FF:11250-116E8: Difference between revisions
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{{f5samples | {{f5samples | ||
|ancestors_in_anatomy_facet=UBERON: | |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0007100,UBERON:0000948,UBERON:0001637,UBERON:0000483,UBERON:0002384,UBERON:0006562,UBERON:0000033,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0002346,UBERON:0000055,UBERON:0000064,UBERON:0000077,UBERON:0004121,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000025,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000480,UBERON:0000923,UBERON:0003914,UBERON:0002050,UBERON:0005911,UBERON:0004921,UBERON:0005423,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0000490,UBERON:0003103,UBERON:0005291,UBERON:0003102,UBERON:0003509,UBERON:0000078,UBERON:0000485,UBERON:0003929,UBERON:0000072,UBERON:0003498,UBERON:0001981,UBERON:0002049,UBERON:0004807,UBERON:0007500,UBERON:0003104,UBERON:0010188,UBERON:0007497,UBERON:0001048,UBERON:0000925,UBERON:0003643,UBERON:0005985,UBERON:0003504,UBERON:0006598,UBERON:0002539,UBERON:0003351,UBERON:0003469,UBERON:0003496,UBERON:0004797,UBERON:0007798,UBERON:0004185,UBERON:0005157,UBERON:0004145,UBERON:0002532,UBERON:0001555,UBERON:0000065,UBERON:0002012,UBERON:0001004,UBERON:0000153,UBERON:0007811,UBERON:0000924,UBERON:0004535,UBERON:0007026,UBERON:0001041,UBERON:0004572,UBERON:0001557,UBERON:0001042,UBERON:0004537,UBERON:0008886,UBERON:0005498,UBERON:0008814,UBERON:0008816,UBERON:0003075,UBERON:0002342,UBERON:0009142,UBERON:0003081,UBERON:0007303,UBERON:0001009,UBERON:0004140,UBERON:0009881,UBERON:0009722,UBERON:0006601,UBERON:0006595,UBERON:0006603,UBERON:0004141,UBERON:0009145,UBERON:0004872,UBERON:0006965,UBERON:0002061,UBERON:0005432,UBERON:0003084,UBERON:0005062,UBERON:0007284,UBERON:0007005,UBERON:0007690,UBERON:0004139,UBERON:0004363,UBERON:0004291 | ||
|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:0002320,CL:0000063,CL:0002371,CL:0000219,CL:0000004,CL:0000134,CL:0000255,CL:0000057,CL:0002557 | ||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
|comment= | |comment= | ||
Revision as of 16:45, 8 June 2012
| Name: | Fibroblast - Pulmonary Artery, donor1 |
|---|---|
| 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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Relative expression to median (log10)
Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
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
library id: CNhs10878
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: CNhs10878
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.234 |
| 10 | 10 | 0.521 |
| 100 | 100 | 0.262 |
| 101 | 101 | 0.499 |
| 102 | 102 | 0.4 |
| 103 | 103 | 0.113 |
| 104 | 104 | 0.453 |
| 105 | 105 | 0.494 |
| 106 | 106 | 0.123 |
| 107 | 107 | 0.0304 |
| 108 | 108 | 0.819 |
| 109 | 109 | 0.0541 |
| 11 | 11 | 0.299 |
| 110 | 110 | 0.107 |
| 111 | 111 | 0.147 |
| 112 | 112 | 0.857 |
| 113 | 113 | 0.124 |
| 114 | 114 | 0.774 |
| 115 | 115 | 0.446 |
| 116 | 116 | 0.0902 |
| 117 | 117 | 0.965 |
| 118 | 118 | 0.774 |
| 119 | 119 | 0.994 |
| 12 | 12 | 0.195 |
| 120 | 120 | 0.178 |
| 121 | 121 | 0.387 |
| 122 | 122 | 0.558 |
