FF:10262-104D1: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
Line 3: | Line 3: | ||
|name=Follicle Associated Epithelium, pool2 | |name=Follicle Associated Epithelium, pool2 | ||
|sample_id=10262 | |sample_id=10262 | ||
|rna_tube_id= | |rna_tube_id=104D1 | ||
|rna_box=104 | |rna_box=104 | ||
|rna_position=D1 | |rna_position=D1 | ||
Line 20: | Line 20: | ||
|sample_ethnicity= | |sample_ethnicity= | ||
|rna_rin= | |rna_rin= | ||
|rna_od260/230=1. | |rna_od260/230=1.61 | ||
|rna_od260/280=2. | |rna_od260/280=2.14 | ||
|sample_cell_type=CELL MIXTURE - tissue sample | |sample_cell_type=CELL MIXTURE - tissue sample | ||
|sample_cell_line= | |sample_cell_line= | ||
Line 29: | Line 29: | ||
|rna_sample_type=total RNA | |rna_sample_type=total RNA | ||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | |rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | ||
|rna_weight_ug=2. | |rna_weight_ug=2.2055 | ||
|rna_concentration= | |rna_concentration=0.2005 | ||
|sample_note= | |sample_note= | ||
|profile_hcage=CNhs13211,LSID1005,, | |profile_hcage=CNhs13211,LSID1005,release012,COMPLETED | ||
|profile_cagescan=,,, | |profile_cagescan=,,, | ||
|profile_srnaseq=,,, | |profile_srnaseq=,,, |
Revision as of 17:37, 27 February 2012
Name: | Follicle Associated Epithelium, pool2 |
---|---|
Species: | Mouse (Mus musculus) |
Library ID: | {{{library_id}}} |
Sample type: | {{{sample_category}}} |
Genomic View: | UCSC |
CAGEd-oPOSSUM: | link |
ExpandAdditional information |
---|
ExpandDownload raw sequence, BAM & CTSS |
---|
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
CNhs13211
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: CNhs13211
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: CNhs13211
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: CNhs13211
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
{{{is_a}}}
part_of relathionship
{{{part_of}}}
has_quality relathionship
{{{has_quality}}}
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
UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000344 (mucosa)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001555 (digestive tract)
0001744 (lymphoid tissue)
0001961 (mucosa-associated lymphoid tissue)
0001962 (gut-associated lymphoid tissue)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002405 (immune system)
0002465 (lymphoid system)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004923 (organ component layer)
0005423 (developing anatomical structure)
0007023 (adult organism)
0007026 (primitive gut)
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