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Q:
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Can I download all the sequences in PhosphoregDB?
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A:
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Yes all peptide sequences are provided and can be downloaded as plain text by performing a query on the advanced search page.
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Q:
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How were the protein kinases and phosphatases in this database identified?
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A:
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The phosphoregulator set was identified as part of the FANTOM2 initiative. The initial paper (Forrest et al. 2003) identified protein kinases and phosphatases by the presence of catalytic domains predicted by Interpro. These proteins were then mapped to the genome and clustered using TribeMCL. This set of protein kinases and phosphatases has now been expanded to include the atypical protein kinases identified by (Caenepeel et al. 2004)
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Q:
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How were the nuclear localization signals (NLS) and nuclear export sequences (NES) predictions done?
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A:
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NLS predictions were done using predictNLS (Cokol et al. 2000) and scanprosite for the bipartite NLS PS00015. NES predictions were done using NetNES (La Cour et al. 2004). We provide a simplified output for these predictions, if the protein contains a predicted NES or NLS we suggest re-running the prediction to get the full output.
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Q:
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How were the membrane organisation predictions carried out and what does the result mean?
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A:
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All sequences were screened with TMHMM (Krogh et al. 2001) and signalP (Bendtsen et al. 2004) online at CBS. The result Y_Y_PredHel=1, refers to positive signal peptide predictions from both the neural net and hidden markov predictors of signalP, and TMHMM prediction of a single transmembrane region.
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Q:
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Why aren't the predicted domain architectures shown in PhosphoregDB?
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A:
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In the next version of phosphoregDB we hope to provide InterPro domains, signal peptides, transmembrane regions, Nuclear export sequences and Nuclear localization signals. For the meantime, follow the peptide links to the ENSEMBL entry or FANTOMDB entry to get a domain view of the protein.
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Q:
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Why were HeLa cells used for the localization screen?
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A:
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Most transfection studies previously have used HeLa, CHO or COS cell lines, choosing one of these makes comparison between sets possible. Additionally many labs are familiar with HeLa cell morphology and subcellular architecture. Finally for co-localization, we have access to more human markers than mouse ones.
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Q:
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Why do some experimental localizations not agree with the previously published localization?
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A:
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In all cases we recommend reviewing the peptide sequences used, species, cell type, methodology and conditions used to record the localization. In some cases splice variants target to different locations so reviewing the peptide sequence is critical. Also there are many examples of different condtions resulting in different localizations. In all cases we provide the peptide sequence of the clone tested and we have consistently used the same methodology, conditions, transfection time, and reagents to record all localizations. We also provide multiple images for the user to review.
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Q:
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Can I link into PhosphoregDB?
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A:
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Yes, but please tell us and reference the database accordingly.
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Q:
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Can I get the clones used in the experimental localization screen?
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A:
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Only proteins from the RIKEN FANTOM2 project were experimentally tested in this database. FANTOM clones are available from DNAFORM by following the links at the following page, DISTRIBUTION SYSTEM FOR RIKEN FANTOM2 CLONES
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Q:
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What are retired entries?
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A:
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Entries marked as retired have been removed either because they represent false positives ( see Caenepeel et al. 2004), fragments or duplicates.
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