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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000065,UBERON:0000072,UBERON:0000077,UBERON:0000078,UBERON:0000119,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000490,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0000974,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001042,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0001557,UBERON:0002050,UBERON:0002193,UBERON:0002342,UBERON:0002346,UBERON:0002368,UBERON:0002370,UBERON:0002384,UBERON:0002390,UBERON:0002405,UBERON:0002530,UBERON:0002532,UBERON:0003075,UBERON:0003104,UBERON:0003295,UBERON:0003351,UBERON:0003408,UBERON:0003929,UBERON:0004119,UBERON:0004120,UBERON:0004121,UBERON:0004177,UBERON:0004185,UBERON:0004807,UBERON:0004921,UBERON:0005057,UBERON:0005058,UBERON:0005291,UBERON:0005423,UBERON:0005428,UBERON:0005434,UBERON:0005562,UBERON:0005911,UBERON:0006562,UBERON:0006598,UBERON:0007026,UBERON:0007284,UBERON:0007690,UBERON:0009113,UBERON:0009142,UBERON:0009145
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000051,CL:0000063,CL:0000084,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000624,CL:0000723,CL:0000738,CL:0000789,CL:0000790,CL:0000791,CL:0000805,CL:0000806,CL:0000807,CL:0000808,CL:0000809,CL:0000810,CL:0000827,CL:0000837,CL:0000838,CL:0000893,CL:0000894,CL:0000895,CL:0000898,CL:0000988,CL:0002031,CL:0002032,CL:0002087,CL:0002320,CL:0002371,CL:0002419,CL:0002420,CL:0002425,CL:0002427,CL:0002428,CL:0002429,CL:0002431,CL:0002432,CL:0002433,CL:0002436,CL:0002489
|ancestors_in_cell_lineage_facet=
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|ancestors_in_ff_facet=FF:11918-125H1
|comment=Changed from previous label. TODO: full classification
|comment=Changed from previous label. TODO: full classification
|created_by=
|created_by=

Revision as of 22:30, 4 July 2012


Name:CD4+CD25-CD45RA- memory conventional T cells expanded, donor3
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexmale
age23
cell typeT cell
cell lineNA
companyNA
collaborationMichael Rehli (University of Regensberg)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number63-64
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} 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>dataNo results for this sample

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: CNhs13921This 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: CNhs13921This 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: CNhs13921


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

FF: FANTOM5
11918-125H1 (CD4+CD25-CD45RA- memory conventional T cells expanded, donor3)

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

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