| 123 | 123 | 4.18901e-4 |
| 124 | 124 | 0.412 |
| 125 | 125 | 0.456 |
| 126 | 126 | 0.749 |
| 127 | 127 | 0.923 |
| 128 | 128 | 0.78 |
| 129 | 129 | 0.895 |
| 13 | 13 | 0.024 |
| 130 | 130 | 0.048 |
| 131 | 131 | 0.919 |
| 132 | 132 | 0.619 |
| 133 | 133 | 0.503 |
| 134 | 134 | 0.305 |
| 135 | 135 | 0.792 |
| 136 | 136 | 0.199 |
| 137 | 137 | 0.195 |
| 138 | 138 | 0.246 |
| 139 | 139 | 0.16 |
| 14 | 14 | 0.169 |
| 140 | 140 | 0.983 |
| 141 | 141 | 0.884 |
| 142 | 142 | 0.421 |
| 143 | 143 | 0.126 |
| 144 | 144 | 0.516 |
| 145 | 145 | 0.678 |
| 146 | 146 | 0.347 |
| 147 | 147 | 0.167 |
| 148 | 148 | 0.181 |
| 149 | 149 | 0.231 |
| 15 | 15 | 0.55 |
| 150 | 150 | 0.0812 |
| 151 | 151 | 0.952 |
| 152 | 152 | 0.0702 |
| 153 | 153 | 0.477 |
| 154 | 154 | 0.435 |
| 155 | 155 | 0.0543 |
| 156 | 156 | 0.717 |
| 157 | 157 | 0.0909 |
| 158 | 158 | 0.00656 |
| 159 | 159 | 0.154 |
| 16 | 16 | 0.0764 |
| 160 | 160 | 0.0273 |
| 161 | 161 | 0.922 |
| 162 | 162 | 0.77 |
| 163 | 163 | 0.596 |
| 164 | 164 | 0.533 |
| 165 | 165 | 0.825 |
| 166 | 166 | 0.449 |
| 167 | 167 | 0.728 |
| 168 | 168 | 0.482 |
| 169 | 169 | 0.098 |
| 17 | 17 | 0.476 |
| 18 | 18 | 0.502 |
| 19 | 19 | 0.0513 |
| 2 | 2 | 0.699 |
| 20 | 20 | 0.898 |
| 21 | 21 | 0.269 |
| 22 | 22 | 0.75 |
| 23 | 23 | 0.736 |
| 24 | 24 | 0.0738 |
| 25 | 25 | 0.705 |
| 26 | 26 | 0.207 |
| 27 | 27 | 0.931 |
| 28 | 28 | 0.122 |
| 29 | 29 | 0.263 |
| 3 | 3 | 0.306 |
| 30 | 30 | 0.836 |
| 31 | 31 | 0.864 |
| 32 | 32 | 1.52994e-5 |
| 33 | 33 | 0.0579 |
| 34 | 34 | 0.866 |
| 35 | 35 | 0.291 |
| 36 | 36 | 0.552 |
| 37 | 37 | 0.0762 |
| 38 | 38 | 0.9 |
| 39 | 39 | 0.0716 |
| 4 | 4 | 0.822 |
| 40 | 40 | 0.47 |
| 41 | 41 | 0.67 |
| 42 | 42 | 0.378 |
| 43 | 43 | 0.886 |
| 44 | 44 | 0.165 |
| 45 | 45 | 0.683 |
| 46 | 46 | 0.185 |
| 47 | 47 | 0.432 |
| 48 | 48 | 0.214 |
| 49 | 49 | 0.749 |
| 5 | 5 | 0.472 |
| 50 | 50 | 0.656 |
| 51 | 51 | 0.926 |
| 52 | 52 | 0.77 |
| 53 | 53 | 0.135 |
| 54 | 54 | 0.654 |
| 55 | 55 | 0.684 |
| 56 | 56 | 0.825 |
| 57 | 57 | 0.535 |
| 58 | 58 | 0.22 |
| 59 | 59 | 0.378 |
| 6 | 6 | 0.6 |
| 60 | 60 | 0.668 |
| 61 | 61 | 0.9 |
| 62 | 62 | 0.63 |
| 63 | 63 | 0.222 |
| 64 | 64 | 0.593 |
| 65 | 65 | 0.954 |
| 66 | 66 | 0.182 |
| 67 | 67 | 0.504 |
| 68 | 68 | 0.675 |
| 69 | 69 | 0.35 |
| 7 | 7 | 0.697 |
| 70 | 70 | 0.596 |
| 71 | 71 | 0.137 |
| 72 | 72 | 0.5 |
| 73 | 73 | 0.00837 |
| 74 | 74 | 0.486 |
| 75 | 75 | 0.486 |
| 76 | 76 | 0.413 |
| 77 | 77 | 0.154 |
| 78 | 78 | 0.629 |
| 79 | 79 | 0.0878 |
| 8 | 8 | 0.0158 |
| 80 | 80 | 0.68 |
| 81 | 81 | 0.986 |
| 82 | 82 | 0.661 |
| 83 | 83 | 0.247 |
| 84 | 84 | 0.495 |
| 85 | 85 | 0.963 |
| 86 | 86 | 0.754 |
| 87 | 87 | 0.0122 |
| 88 | 88 | 0.62 |
| 89 | 89 | 0.24 |
| 9 | 9 | 0.855 |
| 90 | 90 | 0.808 |
| 91 | 91 | 0.716 |
| 92 | 92 | 0.991 |
| 93 | 93 | 0.777 |
| 94 | 94 | 0.715 |
| 95 | 95 | 0.0193 |
| 96 | 96 | 0.718 |
| 97 | 97 | 0.544 |
| 98 | 98 | 0.0929 |
| 99 | 99 | 0.00161 |
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: CNhs10878
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000002 in vivo cell sample
FF:0000068 human fibroblast of pulmonary artery 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)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000219 (motile cell)
