FF:13097-140D1: Difference between revisions
From FANTOM5_SSTAR
(Created page with "{{f5samples
|id=FF:13097-140D1
|name=MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep2
|sample_id=13097
|rna_tube_id=140D1
|rna_box=140
|rna_position=D...") |
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|sample_ethnicity= | |sample_ethnicity= | ||
|rna_rin= | |rna_rin= | ||
|rna_od260/230=1. | |rna_od260/230=1.76 | ||
|rna_od260/280=2. | |rna_od260/280=2.03 | ||
|sample_cell_type=mammary gland epithelial cell | |sample_cell_type=mammary gland epithelial cell | ||
|sample_cell_line=MCF7 | |sample_cell_line=MCF7 | ||
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|rna_sample_type= | |rna_sample_type= | ||
|rna_extraction_protocol=Repurified by minelute | |rna_extraction_protocol=Repurified by minelute | ||
|rna_weight_ug=8. | |rna_weight_ug=8.04 | ||
|rna_concentration=0. | |rna_concentration=0.80 | ||
|sample_note= | |sample_note= | ||
|profile_hcage=CNhs12475,LSID916,release011,COMPLETED | |profile_hcage=CNhs12475,LSID916,release011,COMPLETED | ||
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|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:1612,DOID:162,DOID:299,DOID:305,DOID:4,DOID:5093,DOID:7 | |ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:1612,DOID:162,DOID:299,DOID:305,DOID:4,DOID:5093,DOID:7 | ||
|sample_description= | |sample_description= | ||
|fonse_cell_line=FF:0100816,FF:0101120 | |fonse_cell_line=FF:0100816,FF:0101120 | ||
|fonse_cell_line_closure=FF:0100816,FF:0101120 | |fonse_cell_line_closure=FF:0100816,FF:0101120 | ||
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|fonse_treatment=EFO:0000369,FF:0000330,FF:0000426,FF:13097-140D1 | |fonse_treatment=EFO:0000369,FF:0000330,FF:0000426,FF:13097-140D1 | ||
|fonse_treatment_closure=EFO:0000369,FF:0000330,FF:0000426,FF:13097-140D1 | |fonse_treatment_closure=EFO:0000369,FF:0000330,FF:0000426,FF:13097-140D1 | ||
|top_motifs= | |||
}} | }} | ||
Revision as of 17:42, 27 February 2012
| Name: | MCF7 breast cancer cell line response to EGF1, 00hr00min, biol_rep2 |
|---|---|
| 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
library id: CNhs12475
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: CNhs12475
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.172 |
| 10 | 10 | 0.619 |
| 100 | 100 | 0.571 |
| 101 | 101 | 0.139 |
| 102 | 102 | 0.334 |
| 103 | 103 | 0.165 |
| 104 | 104 | 0.872 |
| 105 | 105 | 0.154 |
| 106 | 106 | 0.0264 |
| 107 | 107 | 0.0823 |
| 108 | 108 | 0.665 |
| 109 | 109 | 0.092 |
| 11 | 11 | 0.505 |
| 110 | 110 | 0.976 |
| 111 | 111 | 0.0279 |
| 112 | 112 | 0.24 |
| 113 | 113 | 0.0848 |
| 114 | 114 | 0.0131 |
| 115 | 115 | 0.246 |
| 116 | 116 | 0.547 |
| 117 | 117 | 0.387 |
| 118 | 118 | 0.319 |
| 119 | 119 | 0.313 |
| 12 | 12 | 0.788 |
| 120 | 120 | 0.864 |
| 121 | 121 | 0.805 |
| 122 | 122 | 0.453 |
| 123 | 123 | 0.101 |
| 124 | 124 | 0.12 |
| 125 | 125 | 0.291 |
| 126 | 126 | 0.779 |
| 127 | 127 | 0.802 |
| 128 | 128 | 0.0696 |
| 129 | 129 | 0.505 |
| 13 | 13 | 0.572 |
| 130 | 130 | 0.00194 |
| 131 | 131 | 0.21 |
| 132 | 132 | 0.814 |
| 133 | 133 | 0.0092 |
| 134 | 134 | 0.154 |
| 135 | 135 | 0.299 |
| 136 | 136 | 0.00155 |
