs specifically in
algae with higher sensitivity and specificity (Petroll et al., 2021).
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TAPscan v4
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TAPscan v4 is the latest version and was published in 2024 (Petroll et al., preprint) and enables the detection of 138 TAP families.
In addition, an updated web interface is available, making through the incorporation of the Genomezoo database
even more TAP data available for the community. TAPscan v4 has also been made available as a Galaxy tool as
part of the European Galaxy server (usegalaxy.eu).
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Source code and data availability
All code and data used and referenced in this website is freely available from GitHub:
Licensing
The TAPscan v4 website and classification tool are licensed GPLv3; the underlying data (Genome Zoo) is licensed CC-BY-NC 4.0.
Contact
For more information about tapscan, please send us an email at
tapscan@plantco.de
