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FANTOM5 SSTAR (Semantic catalog of Samples, Transcription initiation And Regulators) provide a way to explore samples, transcriptional initiations, and regulators analyzed in [http://fantom.gsc.riken.jp/5/ the FANTOM5 project]. If you have any questions or comments, please contact to fantom-help@riken.jp
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<table cellspacing="0" id="front-table">
<html>
  <tr>
    <th ><b>Search genes</b></th>
    <th  colspan="3"><form method="get" action="/5/sstar/RB_SearchResults"><input type="text" name="sq" value="" style="width: 440px;">&nbsp;&nbsp;&nbsp;&nbsp;<input type="submit" value="search"></th>
</form>
  </tr>
  <tr> &nbsp; </tr>
  <tr>
    <th style="width: 120px;"></td>
    <th style="width: 300px;"></td>
    <th style="width: 160px; padding-left: 19px;">Examples</td>
    <th style="width: 160px;">Browse</td>
  </tr></html>
<tr>
    <td>'''Time courses '''</td>
    <td>Promoters and enhancers activity in 19 human and 14 mouse time courses
covering a wide range of cell types and biological stimuli</td>
    <td style="width: 160px;">  <ul><li>[[Human_iPS_to_neuron_(Down's_syndrome)_1|Human iPS to neuron (Down's syndrome)]] </li></ul>    </td>
    <td>
[[Time_Courses_chart|Timecourses chart]]
</td>
  </tr>
  <tr>
    <td>'''Samples'''</td>
    <td> Details of profiled samples (incl. primary cells, cell lines, and tissues) </td>
    <td style="width: 160px;">  <ul><li>[[FF:11210-116A4|Smooth Muscle Cells - Aortic, donor0]] </li></ul>    </td>
    <td>
[[Browse_samples|human]]


Genes, TSS regions, motifs, samples, etc profiled in FANTOM5.
[[Browse_samples_mm9|mouse]]
</td>
  </tr>


=== Usage ===
  <tr>
* Just click any in the left menue
    <td>'''Sample classifications'''</td>
* Or, keyword search on top of this page.
    <td>
* Or, make a complex query at [[Special:Ask]], if you are familiar with [http://semantic-mediawiki.org/ Semantic MediaWIki]
Samples profiled in FANTOM5 are systematically classified by defining FANTON5 sample ontology (FF), consisting of Cell type (CL), Diseases (DOID), and Anatomy (UBERON).
    </td>
    <td> <ul><li>[[CL:0000192|smooth muscle cell]]</li></ul>    </td>
    <td>
[[Cell_Ontology_terms_list|Cell Type (CL)]]


=== Note ===
[[Human_Disease_Ontology_terms_list|Disease (DOID)]]
* 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 ===
[[Uber_Anatomy_Ontology_terms_list|Anatomy (UBERON)]]
* 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)
** http://www.swissregulon.unibas.ch/
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/MotifActivity/
* FF Ontology
** https://fantom5-collaboration.gsc.riken.jp/files/data/shared/contrib/sample_ontology/FANTOM5v5/
* facet classification based on FF ontology
** http://yuri.lbl.gov:8600/fonse/ FONSE (Fantomy ONtology Sample Explorer)


[[FF_Ontology_terms_list|FANTOM5 (FF)]]
</td>
  </tr>


== 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>
  <tr>
</html>
    <td>'''Co-expression'''</td>
    <td>
CAGE peaks (TSS regions) are grouped based on expression, by using MCL
    </td>
    <td> <ul><li>[[Coexpression_cluster:C18|C18 (in human)]] </li></ul></td>
    <td>
[[Browse_coexpression_clusters|Human]]


[[Browse_MCL_coexpression_mouse|Mouse]]
</td>
  </tr>
  <tr>
    <td>'''Motifs'''</td>
    <td>
known and de-novo motifs discovered in the proximal region to the CAGE peaks
    </td>
    <td> <ul><li> [[Novel_motif:1]] </li>  <li> [[JASPAR_motif:MA0002.2|RUNX1]] </li> </ul> </td>
    <td>
<ul>
<li>[[Browse_Novel_motifs|Novel motifs]]</li>
<li>[[Browse_JASPAR_motifs|JASPAR motifs]]</li>
</ul>
</td>
  </tr>
<tr>
    <td>'''Transcription factors'''</td>
    <td>
Transcription factors.
    </td>
    <td> <ul><li>[[EntrezGene:6657|SOX2]]</li></ul>
    </td>
    <td>
[[Browse_Transcription_Factors_hg19|human]]


= Other browsers/resources =
[[Browse_Transcription_Factors_mm9|mouse]]
* [https://fantom5-collaboration.gsc.riken.jp/wiki FANTOM5 collaboration wiki]
</td>
* [https://fantom5-collaboration.gsc.riken.jp/zenbu zenbu]
  </tr>
* [https://fantom5-collaboration.gsc.riken.jp/ucsc UCSC mirror (at RIKEN)]
* [http://yuri.lbl.gov:8600/fonse/ FONSE (Fantomy ONtology Sample Explorer)] (user:terry , pass: T34s377)
* [http://www.biolayout.org/fantom5/ BioLayout]


* [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/FREEZE_PHASE1/ phase1 data freeze]
</table>
* [https://fantom5-collaboration.gsc.riken.jp/files/data/shared/LATEST_UPDATE/ latest update]
== Please cite SSTAR as: ==
Abugessaisa, I., H. Shimoji, S. Sahin, A. Kondo, J. Harshbarger, M. Lizio, Y. Hayashizaki, P. Carninci, F. consortium, A. Forrest, T. Kasukawa and H. Kawaji (2016). "FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki." Database (Oxford) 2016

Latest revision as of 15:23, 14 November 2019

FANTOM5 SSTAR (Semantic catalog of Samples, Transcription initiation And Regulators) provide a way to explore samples, transcriptional initiations, and regulators analyzed in the FANTOM5 project. If you have any questions or comments, please contact to fantom-help@riken.jp

 
Search genes
    
Examples Browse
Time courses Promoters and enhancers activity in 19 human and 14 mouse time courses covering a wide range of cell types and biological stimuli

Timecourses chart

Samples Details of profiled samples (incl. primary cells, cell lines, and tissues)

human

mouse

Sample classifications

Samples profiled in FANTOM5 are systematically classified by defining FANTON5 sample ontology (FF), consisting of Cell type (CL), Diseases (DOID), and Anatomy (UBERON).

Cell Type (CL)

Disease (DOID)

Anatomy (UBERON)

FANTOM5 (FF)

Co-expression

CAGE peaks (TSS regions) are grouped based on expression, by using MCL

Human

Mouse

Motifs

known and de-novo motifs discovered in the proximal region to the CAGE peaks

Transcription factors

Transcription factors.

human

mouse

Please cite SSTAR as:

Abugessaisa, I., H. Shimoji, S. Sahin, A. Kondo, J. Harshbarger, M. Lizio, Y. Hayashizaki, P. Carninci, F. consortium, A. Forrest, T. Kasukawa and H. Kawaji (2016). "FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki." Database (Oxford) 2016

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