Difference between revisions of "FF:11216-116B1"
From FANTOM5_SSTAR
(Created page with "{{f5samples
|id=FF:11216-116B1
|name=Urothelial cells, donor0
|sample_id=11216
|rna_tube_id=116B1
|rna_box=116
|rna_position=B1
|sample_cell_lot=N/A
|sample_cell_catal...") |
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|sample_company=Sciencell | |sample_company=Sciencell | ||
|rna_lot_number= | |rna_lot_number= | ||
| − | |rna_catalog_number=4325 | + | |rna_catalog_number=4325 |
|sample_species=Human (Homo sapiens) | |sample_species=Human (Homo sapiens) | ||
|sample_strain= | |sample_strain= | ||
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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=0. | + | |rna_concentration=0.8 |
|sample_note=machine failed, remainder reloaded, low amount | |sample_note=machine failed, remainder reloaded, low amount | ||
| − | |profile_hcage=CNhs10843,LSID700, | + | |profile_hcage=CNhs10843,LSID700,release009,COMPLETED |
|profile_cagescan=,,, | |profile_cagescan=,,, | ||
|profile_srnaseq=SRhi10009,,, | |profile_srnaseq=SRhi10009,,, | ||
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|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
|sample_description= | |sample_description= | ||
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|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
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|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
| + | |top_motifs= | ||
}} | }} | ||
Revision as of 08:59, 27 February 2012
| Name: | Urothelial cells, donor0 |
|---|---|
| Species: | Human (Homo sapiens) |
| Library ID: | {{{library_id}}} |
| Sample type: | {{{sample_category}}} |
| Genomic View: | UCSC |
| CAGEd-oPOSSUM: | link |
| Additional information | ||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample information
RNA information
|
| Download raw sequence, BAM & CTSS | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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.
Analyst:NA
link to dataset.
data
Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to
the median expression in the FANTOM5 collection is shown. Value is log10
transformed.
Analyst:NA
link to dataset.
data
no result for this sample
TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample
JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this
sample. Pearson's correlation between the number of TFBSs estimated by
using the position-weight matrix for each promoter and its expression is
expressed as Z-score by taking the ones based on random position-weight
matrix, and the tail probability of the normal distribution corresponding
to the Z-score is taken as the resulting P-value. Lower P-value indicates
more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon
link to dataset.
data
library id: CNhs10843
FANTOM5 phase1 novel unique motifsSummary: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 in
169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon
link to dataset.
data
library id: CNhs10843
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.859 |
| 10 | 10 | 0.382 |
| 100 | 100 | 0.563 |
| 101 | 101 | 0.481 |
| 102 | 102 | 0.382 |
| 103 | 103 | 0.0634 |
| 104 | 104 | 0.721 |
| 105 | 105 | 0.46 |
| 106 | 106 | 0.0323 |
| 107 | 107 | 0.00757 |
| 108 | 108 | 0.176 |
| 109 | 109 | 0.0662 |
| 11 | 11 | 0.471 |
| 110 | 110 | 0.464 |
| 111 | 111 | 0.0255 |
| 112 | 112 | 0.592 |
| 113 | 113 | 0.0146 |
| 114 | 114 | 0.135 |
| 115 | 115 | 0.341 |
| 116 | 116 | 0.756 |
| 117 | 117 | 0.506 |
| 118 | 118 | 0.592 |
| 119 | 119 | 0.107 |
| 12 | 12 | 0.405 |
| 120 | 120 | 0.00942 |
| 121 | 121 | 0.587 |
| 122 | 122 | 0.971 |
| 123 | 123 | 0.64 |
| 124 | 124 | 0.131 |
