FF:11528-119I7: Difference between revisions
From FANTOM5_SSTAR
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|id=FF:11528-119I7
|name=Retinal Pigment Epithelial Cells, donor1
|sample_id=11528
|rna_tube_id=119I7
|rna_box=119
|rna_position=I7
|sample_cell_lot=lot:353...") |
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|rna_rin=9. | |rna_rin=9.7 | ||
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|rna_sample_type=total RNA | |rna_sample_type=total RNA | ||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0 | |rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0 | ||
|rna_weight_ug=10 | |rna_weight_ug=10 | ||
|rna_concentration=1. | |rna_concentration=1.43 | ||
|sample_note= | |sample_note= | ||
|profile_hcage=,LSID768, | |profile_hcage=CNhs11338,LSID768,release014,COMPLETED | ||
|profile_cagescan=,,, | |profile_cagescan=,,, | ||
|profile_srnaseq=SRhi10015,,, | |profile_srnaseq=SRhi10015,,, | ||
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|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
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Revision as of 17:51, 27 February 2012
| Name: | Retinal Pigment Epithelial Cells, 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
|
| 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
library id: CNhs11338
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: CNhs11338
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.216 |
| 10 | 10 | 0.0126 |
| 100 | 100 | 0.9 |
| 101 | 101 | 0.498 |
| 102 | 102 | 0.746 |
| 103 | 103 | 0.963 |
| 104 | 104 | 0.886 |
| 105 | 105 | 0.0435 |
| 106 | 106 | 0.749 |
| 107 | 107 | 0.0432 |
| 108 | 108 | 0.691 |
| 109 | 109 | 0.349 |
| 11 | 11 | 0.703 |
| 110 | 110 | 0.361 |
| 111 | 111 | 0.0946 |
| 112 | 112 | 0.0732 |
| 113 | 113 | 0.181 |
| 114 | 114 | 0.521 |
| 115 | 115 | 0.936 |
| 116 | 116 | 0.284 |
| 117 | 117 | 0.185 |
| 118 | 118 | 0.58 |
| 119 | 119 | 0.896 |
| 12 | 12 | 0.995 |
| 120 | 120 | 0.684 |
| 121 | 121 | 0.535 |
| 122 | 122 | 0.123 |
| 123 | 123 | 0.0257 |
| 124 | 124 | 0.403 |
| 125 | 125 | 0.0775 |
| 126 | 126 | 0.158 |
| 127 | 127 | 0.97 |
| 128 | 128 | 0.638 |
| 129 | 129 | 0.947 |
| 13 | 13 | 0.717 |
| 130 | 130 | 0.152 |
| 131 | 131 | 0.734 |
| 132 | 132 | 0.0882 |
| 133 | 133 | 0.969 |
| 134 | 134 | 0.777 |
| 135 | 135 | 0.162 |
| 136 | 136 | 0.971 |
| 137 | 137 | 0.157 |
| 138 | 138 | 0.0127 |
| 139 | 139 | 0.803 |
| 14 | 14 | 0.408 |
| 140 | 140 | 0.819 |
| 141 | 141 | 0.122 |
| 142 | 142 | 0.656 |
| 143 | 143 | 0.882 |
| 144 | 144 | 0.87 |
| 145 | 145 | 0.631 |
| 146 | 146 | 0.332 |
| 147 | 147 | 0.934 |
| 148 | 148 | 0.18 |
| 149 | 149 | 0.0788 |
| 15 | 15 | 0.788 |
| 150 | 150 | 0.667 |
| 151 | 151 | 0.557 |
| 152 | 152 | 0.086 |
| 153 | 153 | 0.415 |
| 154 | 154 | 0.108 |
| 155 | 155 | 0.295 |
| 156 | 156 | 0.445 |
| 157 | 157 | 0.0205 |
| 158 | 158 | 0.0416 |
| 159 | 159 | 0.56 |
| 16 | 16 | 0.454 |
| 160 | 160 | 0.0771 |
| 161 | 161 | 0.502 |
| 162 | 162 | 0.0485 |
| 163 | 163 | 0.737 |
| 164 | 164 | 0.0626 |
| 165 | 165 | 0.0454 |
| 166 | 166 | 0.951 |
| 167 | 167 | 0.315 |
| 168 | 168 | 0.185 |
| 169 | 169 | 0.296 |
| 17 | 17 | 0.511 |
| 18 | 18 | 0.544 |
| 19 | 19 | 0.821 |
| 2 | 2 | 0.414 |
| 20 | 20 | 0.438 |
| 21 | 21 | 0.379 |
| 22 | 22 | 0.253 |
| 23 | 23 | 0.817 |
| 24 | 24 | 0.88 |
| 25 | 25 | 0.44 |
