FF:11366-117I7: Difference between revisions
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{{f5samples | {{f5samples | ||
|ancestors_in_anatomy_facet=UBERON: | |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0001134,UBERON:0001637,UBERON:0002100,UBERON:0000483,UBERON:0000926,UBERON:0000479,UBERON:0000055,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000025,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0003914,UBERON:0002050,UBERON:0005423,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0000490,UBERON:0009569,UBERON:0005291,UBERON:0003509,UBERON:0004573,UBERON:0002036,UBERON:0002385,UBERON:0003834,UBERON:0001981,UBERON:0002049,UBERON:0000486,UBERON:0007500,UBERON:0003104,UBERON:0000914,UBERON:0005256,UBERON:0003513,UBERON:0006598,UBERON:0007798,UBERON:0001015,UBERON:0002532,UBERON:0001533,UBERON:0002329,UBERON:0002204,UBERON:0004535,UBERON:0004571,UBERON:0000383,UBERON:0000915,UBERON:0004572,UBERON:0004537,UBERON:0003077,UBERON:0004290,UBERON:0009142,UBERON:0003081,UBERON:0001009,UBERON:0006603,UBERON:0003082,UBERON:0004872,UBERON:0006965,UBERON:0003059,UBERON:0007282,UBERON:0009618,UBERON:0007285 | ||
|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:0000359,CL:0000222,CL:0002595,CL:0000355,CL:0000514 | ||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
|comment= | |comment= | ||
Revision as of 16:55, 8 June 2012
| Name: | Smooth Muscle Cells - Subclavian Artery, donor2 |
|---|---|
| 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: CNhs11990
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: CNhs11990
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.229 |
| 10 | 10 | 0.645 |
| 100 | 100 | 0.973 |
| 101 | 101 | 0.848 |
| 102 | 102 | 0.955 |
| 103 | 103 | 0.0246 |
| 104 | 104 | 0.443 |
| 105 | 105 | 0.296 |
| 106 | 106 | 0.0219 |
| 107 | 107 | 0.0259 |
| 108 | 108 | 0.216 |
| 109 | 109 | 0.0857 |
| 11 | 11 | 0.0694 |
| 110 | 110 | 0.203 |
| 111 | 111 | 0.924 |
| 112 | 112 | 0.369 |
| 113 | 113 | 0.169 |
| 114 | 114 | 0.148 |
| 115 | 115 | 0.0198 |
| 116 | 116 | 0.0564 |
| 117 | 117 | 0.546 |
| 118 | 118 | 0.46 |
| 119 | 119 | 0.266 |
| 12 | 12 | 0.456 |
| 120 | 120 | 0.0446 |
| 121 | 121 | 0.571 |
| 122 | 122 | 0.217 |
| 123 | 123 | 0.193 |
| 124 | 124 | 0.752 |
| 125 | 125 | 0.319 |
| 126 | 126 | 0.623 |
| 127 | 127 | 0.483 |
| 128 | 128 | 0.0728 |
| 129 | 129 | 0.727 |
| 13 | 13 | 0.896 |
| 130 | 130 | 0.907 |
| 131 | 131 | 0.651 |
| 132 | 132 | 0.781 |
| 133 | 133 | 0.394 |
| 134 | 134 | 0.529 |
| 135 | 135 | 0.109 |
| 136 | 136 | 0.982 |
| 137 | 137 | 0.424 |
| 138 | 138 | 0.813 |
| 139 | 139 | 0.126 |
| 14 | 14 | 0.931 |
| 140 | 140 | 0.878 |
| 141 | 141 | 0.857 |
| 142 | 142 | 0.349 |
| 143 | 143 | 0.0341 |
| 144 | 144 | 0.821 |
| 145 | 145 | 0.122 |
| 146 | 146 | 0.534 |
| 147 | 147 | 0.0481 |
| 148 | 148 | 0.0278 |
| 149 | 149 | 0.0242 |
| 15 | 15 | 0.288 |
| 150 | 150 | 0.275 |
| 151 | 151 | 0.325 |
| 152 | 152 | 0.0332 |
| 153 | 153 | 0.613 |
| 154 | 154 | 0.916 |
| 155 | 155 | 0.242 |
| 156 | 156 | 0.739 |
| 157 | 157 | 0.603 |
| 158 | 158 | 0.033 |
| 159 | 159 | 0.307 |
| 16 | 16 | 0.046 |
| 160 | 160 | 0.0727 |
| 161 | 161 | 0.682 |
| 162 | 162 | 0.95 |
| 163 | 163 | 0.703 |
| 164 | 164 | 0.0792 |
| 165 | 165 | 0.971 |
| 166 | 166 | 0.386 |
| 167 | 167 | 0.985 |
| 168 | 168 | 0.542 |
| 169 | 169 | 0.0258 |
| 17 | 17 | 0.166 |
| 18 | 18 | 0.0764 |
| 19 | 19 | 0.0362 |
| 2 | 2 | 0.32 |
| 20 | 20 | 0.563 |
| 21 | 21 | 0.229 |
| 22 | 22 | 0.227 |
| 23 | 23 | 0.0717 |
| 24 | 24 | 0.699 |
| 25 | 25 | 0.517 |
| 26 | 26 | 0.189 |
| 27 | 27 | 0.415 |
| 28 | 28 | 0.258 |
| 29 | 29 | 0.151 |
| 3 | 3 | 0.247 |
| 30 | 30 | 0.543 |
