FF:11465-119B7: Difference between revisions
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{{f5samples | {{f5samples | ||
|ancestors_in_anatomy_facet=UBERON: | |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002367,UBERON:0001134,UBERON:0002100,UBERON:0000483,UBERON:0002530,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0005156,UBERON:0000077,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0006554,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0000990,UBERON:0002050,UBERON:0005153,UBERON:0005911,UBERON:0004921,UBERON:0000161,UBERON:0000162,UBERON:0005423,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0000490,UBERON:0005291,UBERON:0003102,UBERON:0002036,UBERON:0002385,UBERON:0003929,UBERON:0000486,UBERON:0003104,UBERON:0000914,UBERON:0010147,UBERON:0005256,UBERON:0000925,UBERON:0006598,UBERON:0009846,UBERON:0004185,UBERON:0005157,UBERON:0003937,UBERON:0005399,UBERON:0001015,UBERON:0002532,UBERON:0003353,UBERON:0004902,UBERON:0001555,UBERON:0002329,UBERON:0002204,UBERON:0001008,UBERON:0003101,UBERON:0004122,UBERON:0001353,UBERON:0000163,UBERON:0000079,UBERON:0007026,UBERON:0000383,UBERON:0006866,UBERON:0003077,UBERON:0004290,UBERON:0009142,UBERON:0001046,UBERON:0000164,UBERON:0003064,UBERON:0006595,UBERON:0006603,UBERON:0003082,UBERON:0000931,UBERON:0003059,UBERON:0003820,UBERON:0007282,UBERON:0009618,UBERON:0007285,UBERON:0009847 | ||
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL: | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000055,CL:0000144,CL:0000723,CL:0000048,CL:0000548,CL:0000034,CL:0000012,CL:0000680,CL:0002321,CL:0002371,CL:0000393,CL:0000183,CL:0000187,CL:0000220,CL:0000004,CL:0000192,CL:0000211,CL:0000056,CL:0000255,CL:0000222,CL:1000487,CL:0000355,CL:0000514 | ||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
|comment= | |comment= | ||
Revision as of 17:04, 8 June 2012
| Name: | Smooth Muscle Cells - Prostate, donor3 |
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| 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>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: CNhs11910This 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: CNhs11910This 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: CNhs11910
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000002 in vivo cell sample
FF:0000183 human smooth muscle cell of prostate sample
FF:0000210 human 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
CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000055 (non-terminally differentiated cell)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0000034 (stem cell)
0000680 (muscle precursor cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0000393 (electrically responsive cell)
0000183 (contractile cell)
0000187 (muscle cell)
0000192 (smooth muscle cell)
0000211 (electrically active cell)
0000056 (myoblast)
0000255 (eukaryotic cell)
0000222 (mesodermal cell)
1000487 (smooth muscle cell of prostate)
0000355 (multi-potent skeletal muscle stem cell)
0000514 (smooth muscle myoblast)
UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002367 (prostate gland)
0001134 (skeletal muscle tissue)
0002100 (trunk)
0000483 (epithelium)
0002530 (gland)
0000926 (mesoderm)
0000479 (tissue)
0001007 (digestive system)
0005156 (reproductive structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0006554 (urinary system structure)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0000990 (reproductive system)
0002050 (embryonic structure)
0005153 (epithelial bud)
0005911 (endo-epithelium)
0004921 (subdivision of digestive tract)
0000161 (orifice)
0000162 (cloaca)
0005423 (developing anatomical structure)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0005291 (embryonic tissue)
0003102 (surface structure)
0002036 (striated muscle tissue)
0002385 (muscle tissue)
0003929 (gut epithelium)
0000486 (multilaminar epithelium)
0003104 (mesenchyme)
0010147 (male accessory sex gland)
0005256 (trunk mesenchyme)
0000925 (endoderm)
0006598 (presumptive structure)
0009846 (embryonic cloacal epithelium)
0004185 (endodermal part of digestive tract)
0005157 (epithelial fold)
0003937 (sex gland)
0005399 (male reproductive gland)
0001015 (musculature)
0002532 (epiblast (generic))
0003353 (epithelium of hindgut)
0004902 (urogenital sinus epithelium)
0001555 (digestive tract)
0002329 (somite)
0002204 (musculoskeletal system)
0001008 (renal system)
0003101 (male organism)
0004122 (genitourinary system)
0001353 (anal region)
0000163 (embryonic cloaca)
0000079 (male reproductive system)
0007026 (primitive gut)
0000383 (musculature of body)
0006866 (terminal part of digestive tract)
0003077 (paraxial mesoderm)
0004290 (dermomyotome)
0009142 (entire embryonic mesenchyme)
0001046 (hindgut)
0000164 (primitive urogenital sinus)
0003064 (intermediate mesoderm)
0006595 (presumptive endoderm)
0006603 (presumptive mesoderm)
0003082 (myotome)
0000931 (proctodeum)
0003059 (presomitic mesoderm)
0003820 (prostate bud)
0007282 (presumptive segmental plate)
0009618 (trunk paraxial mesoderm)
0007285 (presumptive paraxial mesoderm)
0009847 (prostate field)
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
