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* facet classification based on FF ontology | * facet classification based on FF ontology | ||
** http://yuri.lbl.gov:8600/fonse/ FONSE (Fantomy ONtology Sample Explorer) | ** http://yuri.lbl.gov:8600/fonse/ FONSE (Fantomy ONtology Sample Explorer) | ||
== Search within Sample/gene/motif names (beta) == | |||
<html> | |||
<form method="get" action="/resource_browser/index.php/User:Hisa/SemanticResults"> | |||
<p>Key Word：<input type="text" name="sq" value="</html>{{#urldecode:{{#urlget:sq}}}}<html>"><input type="submit" value="search"></p> | |||
</form> | |||
</html> | |||
Revision as of 13:35, 16 March 2012
Genes, TSS regions, motifs, samples, etc profiled in FANTOM5.
Usage
- Just click any in the left menue
- Or, keyword search on top of this page.
- Or, make a complex query at Special:Ask, if you are familiar with Semantic MediaWIki
Note
- we are focusing on phase1 freeze, and we are still keep updating this.
- expression view on genes are little bit slow now. We are now investigating alternative ways.
- contact: KAWAJI, Hideya <kawaji@gsc.riken.jp>, SHIMOJI, Hisashi <hisashi.shimoji@dnaform.jp>, or WP4 <fantom5-wp4@gsc.riken.jp>
Data source
- CAGE peaks (only the robust set), their association with genes, and their expression based on RLE TPM.
- https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.osc.txt.gz
- https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.osc.txt.gz
- Swissregulon motifs, and Motif Activity Response Analysis (MARA)
- FF Ontology
- facet classification based on FF ontology
- http://yuri.lbl.gov:8600/fonse/ FONSE (Fantomy ONtology Sample Explorer)
Search within Sample/gene/motif names (beta)
Other browsers/resources
- FANTOM5 collaboration wiki
- zenbu
- UCSC mirror (at RIKEN)
- FONSE (Fantomy ONtology Sample Explorer) (user:terry , pass: T34s377)
- BioLayout