| 31 | 31 | 0.455 |
| 32 | 32 | 4.64691e-5 |
| 33 | 33 | 0.827 |
| 34 | 34 | 0.772 |
| 35 | 35 | 0.324 |
| 36 | 36 | 0.367 |
| 37 | 37 | 0.0619 |
| 38 | 38 | 0.668 |
| 39 | 39 | 0.292 |
| 4 | 4 | 0.956 |
| 40 | 40 | 0.551 |
| 41 | 41 | 0.507 |
| 42 | 42 | 0.549 |
| 43 | 43 | 0.185 |
| 44 | 44 | 0.0418 |
| 45 | 45 | 0.552 |
| 46 | 46 | 0.0809 |
| 47 | 47 | 0.214 |
| 48 | 48 | 0.273 |
| 49 | 49 | 0.482 |
| 5 | 5 | 0.589 |
| 50 | 50 | 0.69 |
| 51 | 51 | 0.636 |
| 52 | 52 | 0.963 |
| 53 | 53 | 0.425 |
| 54 | 54 | 0.432 |
| 55 | 55 | 0.271 |
| 56 | 56 | 0.536 |
| 57 | 57 | 0.461 |
| 58 | 58 | 0.982 |
| 59 | 59 | 0.0256 |
| 6 | 6 | 0.615 |
| 60 | 60 | 0.306 |
| 61 | 61 | 0.868 |
| 62 | 62 | 0.505 |
| 63 | 63 | 0.158 |
| 64 | 64 | 0.44 |
| 65 | 65 | 0.283 |
| 66 | 66 | 0.789 |
| 67 | 67 | 0.0999 |
| 68 | 68 | 0.701 |
| 69 | 69 | 0.183 |
| 7 | 7 | 0.952 |
| 70 | 70 | 0.0567 |
| 71 | 71 | 0.264 |
| 72 | 72 | 0.923 |
| 73 | 73 | 0.0114 |
| 74 | 74 | 0.289 |
| 75 | 75 | 0.223 |
| 76 | 76 | 0.996 |
| 77 | 77 | 0.00402 |
| 78 | 78 | 0.64 |
| 79 | 79 | 0.00175 |
| 8 | 8 | 0.0517 |
| 80 | 80 | 0.715 |
| 81 | 81 | 0.267 |
| 82 | 82 | 0.309 |
| 83 | 83 | 0.298 |
| 84 | 84 | 0.583 |
| 85 | 85 | 0.0168 |
| 86 | 86 | 0.469 |
| 87 | 87 | 0.0347 |
| 88 | 88 | 0.0978 |
| 89 | 89 | 0.00488 |
| 9 | 9 | 0.485 |
| 90 | 90 | 0.593 |
| 91 | 91 | 0.271 |
| 92 | 92 | 0.0995 |
| 93 | 93 | 0.419 |
| 94 | 94 | 0.339 |
| 95 | 95 | 0.181 |
| 96 | 96 | 0.763 |
| 97 | 97 | 0.725 |
| 98 | 98 | 0.932 |
| 99 | 99 | 0.00966 |
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: CNhs11990
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000002 in vivo cell sample
FF:0000175 human smooth muscle cell of subclavian 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)
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)
0000359 (vascular associated smooth muscle cell)
0000222 (mesodermal cell)
0002595 (smooth muscle cell of the subclavian artery)
0000355 (multi-potent skeletal muscle stem cell)
0000514 (smooth muscle myoblast)
UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0001134 (skeletal muscle tissue)
0001637 (artery)
0002100 (trunk)
0000483 (epithelium)
0000926 (mesoderm)
0000479 (tissue)
0000055 (vessel)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000025 (tube)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0003914 (epithelial tube)
0002050 (embryonic structure)
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)
0003509 (arterial blood vessel)
0004573 (systemic artery)
0002036 (striated muscle tissue)
0002385 (muscle tissue)
0003834 (thoracic segment blood vessel)
0001981 (blood vessel)
0002049 (vasculature)
0000486 (multilaminar epithelium)
0007500 (epithelial tube open at both ends)
0003104 (mesenchyme)
0005256 (trunk mesenchyme)
0003513 (trunk blood vessel)
0006598 (presumptive structure)
0007798 (vascular system)
0001015 (musculature)
0002532 (epiblast (generic))
0001533 (subclavian artery)
0002329 (somite)
0002204 (musculoskeletal system)
0004535 (cardiovascular system)
0004571 (systemic arterial system)
0000383 (musculature of body)
0000915 (thoracic segment of trunk)
0004572 (arterial system)
0004537 (blood vasculature)
0003077 (paraxial mesoderm)
0004290 (dermomyotome)
0009142 (entire embryonic mesenchyme)
0003081 (lateral plate mesoderm)
0001009 (circulatory system)
0006603 (presumptive mesoderm)
0003082 (myotome)
0004872 (splanchnic layer of lateral plate mesoderm)
0006965 (vascular cord)
0003059 (presomitic mesoderm)
0007282 (presumptive segmental plate)
0009618 (trunk paraxial mesoderm)
0007285 (presumptive paraxial mesoderm)
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
