FF:10630-108H9: Difference between revisions
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{{f5samples | {{f5samples | ||
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002107,UBERON:0002100,UBERON:0000483,UBERON:0002530,UBERON:0002384,UBERON:0001282,UBERON:0002394,UBERON:0000926,UBERON:0000479,UBERON:0000058,UBERON:0001007,UBERON:0000064,UBERON:0000077,UBERON:0002368,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000025,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0003914,UBERON:0007499,UBERON:0002050,UBERON:0005911,UBERON:0004921,UBERON:0005423,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0000490,UBERON:0009569,UBERON:0005291,UBERON:0009854,UBERON:0009842,UBERON:0003929,UBERON:0000353,UBERON:0003704,UBERON:0005177,UBERON:0002365,UBERON:0003104,UBERON:0005057,UBERON:0005172,UBERON:0006925,UBERON:0003928,UBERON:0005256,UBERON:0001048,UBERON:0000925,UBERON:0006598,UBERON:0009497,UBERON:0004185,UBERON:0005173,UBERON:0000015,UBERON:0009856,UBERON:0002532,UBERON:0001555,UBERON:0002417,UBERON:0007026,UBERON:0001041,UBERON:0000949,UBERON:0001280,UBERON:0001171,UBERON:0004647,UBERON:0002294,UBERON:0001173,UBERON:0001172,UBERON:0002330,UBERON:0000916,UBERON:0002405,UBERON:0002423,UBERON:0009142,UBERON:0006235,UBERON:0004912,UBERON:0006595,UBERON:0006603,UBERON:0008835,UBERON:0003894,UBERON:0004161,UBERON:0008836 | |||
|ancestors_in_anatomy_facet=UBERON: | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000723,CL:0000048,CL:0000548,CL:0000034,CL:0000012,CL:0002321,CL:0002320,CL:0000063,CL:0000066,CL:0002371,CL:0000219,CL:0000181,CL:0000417,CL:0000668,CL:0000220,CL:0000004,CL:0000134,CL:0000414,CL:0000412,CL:0000255,CL:0000182,CL:0000223 | ||
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL: | |ancestors_in_disease_facet=DOID:4,DOID:162,DOID:14566,DOID:0050687,DOID:7,DOID:305 | ||
|ancestors_in_disease_facet=DOID: | |||
|comment= | |comment= | ||
|created_by= | |created_by= | ||
|creation_date= | |creation_date= | ||
|def= | |def= | ||
|f5samples= | |||
|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
Revision as of 16:28, 8 June 2012
| Name: | |
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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>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:0000210 human sample
FF:0102842 cholangioma cell 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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0000034 (stem cell)
0002321 (embryonic cell)
0002320 (connective tissue cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000219 (motile cell)
0000181 (metabolising cell)
0000417 (endopolyploid cell)
0000668 (parenchymal cell)
0000134 (mesenchymal cell)
0000412 (polyploid cell)
0000255 (eukaryotic cell)
0000182 (hepatocyte)
0000223 (endodermal cell)
DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
7 (disease of anatomical entity)
305 (carcinoma)
UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002107 (liver)
0002100 (trunk)
0000483 (epithelium)
0002530 (gland)
0002384 (connective tissue)
0001282 (intralobular bile duct)
0002394 (bile duct)
0000926 (mesoderm)
0000479 (tissue)
0000058 (duct)
0001007 (digestive system)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0002368 (endocrine gland)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000025 (tube)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0003914 (epithelial tube)
0007499 (epithelial sac)
0002050 (embryonic structure)
0005911 (endo-epithelium)
0004921 (subdivision of digestive tract)
0005423 (developing anatomical structure)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0009569 (subdivision of trunk)
0005291 (embryonic tissue)
0009854 (digestive tract diverticulum)
0009842 (acinus)
0003929 (gut epithelium)
0000353 (parenchyma)
0003704 (intrahepatic bile duct)
0005177 (trunk region element)
0002365 (exocrine gland)
0003104 (mesenchyme)
0005057 (immune organ)
0005172 (abdomen element)
0006925 (digestive gland)
0003928 (digestive system duct)
0005256 (trunk mesenchyme)
0001048 (primordium)
0000925 (endoderm)
0006598 (presumptive structure)
0009497 (epithelium of foregut-midgut junction)
0004185 (endodermal part of digestive tract)
0005173 (abdominal segment element)
0000015 (anatomical boundary)
0009856 (sac)
0002532 (epiblast (generic))
0001555 (digestive tract)
0002417 (abdominal segment of trunk)
0007026 (primitive gut)
0001041 (foregut)
0000949 (endocrine system)
0001280 (liver parenchyma)
0001171 (portal lobule)
0004647 (liver lobule)
0002294 (biliary system)
0001173 (biliary tree)
0001172 (hepatic acinus)
0002330 (exocrine system)
0000916 (abdomen)
0002405 (immune system)
0002423 (hepatobiliary system)
0009142 (entire embryonic mesenchyme)
0006235 (foregut-midgut junction)
0004912 (biliary bud)
0006595 (presumptive endoderm)
0006603 (presumptive mesoderm)
0008835 (hepatic diverticulum)
0003894 (liver primordium)
0004161 (septum transversum)
0008836 (liver bud)
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