| 125 | 125 | 0.334 |
| 126 | 126 | 0.47 |
| 127 | 127 | 0.168 |
| 128 | 128 | 0.0839 |
| 129 | 129 | 0.0621 |
| 13 | 13 | 0.672 |
| 130 | 130 | 0.247 |
| 131 | 131 | 0.715 |
| 132 | 132 | 0.168 |
| 133 | 133 | 0.0548 |
| 134 | 134 | 0.112 |
| 135 | 135 | 0.559 |
| 136 | 136 | 0.64 |
| 137 | 137 | 0.265 |
| 138 | 138 | 0.818 |
| 139 | 139 | 0.951 |
| 14 | 14 | 0.828 |
| 140 | 140 | 0.419 |
| 141 | 141 | 0.714 |
| 142 | 142 | 0.638 |
| 143 | 143 | 0.978 |
| 144 | 144 | 0.646 |
| 145 | 145 | 0.0972 |
| 146 | 146 | 0.122 |
| 147 | 147 | 0.265 |
| 148 | 148 | 0.139 |
| 149 | 149 | 0.555 |
| 15 | 15 | 0.6 |
| 150 | 150 | 0.129 |
| 151 | 151 | 0.276 |
| 152 | 152 | 0.0126 |
| 153 | 153 | 0.818 |
| 154 | 154 | 0.646 |
| 155 | 155 | 0.613 |
| 156 | 156 | 0.589 |
| 157 | 157 | 0.721 |
| 158 | 158 | 0.663 |
| 159 | 159 | 0.894 |
| 16 | 16 | 0.179 |
| 160 | 160 | 0.702 |
| 161 | 161 | 0.976 |
| 162 | 162 | 0.894 |
| 163 | 163 | 0.717 |
| 164 | 164 | 0.764 |
| 165 | 165 | 0.662 |
| 166 | 166 | 0.688 |
| 167 | 167 | 0.223 |
| 168 | 168 | 0.146 |
| 169 | 169 | 0.0976 |
| 17 | 17 | 0.0636 |
| 18 | 18 | 0.31 |
| 19 | 19 | 0.881 |
| 2 | 2 | 0.223 |
| 20 | 20 | 0.792 |
| 21 | 21 | 0.552 |
| 22 | 22 | 0.545 |
| 23 | 23 | 0.0131 |
| 24 | 24 | 0.0809 |
| 25 | 25 | 0.68 |
| 26 | 26 | 0.545 |
| 27 | 27 | 0.529 |
| 28 | 28 | 0.389 |
| 29 | 29 | 0.456 |
| 3 | 3 | 0.252 |
| 30 | 30 | 0.154 |
| 31 | 31 | 0.476 |
| 32 | 32 | 0.239 |
| 33 | 33 | 0.399 |
| 34 | 34 | 0.901 |
| 35 | 35 | 0.175 |
| 36 | 36 | 0.854 |
| 37 | 37 | 0.495 |
| 38 | 38 | 0.218 |
| 39 | 39 | 0.264 |
| 4 | 4 | 0.74 |
| 40 | 40 | 0.124 |
| 41 | 41 | 0.871 |
| 42 | 42 | 0.46 |
| 43 | 43 | 0.37 |
| 44 | 44 | 0.26 |
| 45 | 45 | 0.0948 |
| 46 | 46 | 0.511 |
| 47 | 47 | 0.594 |
| 48 | 48 | 0.26 |
| 49 | 49 | 0.587 |
| 5 | 5 | 0.641 |
| 50 | 50 | 0.332 |
| 51 | 51 | 0.429 |
| 52 | 52 | 0.184 |
| 53 | 53 | 0.657 |
| 54 | 54 | 0.419 |
| 55 | 55 | 0.321 |
| 56 | 56 | 0.219 |
| 57 | 57 | 0.521 |
| 58 | 58 | 0.823 |
| 59 | 59 | 0.249 |
| 6 | 6 | 0.229 |
| 60 | 60 | 0.255 |
| 61 | 61 | 0.953 |
| 62 | 62 | 0.981 |
| 63 | 63 | 0.124 |
| 64 | 64 | 0.937 |
| 65 | 65 | 0.212 |
| 66 | 66 | 0.504 |
| 67 | 67 | 0.513 |
| 68 | 68 | 0.265 |
| 69 | 69 | 0.26 |
| 7 | 7 | 0.71 |
| 70 | 70 | 0.00937 |
| 71 | 71 | 0.582 |
| 72 | 72 | 0.896 |
| 73 | 73 | 0.0202 |
| 74 | 74 | 0.171 |
| 75 | 75 | 0.181 |
| 76 | 76 | 0.671 |
| 77 | 77 | 0.046 |
| 78 | 78 | 0.0291 |
| 79 | 79 | 0.874 |
| 8 | 8 | 0.543 |
| 80 | 80 | 0.781 |
| 81 | 81 | 0.91 |
| 82 | 82 | 0.604 |
| 83 | 83 | 0.657 |
| 84 | 84 | 0.562 |
| 85 | 85 | 0.33 |
| 86 | 86 | 0.475 |
| 87 | 87 | 0.73 |
| 88 | 88 | 0.578 |
| 89 | 89 | 0.0306 |
| 9 | 9 | 0.846 |
| 90 | 90 | 0.683 |
| 91 | 91 | 0.472 |
| 92 | 92 | 0.228 |
| 93 | 93 | 0.958 |
| 94 | 94 | 0.522 |
| 95 | 95 | 0.336 |
| 96 | 96 | 0.956 |
| 97 | 97 | 0.921 |
| 98 | 98 | 0.826 |
| 99 | 99 | 0.286 |
de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs10843
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)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji
link to source data
data
CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000244 (transitional epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000731 (urothelial cell)
0002371 (somatic cell)
UBERON: Anatomy
0000061 (anatomical structure)
0000119 (cell layer)
0000365 (urothelium)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001008 (renal system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0005423 (developing anatomical structure)
0005910 (transitional epithelium)
0005911 (endo-epithelium)
0006554 (urinary system structure)
FF: FANTOM5
NA
Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji
link to source data
data
NA