| 137 | 137 | 0.0975 |
| 138 | 138 | 0.133 |
| 139 | 139 | 0.0596 |
| 14 | 14 | 1 |
| 140 | 140 | 0.299 |
| 141 | 141 | 0.789 |
| 142 | 142 | 0.267 |
| 143 | 143 | 0.0359 |
| 144 | 144 | 0.345 |
| 145 | 145 | 0.273 |
| 146 | 146 | 0.488 |
| 147 | 147 | 0.746 |
| 148 | 148 | 4.61885e-4 |
| 149 | 149 | 0.215 |
| 15 | 15 | 0.404 |
| 150 | 150 | 0.978 |
| 151 | 151 | 0.157 |
| 152 | 152 | 0.778 |
| 153 | 153 | 0.0883 |
| 154 | 154 | 0.394 |
| 155 | 155 | 0.0492 |
| 156 | 156 | 0.768 |
| 157 | 157 | 0.423 |
| 158 | 158 | 0.268 |
| 159 | 159 | 0.655 |
| 16 | 16 | 0.491 |
| 160 | 160 | 0.441 |
| 161 | 161 | 0.639 |
| 162 | 162 | 0.893 |
| 163 | 163 | 0.667 |
| 164 | 164 | 0.449 |
| 165 | 165 | 0.37 |
| 166 | 166 | 0.157 |
| 167 | 167 | 0.891 |
| 168 | 168 | 0.235 |
| 169 | 169 | 0.967 |
| 17 | 17 | 0.829 |
| 18 | 18 | 0.0868 |
| 19 | 19 | 0.236 |
| 2 | 2 | 0.44 |
| 20 | 20 | 0.28 |
| 21 | 21 | 0.248 |
| 22 | 22 | 0.637 |
| 23 | 23 | 0.00184 |
| 24 | 24 | 0.946 |
| 25 | 25 | 0.937 |
| 26 | 26 | 0.317 |
| 27 | 27 | 0.571 |
| 28 | 28 | 0.845 |
| 29 | 29 | 0.842 |
| 3 | 3 | 0.112 |
| 30 | 30 | 0.436 |
| 31 | 31 | 0.471 |
| 32 | 32 | 0.152 |
| 33 | 33 | 0.523 |
| 34 | 34 | 0.242 |
| 35 | 35 | 0.103 |
| 36 | 36 | 0.281 |
| 37 | 37 | 0.16 |
| 38 | 38 | 0.994 |
| 39 | 39 | 0.516 |
| 4 | 4 | 0.621 |
| 40 | 40 | 0.243 |
| 41 | 41 | 0.174 |
| 42 | 42 | 0.194 |
| 43 | 43 | 0.104 |
| 44 | 44 | 0.266 |
| 45 | 45 | 0.903 |
| 46 | 46 | 0.139 |
| 47 | 47 | 0.883 |
| 48 | 48 | 0.977 |
| 49 | 49 | 0.146 |
| 5 | 5 | 0.126 |
| 50 | 50 | 0.479 |
| 51 | 51 | 0.539 |
| 52 | 52 | 0.313 |
| 53 | 53 | 0.132 |
| 54 | 54 | 0.377 |
| 55 | 55 | 0.439 |
| 56 | 56 | 0.41 |
| 57 | 57 | 0.347 |
| 58 | 58 | 0.297 |
| 59 | 59 | 0.317 |
| 6 | 6 | 0.531 |
| 60 | 60 | 0.0373 |
| 61 | 61 | 0.721 |
| 62 | 62 | 0.068 |
| 63 | 63 | 0.239 |
| 64 | 64 | 0.784 |
| 65 | 65 | 0.268 |
| 66 | 66 | 0.0307 |
| 67 | 67 | 0.514 |
| 68 | 68 | 0.961 |
| 69 | 69 | 0.639 |
| 7 | 7 | 0.655 |
| 70 | 70 | 0.0424 |
| 71 | 71 | 0.361 |
| 72 | 72 | 0.578 |
| 73 | 73 | 0.791 |
| 74 | 74 | 0.0659 |
| 75 | 75 | 0.99 |
| 76 | 76 | 0.979 |
| 77 | 77 | 0.411 |
| 78 | 78 | 0.944 |
| 79 | 79 | 0.263 |
| 8 | 8 | 0.415 |
| 80 | 80 | 0.0469 |
| 81 | 81 | 0.134 |
| 82 | 82 | 0.286 |
| 83 | 83 | 0.367 |
| 84 | 84 | 0.818 |
| 85 | 85 | 0.0701 |
| 86 | 86 | 0.464 |
| 87 | 87 | 0.00296 |
| 88 | 88 | 0.667 |
| 89 | 89 | 0.0853 |
| 9 | 9 | 0.151 |
| 90 | 90 | 7.07333e-5 |
| 91 | 91 | 0.0964 |
| 92 | 92 | 0.0211 |
| 93 | 93 | 0.188 |
| 94 | 94 | 0.121 |
| 95 | 95 | 0.02 |
| 96 | 96 | 0.0849 |
| 97 | 97 | 0.964 |
| 98 | 98 | 0.28 |
| 99 | 99 | 0.937 |
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: CNhs12475
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)
0000255 (eukaryotic cell)
0000548 (animal cell)
DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
1612 (breast cancer)
162 (cancer)
299 (adenocarcinoma)
305 (carcinoma)
4 (disease)
5093 (thoracic cancer)
7 (disease of anatomical entity)
UBERON: Anatomy
0000061 (anatomical structure)
0000310 (breast)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000915 (thoracic segment of trunk)
0001062 (anatomical entity)
0001443 (chest)
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
