Personal tools

Main Page: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
mNo edit summary
 
(43 intermediate revisions by 5 users not shown)
Line 1: Line 1:
 
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
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]
 
<html><style>
<html><style>
#front-table td { border-top: 1px solid #AAA; vertical-align:middle; padding: 0.5em 0 0.5em 0; }
#front-table td { border-top: 1px solid #AAA; vertical-align:middle; padding: 0.5em; height: 85px; }
#front-table th { text-align: left; padding: 2em 0 0.3em 0; }
#front-table th { text-align: left; padding: 2em 0 0.3em 0.5em; }
#front-table li { line-height: 1.2em; }
#front-table li { line-height: 1.2em; }
#front-table tbody tr:nth-child(even) td, tbody tr.even td {
background: #E5ECF9;
}
</style></html>
</style></html>
<table cellspacing="0" id="front-table">  
<table cellspacing="0" id="front-table">  
<html>
<html>
<form method="get" action="/resource_browser/RB_SearchResults">
   <tr>
   <tr>
     <th ><b>Gene Search</b></td>
     <th ><b>Search genes</b></th>
     <th  colspan="2"><input type="text" name="sq" value="" style="width: 440px;"></td>
     <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>
    <th ><input type="submit" value="search"></td>
</form>
   </tr>
   </tr>
</form>
 
  <tr> &nbsp; </tr>
 
   <tr>
   <tr>
     <th style="width: 120px;"></td>
     <th style="width: 120px;"></td>
Line 24: Line 24:
     <th style="width: 160px;">Browse</td>
     <th style="width: 160px;">Browse</td>
   </tr></html>
   </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>
   <tr>
     <td>'''Samples'''</td>
     <td>'''Samples'''</td>
     <td> Details of profiled samples (incl. primary cells, cell lines, and tissues) are accesible  </td>
     <td> Details of profiled samples (incl. primary cells, cell lines, and tissues) </td>
     <td style="width: 160px;">
     <td style="width: 160px;"> <ul><li>[[FF:11210-116A4|Smooth Muscle Cells - Aortic, donor0]] </li></ul>    </td>
{{#ask:[[Category:FF Samples]]
| limit=3
| format=ul
| searchlabel=
| order=random
}}
    </td>
     <td>
     <td>
[[Browse_samples|Samples by name]]
[[Browse_samples|human]]


[[Browse_facet|Samples by categories]]
[[Browse_samples_mm9|mouse]]
</td>
  </tr>


[[Browse_series|Samples by series]]
  <tr>
    <td>'''Sample classifications'''</td>
    <td>
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)]]
 
[[Human_Disease_Ontology_terms_list|Disease (DOID)]]


[[Browse_datatype|Samples by data type]]
[[Uber_Anatomy_Ontology_terms_list|Anatomy (UBERON)]]


[[FF_Ontology_terms_list|FANTOM5 (FF)]]
</td>
</td>
   </tr>
   </tr>
  <tr>
 
 
 
  <tr>
     <td>'''Co-expression'''</td>
     <td>'''Co-expression'''</td>
     <td>
     <td>
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor.
CAGE peaks (TSS regions) are grouped based on expression, by using MCL
    </td>
    <td>
{{#ask:[[Category:Coexpression clusters]]
| limit=3
| format=ul
| searchlabel=
| order=random
}}
     </td>
     </td>
    <td> <ul><li>[[Coexpression_cluster:C18|C18 (in human)]] </li></ul></td>
     <td>
     <td>
[[Browse_coexpression_clusters|Human]]
[[Browse_coexpression_clusters|Human]]
Line 67: Line 80:
   </tr>
   </tr>
   <tr>
   <tr>
     <td>'''MOTIFs'''</td>
     <td>'''Motifs'''</td>
     <td>
     <td>
Duis aute irure dolor in reprehenderit in voluptate velit esse cillum.
known and de-novo motifs discovered in the proximal region to the CAGE peaks
     </td>
     </td>
    <td> <ul><li> [[Novel_motif:1]] </li>  <li> [[JASPAR_motif:MA0002.2|RUNX1]] </li> </ul> </td>
     <td>
     <td>
{{#ask:[[Category:MacroAPE_1083]]
<ul>
| limit=3
<li>[[Browse_Novel_motifs|Novel motifs]]</li>
| format=ul
<li>[[Browse_JASPAR_motifs|JASPAR motifs]]</li>
| searchlabel=
</ul>
| order=random
}}
    </td>
    <td>
[[Browse_MacroAPE|MacroAPE]]
 
[[Browse_swissregulon|Swissregulon]]
</td>
</td>
   </tr>
   </tr>
  <tr>
<tr>
     <td>'''Genes'''</td>
     <td>'''Transcription factors'''</td>
     <td>
     <td>
Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia.
Transcription factors.
     </td>
     </td>
     <td>
     <td> <ul><li>[[EntrezGene:6657|SOX2]]</li></ul>
{{#ask:[[Category:EntrezGene]]
| limit=3
| format=ul
| searchlabel=
| order=random
}}
     </td>
     </td>
     <td>
     <td>
[[Browse_genes|Genes]]
[[Browse_Transcription_Factors_hg19|human]]


[[Browse_tss|TSSs]]
[[Browse_Transcription_Factors_mm9|mouse]]
 
[[Browse_Transcription_Factors|TFs]]
</td>
</td>
   </tr>
   </tr>
  <tr>
    <td>'''Ontologies'''</td>
    <td>
Duis aute irure dolor in reprehenderit in voluptate.
    </td>
    <td>
{{#ask:[[Category:FF_Terms]]
| limit=3
| format=ul
| searchlabel=
| order=random
}}
    </td>
    <td>
[[FF_Ontology_terms_list|FANTOM5 (FF)]]


[[Cell_Ontology_terms_list|Cell Type (CL)]]
[[Human_Disease_Ontology_terms_list|Disease (DOID)]]
[[Uber_Anatomy_Ontology_terms_list|Anatomy (UBERON)]]
</td>
  </tr>
</table>
</table>
== 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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Main_Page&oldid=4575583"