| 26 | 26 | 0.327 |
| 27 | 27 | 0.391 |
| 28 | 28 | 0.476 |
| 29 | 29 | 0.44 |
| 3 | 3 | 0.318 |
| 30 | 30 | 0.0417 |
| 31 | 31 | 0.874 |
| 32 | 32 | 0.468 |
| 33 | 33 | 0.66 |
| 34 | 34 | 0.111 |
| 35 | 35 | 0.622 |
| 36 | 36 | 0.323 |
| 37 | 37 | 0.643 |
| 38 | 38 | 0.905 |
| 39 | 39 | 0.319 |
| 4 | 4 | 0.456 |
| 40 | 40 | 0.0308 |
| 41 | 41 | 0.119 |
| 42 | 42 | 0.343 |
| 43 | 43 | 0.8 |
| 44 | 44 | 0.67 |
| 45 | 45 | 0.114 |
| 46 | 46 | 0.881 |
| 47 | 47 | 0.83 |
| 48 | 48 | 0.579 |
| 49 | 49 | 0.771 |
| 5 | 5 | 0.435 |
| 50 | 50 | 0.27 |
| 51 | 51 | 0.373 |
| 52 | 52 | 0.545 |
| 53 | 53 | 0.535 |
| 54 | 54 | 0.577 |
| 55 | 55 | 0.474 |
| 56 | 56 | 0.657 |
| 57 | 57 | 0.79 |
| 58 | 58 | 0.244 |
| 59 | 59 | 0.239 |
| 6 | 6 | 0.535 |
| 60 | 60 | 0.533 |
| 61 | 61 | 0.56 |
| 62 | 62 | 0.157 |
| 63 | 63 | 0.119 |
| 64 | 64 | 0.346 |
| 65 | 65 | 0.326 |
| 66 | 66 | 0.222 |
| 67 | 67 | 0.535 |
| 68 | 68 | 0.0658 |
| 69 | 69 | 0.0142 |
| 7 | 7 | 0.938 |
| 70 | 70 | 0.475 |
| 71 | 71 | 0.723 |
| 72 | 72 | 0.173 |
| 73 | 73 | 0.251 |
| 74 | 74 | 0.0896 |
| 75 | 75 | 0.422 |
| 76 | 76 | 0.00765 |
| 77 | 77 | 0.0464 |
| 78 | 78 | 0.322 |
| 79 | 79 | 0.784 |
| 8 | 8 | 0.281 |
| 80 | 80 | 0.246 |
| 81 | 81 | 0.356 |
| 82 | 82 | 0.736 |
| 83 | 83 | 0.503 |
| 84 | 84 | 0.527 |
| 85 | 85 | 0.971 |
| 86 | 86 | 0.564 |
| 87 | 87 | 0.445 |
| 88 | 88 | 0.271 |
| 89 | 89 | 0.336 |
| 9 | 9 | 0.502 |
| 90 | 90 | 0.0238 |
| 91 | 91 | 0.721 |
| 92 | 92 | 0.32 |
| 93 | 93 | 0.513 |
| 94 | 94 | 0.0761 |
| 95 | 95 | 0.812 |
| 96 | 96 | 0.665 |
| 97 | 97 | 0.719 |
| 98 | 98 | 0.95 |
| 99 | 99 | 0.0176 |
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: CNhs11338
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
{{{is_a}}}
part_of relathionship
{{{part_of}}}
has_quality relathionship
{{{has_quality}}}
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)
0000066 (epithelial cell)
0000147 (pigment cell)
0000149 (visual pigment cell)
0000255 (eukaryotic cell)
0000325 (stuff accumulating cell)
0000548 (animal cell)
0002371 (somatic cell)
0002586 (retinal pigment epithelial cell)
UBERON: Anatomy
0000019 (camera-type eye)
0000020 (sense organ)
0000033 (head)
0000047 (simple eye)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000073 (regional part of nervous system)
0000119 (cell layer)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000966 (retina)
0000970 (eye)
0001016 (nervous system)
0001032 (sensory system)
0001048 (primordium)
0001062 (anatomical entity)
0001444 (subdivision of head)
0001456 (face)
0001781 (layer of retina)
0001782 (pigmented layer of retina)
0001802 (posterior segment of eyeball)
0002050 (embryonic structure)
0002104 (visual system)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0003056 (pre-chordal neural plate)
0003071 (eye primordium)
0003072 (optic cup)
0003075 (neural plate)
0004121 (ectoderm-derived structure)
0004128 (optic vesicle)
0004456 (entire sense organ system)
0004923 (organ component layer)
0005085 (ectodermal placode)
0005291 (embryonic tissue)
0005388 (photoreceptor array)
0005423 (developing anatomical structure)
0005424 (presumptive retinal pigmented epithelium)
0006598 (presumptive structure)
0007284 (presumptive neural plate)
0007625 (pigment epithelium of eye)
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
