Main Page: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
mNo edit summary |
||
| (81 intermediate revisions by 6 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 | |||
<html><style> | |||
#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 0.5em; } | |||
#front-table li { line-height: 1.2em; } | |||
#front-table tbody tr:nth-child(even) td, tbody tr.even td { | |||
background: #E5ECF9; | |||
} | |||
</style></html> | |||
<table cellspacing="0" id="front-table"> | |||
<html> | <html> | ||
< | <tr> | ||
</html> | <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;"> <input type="submit" value="search"></th> | |||
</form> | |||
</tr> | |||
<tr> </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]] | |||
[[Browse_samples_mm9|mouse]] | |||
</td> | |||
</tr> | |||
<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)]] | |||
[[Uber_Anatomy_Ontology_terms_list|Anatomy (UBERON)]] | |||
[[FF_Ontology_terms_list|FANTOM5 (FF)]] | |||
</td> | |||
</tr> | |||
<tr> | |||
<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]] | |||
[[Browse_Transcription_Factors_mm9|mouse]] | |||
</td> | |||
</tr> | |||
</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
