FF:10320-105A5: Difference between revisions
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{{f5samples | {{f5samples | ||
| | |F5samples= | ||
| | |ancestors_in_anatomy_facet=UBERON:0000026,UBERON:0000043,UBERON:0000061,UBERON:0000062,UBERON:0000154,UBERON:0000211,UBERON:0000383,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001048,UBERON:0001062,UBERON:0001434,UBERON:0001630,UBERON:0001665,UBERON:0002050,UBERON:0002101,UBERON:0002103,UBERON:0002204,UBERON:0002384,UBERON:0002471,UBERON:0002529,UBERON:0002532,UBERON:0003081,UBERON:0003102,UBERON:0003587,UBERON:0003589,UBERON:0003661,UBERON:0003663,UBERON:0003701,UBERON:0003823,UBERON:0004120,UBERON:0004256,UBERON:0004270,UBERON:0004347,UBERON:0004357,UBERON:0004708,UBERON:0004709,UBERON:0005090,UBERON:0005423,UBERON:0005732,UBERON:0005733,UBERON:0007023,UBERON:0008784,UBERON:0008846 | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
| | |comment= | ||
|created_by= | |||
|creation_date= | |||
|def= | |||
|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
| Line 66: | Line 34: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |has_quality= | ||
|id=FF:10320-105A5 | |||
|is_a=EFO:0002091;;FF:0011147 | |is_a=EFO:0002091;;FF:0011147 | ||
|name= | |||
|namespace= | |namespace= | ||
|part_of= | |part_of= | ||
|profile_cagescan= | |||
|profile_hcage=,,,SKIP_ADDITIONAL | |||
|profile_rnaseq= | |||
|profile_srnaseq= | |||
|rna_box=105 | |||
|rna_catalog_number= | |||
|rna_concentration=0.23572 | |||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | |||
|rna_lot_number=3-At | |||
|rna_od260/230=0.9 | |||
|rna_od260/280=2.03 | |||
|rna_position=A5 | |||
|rna_rin=2.4 | |||
|rna_sample_type=total RNA | |||
|rna_tube_id=105A5 | |||
|rna_weight_ug=6.36444 | |||
|sample_age= | |||
|sample_cell_catalog= | |||
|sample_cell_line= | |||
|sample_cell_lot= | |||
|sample_cell_type=CELL MIXTURE - tissue sample | |||
|sample_collaboration=Alessandro Bonetti | |||
|sample_company= | |||
|sample_description= | |||
|sample_dev_stage= | |||
|sample_disease= | |||
|sample_donor(cell lot)= | |||
|sample_ethnicity= | |||
|sample_experimental_condition= | |||
|sample_id=10320 | |||
|sample_note= | |||
|sample_sex=male | |||
|sample_species=Human (Homo sapiens) | |||
|sample_strain= | |||
|sample_tissue=achilles tendon | |||
|top_motifs= | |||
}} | }} | ||
Revision as of 14:05, 21 March 2012
| Name: | |
|---|---|
| Species: | Human (Homo sapiens) |
| 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
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
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
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>
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0011147 human achilles tendon 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
UBERON: Anatomy
0000026 (appendage)
0000043 (tendon)
0000061 (anatomical structure)
0000062 (organ)
0000154 (posterior region of body)
0000211 (ligament)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001048 (primordium)
0001062 (anatomical entity)
0001434 (skeletal system)
0001630 (muscle organ)
0001665 (triceps surae)
0002050 (embryonic structure)
0002101 (limb)
0002103 (hindlimb)
0002204 (musculoskeletal system)
0002384 (connective tissue)
0002471 (zeugopod)
0002529 (limb segment)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003102 (surface structure)
0003587 (limb connective tissue)
0003589 (hindlimb connective tissue)
0003661 (limb muscle)
0003663 (hindlimb muscle)
0003701 (calcaneal tendon)
0003823 (hindlimb zeugopod)
0004120 (mesoderm-derived structure)
0004256 (hindlimb zeugopod muscle)
0004270 (lower leg connective tissue)
0004347 (limb bud)
0004357 (paired limb/fin bud)
0004708 (paired limb/fin)
0004709 (pelvic appendage)
0005090 (muscle structure)
0005423 (developing anatomical structure)
0005732 (limb/fin field)
0005733 (limb field)
0007023 (adult organism)
0008784 (lower limb segment)
0008846 (skeletal ligament)
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
