FF:11950-126B6: Difference between revisions
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{{f5samples | {{f5samples | ||
|ancestors_in_anatomy_facet= | |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0001987,UBERON:0005795,UBERON:0000995,UBERON:0002384,UBERON:0003134,UBERON:0000926,UBERON:0000479,UBERON:0005156,UBERON:0000064,UBERON:0000077,UBERON:0000062,UBERON:0004120,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0000990,UBERON:0002050,UBERON:0004923,UBERON:0005423,UBERON:0005631,UBERON:0000467,UBERON:0001062,UBERON:0000478,UBERON:0005291,UBERON:0003133,UBERON:0003975,UBERON:0004175,UBERON:0000925,UBERON:0006598,UBERON:0000158,UBERON:0002532,UBERON:0003124,UBERON:0003100,UBERON:0000474,UBERON:0003081,UBERON:0006595,UBERON:0006603,UBERON:0004872,UBERON:0004340 | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000723,CL:0000048,CL:0000988,CL:0000548,CL:0000034,CL:0000012,CL:0002320,CL:0000063,CL:0002371,CL:0000219,CL:0000004,CL:0000134,CL:0000255,CL:0000037,CL:0000566 | ||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
|comment= | |comment= | ||
Revision as of 17:36, 8 June 2012
| Name: | hematopoietic stem cell, placenta derived, embryo E10.5 |
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| Species: | Mouse (Mus musculus) |
| Library ID: | {{{library_id}}} |
| Sample type: | {{{sample_category}}} |
| Genomic View: | UCSC |
| CAGEd-oPOSSUM: | link |
| Additional information | ||||||||||||||||||||||||||||
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Sample information
RNA information
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| Download raw sequence, BAM & CTSS | ||||||||||||
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Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data
CNhs14150
Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data
no result for this sample
TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample
JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data
library id: CNhs14150This sample isn't target for the analysis
FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data
library id: CNhs14150This sample isn't target for the analysis
de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br>
library id: CNhs14150
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
FF:0200028 hematopoietic stem cell, placenta derived sample
Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data
CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000034 (stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000219 (motile cell)
0000134 (mesenchymal cell)
0000255 (eukaryotic cell)
0000037 (hematopoietic stem cell)
0000566 (angioblastic mesenchymal cell)
UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0001987 (placenta)
0005795 (embryonic uterus)
0000995 (uterus)
0002384 (connective tissue)
0003134 (female reproductive organ)
0000926 (mesoderm)
0000479 (tissue)
0005156 (reproductive structure)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000062 (organ)
0004120 (mesoderm-derived structure)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0000990 (reproductive system)
0002050 (embryonic structure)
0004923 (organ component layer)
0005423 (developing anatomical structure)
0005631 (extraembryonic membrane)
0000467 (anatomical system)
0001062 (anatomical entity)
0000478 (extraembryonic structure)
0005291 (embryonic tissue)
0003133 (reproductive organ)
0003975 (internal female genitalia)
0004175 (internal genitalia)
0000925 (endoderm)
0006598 (presumptive structure)
0000158 (membranous layer)
0002532 (epiblast (generic))
0003124 (chorion)
0003100 (female organism)
0000474 (female reproductive system)
0003081 (lateral plate mesoderm)
0006595 (presumptive endoderm)
0006603 (presumptive mesoderm)
0004872 (splanchnic layer of lateral plate mesoderm)
0004340 (allantois)
FF: FANTOM5
NA
Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA
