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|id=FF:11948-126B4
|id=FF:11948-126B4
|is_a=FF:0200027
|is_a=FF:0200027
|is_obsolete=
|name=Pre-hematopoietic stem cell, aorta-gonad-mesonephros (AGM) region derived, embryo E9.5
|name=Pre-hematopoietic stem cell, aorta-gonad-mesonephros (AGM) region derived, embryo E9.5
|namespace=
|namespace=
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|sample_tissue=ANATOMICAL SYSTEM
|sample_tissue=ANATOMICAL SYSTEM
|top_motifs=
|top_motifs=
|xref=
}}
}}

Revision as of 23:41, 27 June 2012


Name:Pre-hematopoietic stem cell, aorta-gonad-mesonephros (AGM) region derived, embryo E9.5
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companyNA
collaborationDaisuke Sugiyama
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs14149



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: CNhs14149This 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: CNhs14149This 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: CNhs14149


FANTOM5 (FF) ontology


Direct parent terms


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)
0002113 (kidney)
0002100 (trunk)
0002384 (connective tissue)
0000926 (mesoderm)
0000080 (mesonephros)
0000479 (tissue)
0000466 (immaterial anatomical entity)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0002553 (anatomical cavity)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0003103 (compound organ)
0009569 (subdivision of trunk)
0005291 (embryonic tissue)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0003104 (mesenchyme)
0005172 (abdomen element)
0000464 (anatomical space)
0005256 (trunk mesenchyme)
0003918 (kidney mesenchyme)
0006598 (presumptive structure)
0003886 (body cavity precursor)
0005173 (abdominal segment element)
0002532 (epiblast (generic))
0001008 (renal system)
0002417 (abdominal segment of trunk)
0000916 (abdomen)
0003887 (intraembryonic coelom)
0002120 (pronephros)
0009142 (entire embryonic mesenchyme)
0003081 (lateral plate mesoderm)
0003064 (intermediate mesoderm)
0004875 (nephrogenic cord)
0006603 (presumptive mesoderm)
0004876 (urogenital ridge)
0005095 (kidney rudiment)
0005721 (pronephric mesoderm)
0005754 (rostral part of nephrogenic cord)
0007687 (kidney field)
0007297 (presumptive pronephric mesoderm)

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