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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 | |||
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] | |||
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<table cellspacing="0" id="front-table"> | <table cellspacing="0" id="front-table"> | ||
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<tr> | <tr> | ||
<th ><b> | <th ><b>Search genes</b></th> | ||
<th colspan=" | <th colspan="3"><form method="get" action="/5/sstar/RB_SearchResults"><input type="text" name="sq" value="" style="width: 440px;"> <input type="submit" value="search"></th> | ||
</form> | |||
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<th style="width: 120px;"></td> | <th style="width: 120px;"></td> | ||
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<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> | |||
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<tr> | <tr> | ||
<td>'''Samples'''</td> | <td>'''Samples'''</td> | ||
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<td>'''Sample classifications'''</td> | <td>'''Sample classifications'''</td> | ||
<td> | <td> | ||
Samples profiled in FANTOM5 are systematically classified by defining FANTON5 sample ontology, consisting of Cell type (CL), Diseases (DOID), and Anatomy (UBERON). | 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> | ||
<td> <ul><li>[[CL:0000192|smooth muscle cell]]</li></ul> </td> | <td> <ul><li>[[CL:0000192|smooth muscle cell]]</li></ul> </td> | ||
<td> | <td> | ||
[[Cell_Ontology_terms_list|Cell Type (CL)]] | [[Cell_Ontology_terms_list|Cell Type (CL)]] | ||
| Line 50: | Line 60: | ||
[[Uber_Anatomy_Ontology_terms_list|Anatomy (UBERON)]] | [[Uber_Anatomy_Ontology_terms_list|Anatomy (UBERON)]] | ||
[[FF_Ontology_terms_list|FANTOM5 (FF)]] | |||
</td> | </td> | ||
</tr> | </tr> | ||
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<td>'''Co-expression'''</td> | <td>'''Co-expression'''</td> | ||
<td> | <td> | ||
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</tr> | </tr> | ||
<tr> | <tr> | ||
<td>''' | <td>'''Motifs'''</td> | ||
<td> | <td> | ||
de-novo motifs discovered in the proximal region to the CAGE peaks | known and de-novo motifs discovered in the proximal region to the CAGE peaks | ||
</td> | </td> | ||
<td> <ul><li>[[ | <td> <ul><li> [[Novel_motif:1]] </li> <li> [[JASPAR_motif:MA0002.2|RUNX1]] </li> </ul> </td> | ||
<td> | <td> | ||
[[ | <ul> | ||
<li>[[Browse_Novel_motifs|Novel motifs]]</li> | |||
<li>[[Browse_JASPAR_motifs|JASPAR motifs]]</li> | |||
</ul> | |||
</td> | </td> | ||
</tr> | </tr> | ||
<tr> | |||
<td>'''Transcription factors'''</td> | <td>'''Transcription factors'''</td> | ||
<td> | <td> | ||
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</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 | ||
| Samples | Details of profiled samples (incl. primary cells, cell lines, and tissues) | ||
| 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). |
||
| Co-expression |
CAGE peaks (TSS regions) are grouped based on expression, by using MCL |
||
| Motifs |
known and de-novo motifs discovered in the proximal region to the CAGE peaks |
||
| Transcription factors |
Transcription factors. |
||
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