0000134 (mesenchymal cell)
0000255 (eukaryotic cell)
0000057 (fibroblast)
0002557 (fibroblast of pulmonary artery)
UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0007100 (primary circulatory organ)
0000948 (heart)
0001637 (artery)
0000483 (epithelium)
0002384 (connective tissue)
0006562 (pharynx)
0000033 (head)
0000926 (mesoderm)
0000479 (tissue)
0001007 (digestive system)
0002346 (neurectoderm)
0000055 (vessel)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0004121 (ectoderm-derived structure)
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)
0000063 (organ segment)
0000480 (anatomical group)
0000923 (germ layer)
0003914 (epithelial tube)
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)
0003103 (compound organ)
0005291 (embryonic tissue)
0003102 (surface structure)
0003509 (arterial blood vessel)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0000485 (simple columnar epithelium)
0003929 (gut epithelium)
0000072 (segment of respiratory tract)
0003498 (heart blood vessel)
0001981 (blood vessel)
0002049 (vasculature)
0004807 (respiratory system epithelium)
0007500 (epithelial tube open at both ends)
0003104 (mesenchyme)
0010188 (protuberance)
0007497 (developing epithelial placode)
0001048 (primordium)
0000925 (endoderm)
0003643 (respiratory system arterial blood vessel)
0005985 (coronary vessel)
0003504 (respiratory system blood vessel)
0006598 (presumptive structure)
0002539 (pharyngeal arch)
0003351 (pharyngeal epithelium)
0003469 (respiratory system artery)
0003496 (head blood vessel)
0004797 (blood vessel layer)
0007798 (vascular system)
0004185 (endodermal part of digestive tract)
0005157 (epithelial fold)
0004145 (outflow tract)
0002532 (epiblast (generic))
0001555 (digestive tract)
0000065 (respiratory tract)
0002012 (pulmonary artery)
0001004 (respiratory system)
0000153 (anterior region of body)
0007811 (craniocervical region)
0000924 (ectoderm)
0004535 (cardiovascular system)
0007026 (primitive gut)
0001041 (foregut)
0004572 (arterial system)
0001557 (upper respiratory tract)
0001042 (chordate pharynx)
0004537 (blood vasculature)
0008886 (pulmonary vascular system)
0005498 (primitive heart tube)
0008814 (pharyngeal arch system)
0008816 (embryonic head)
0003075 (neural plate)
0002342 (neural crest)
0009142 (entire embryonic mesenchyme)
0003081 (lateral plate mesoderm)
0007303 (pharyngeal vasculature)
0001009 (circulatory system)
0004140 (primary heart field)
0009881 (anterior lateral plate mesoderm)
0009722 (entire pharyngeal arch endoderm)
0006601 (presumptive ectoderm)
0006595 (presumptive endoderm)
0006603 (presumptive mesoderm)
0004141 (heart tube)
0009145 (pharyngeal region of foregut)
0004872 (splanchnic layer of lateral plate mesoderm)
0006965 (vascular cord)
0002061 (truncus arteriosus)
0005432 (aortic sac)
0003084 (heart primordium)
0005062 (neural fold)
0007284 (presumptive neural plate)
0007005 (cardiac mesoderm)
0007690 (early pharyngeal endoderm)
0004139 (cardiogenic plate)
0004363 (pharyngeal arch artery)
0004291 (heart rudiment)
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
