FF:10337-105C4: Difference between revisions
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{{f5samples | {{f5samples | ||
| | |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0001379,UBERON:0000479,UBERON:0000062,UBERON:0000026,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003663,UBERON:0005090,UBERON:0001630,UBERON:0004708,UBERON:0002101,UBERON:0004709,UBERON:0003661,UBERON:0010890,UBERON:0010317,UBERON:0010707,UBERON:0002204,UBERON:0002103,UBERON:0000383,UBERON:0001377,UBERON:0000154,UBERON:0010709 | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
| | |ancestors_in_ff_facet=FF:0000102,FF:0000210,FF:0000101,FF:0000001,FF:0000998,FF:0000004,FF:0011172 | ||
|comment= | |||
|created_by= | |||
|creation_date= | |||
|def= | |||
|f5samples= | |||
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006603,UBERON:0010316 | |||
|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
| Line 66: | Line 36: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |has_quality= | ||
|id=FF:10337-105C4 | |||
|is_a=EFO:0002091;;FF:0011172 | |is_a=EFO:0002091;;FF:0011172 | ||
|is_obsolete= | |||
|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=0.75665 | |||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | |||
|rna_lot_number=3-Sm1 | |||
|rna_od260/230=1.78 | |||
|rna_od260/280=2.08 | |||
|rna_position=C4 | |||
|rna_rin=4.8 | |||
|rna_sample_type=total RNA | |||
|rna_tube_id=105C4 | |||
|rna_weight_ug=20.42955 | |||
|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=10337 | |||
|sample_note= | |||
|sample_sex=male | |||
|sample_species=Human (Homo sapiens) | |||
|sample_strain= | |||
|sample_tissue=skeletal muscle - lateralis muscle | |||
|top_motifs= | |||
|xref= | |||
}} | }} | ||
Latest revision as of 18:46, 9 July 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
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
0000468 (multi-cellular organism)
0007023 (adult organism)
0001379 (vastus lateralis)
0000479 (tissue)
0000062 (organ)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003663 (hindlimb muscle)
0005090 (muscle structure)
0001630 (muscle organ)
0004708 (paired limb/fin)
0002101 (limb)
0004709 (pelvic appendage)
0003661 (limb muscle)
0010890 (pelvic complex muscle)
0010317 (germ layer / neural crest derived structure)
0010707 (appendage girdle complex)
0002204 (musculoskeletal system)
0002103 (hindlimb)
0000383 (musculature of body)
0001377 (quadriceps femoris)
0000154 (posterior region of body)
0010709 (pelvic complex)
FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011172 (skeletal muscle - lateralis muscle)
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
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)
