FF:10638-108I8: Difference between revisions
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Revision as of 15:15, 7 March 2012
| Name: | clear cell carcinoma cell line:JHOC-5 |
|---|---|
| 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: CNhs11745
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: CNhs11745
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.0898 |
| 10 | 10 | 0.111 |
| 100 | 100 | 0.00105 |
| 101 | 101 | 0.178 |
| 102 | 102 | 0.638 |
| 103 | 103 | 0.411 |
| 104 | 104 | 0.962 |
| 105 | 105 | 0.143 |
| 106 | 106 | 0.701 |
| 107 | 107 | 0.276 |
| 108 | 108 | 0.534 |
| 109 | 109 | 0.0551 |
| 11 | 11 | 0.163 |
| 110 | 110 | 0.0531 |
| 111 | 111 | 0.15 |
| 112 | 112 | 0.5 |
| 113 | 113 | 0.0218 |
| 114 | 114 | 0.84 |
| 115 | 115 | 0.336 |
| 116 | 116 | 0.39 |
| 117 | 117 | 0.154 |
| 118 | 118 | 0.0148 |
| 119 | 119 | 0.159 |
| 12 | 12 | 0.324 |
| 120 | 120 | 0.0979 |
| 121 | 121 | 0.54 |
| 122 | 122 | 0.263 |
| 123 | 123 | 0.557 |
| 124 | 124 | 0.286 |
| 125 | 125 | 0.272 |
| 126 | 126 | 0.4 |
| 127 | 127 | 0.77 |
| 128 | 128 | 0.766 |
| 129 | 129 | 0.272 |
| 13 | 13 | 8.78508e-4 |
| 130 | 130 | 0.806 |
| 131 | 131 | 0.931 |
| 132 | 132 | 0.852 |
| 133 | 133 | 0.113 |
| 134 | 134 | 0.104 |
| 135 | 135 | 0.0204 |
| 136 | 136 | 0.0104 |
| 137 | 137 | 0.349 |
| 138 | 138 | 0.777 |
| 139 | 139 | 0.0936 |
| 14 | 14 | 0.728 |
| 140 | 140 | 0.788 |
| 141 | 141 | 0.675 |
| 142 | 142 | 0.807 |
| 143 | 143 | 0.0422 |
| 144 | 144 | 0.925 |
| 145 | 145 | 0.5 |
| 146 | 146 | 0.236 |
| 147 | 147 | 0.94 |
| 148 | 148 | 0.569 |
| 149 | 149 | 0.711 |
| 15 | 15 | 0.306 |
| 150 | 150 | 0.603 |
| 151 | 151 | 0.8 |
| 152 | 152 | 0.327 |
| 153 | 153 | 0.775 |
| 154 | 154 | 0.404 |
| 155 | 155 | 0.924 |
| 156 | 156 | 0.971 |
| 157 | 157 | 0.426 |
| 158 | 158 | 0.178 |
| 159 | 159 | 0.188 |
| 16 | 16 | 0.308 |
| 160 | 160 | 0.159 |
| 161 | 161 | 0.58 |
| 162 | 162 | 0.69 |
| 163 | 163 | 0.876 |
| 164 | 164 | 0.0142 |
| 165 | 165 | 0.826 |
| 166 | 166 | 0.996 |
| 167 | 167 | 0.189 |
| 168 | 168 | 0.8 |
| 169 | 169 | 0.8 |
| 17 | 17 | 0.931 |
| 18 | 18 | 0.959 |
| 19 | 19 | 0.914 |
| 2 | 2 | 0.205 |
| 20 | 20 | 0.0313 |
| 21 | 21 | 0.108 |
| 22 | 22 | 0.307 |
| 23 | 23 | 0.878 |
| 24 | 24 | 0.446 |
| 25 | 25 | 0.983 |
| 26 | 26 | 0.0271 |
| 27 | 27 | 0.352 |
| 28 | 28 | 0.711 |
| 29 | 29 | 0.0269 |
| 3 | 3 | 0.503 |
| 30 | 30 | 0.882 |
| 31 | 31 | 0.46 |
| 32 | 32 | 0.337 |
| 33 | 33 | 0.0474 |
| 34 | 34 | 0.0928 |
| 35 | 35 | 0.907 |
| 36 | 36 | 0.123 |
| 37 | 37 | 0.12 |
| 38 | 38 | 0.696 |
| 39 | 39 | 0.509 |
| 4 | 4 | 0.996 |
| 40 | 40 | 0.0222 |
| 41 | 41 | 0.027 |
| 42 | 42 | 0.548 |
| 43 | 43 | 0.964 |
| 44 | 44 | 0.023 |
| 45 | 45 | 0.34 |
| 46 | 46 | 0.419 |
| 47 | 47 | 0.145 |
| 48 | 48 | 0.0763 |
| 49 | 49 | 0.424 |
| 5 | 5 | 0.731 |
| 50 | 50 | 0.628 |
| 51 | 51 | 0.868 |
| 52 | 52 | 0.437 |
| 53 | 53 | 0.315 |
| 54 | 54 | 0.741 |
| 55 | 55 | 0.697 |
| 56 | 56 | 0.757 |
| 57 | 57 | 0.354 |
| 58 | 58 | 0.683 |
| 59 | 59 | 0.722 |
| 6 | 6 | 0.339 |
| 60 | 60 | 0.674 |
| 61 | 61 | 0.627 |
| 62 | 62 | 0.732 |
| 63 | 63 | 0.461 |
| 64 | 64 | 0.526 |
| 65 | 65 | 0.975 |
| 66 | 66 | 0.515 |
| 67 | 67 | 0.906 |
| 68 | 68 | 0.98 |
| 69 | 69 | 0.518 |
| 7 | 7 | 0.63 |
| 70 | 70 | 0.275 |
| 71 | 71 | 0.169 |
| 72 | 72 | 0.264 |
| 73 | 73 | 0.863 |
| 74 | 74 | 0.559 |
| 75 | 75 | 0.0979 |
| 76 | 76 | 0.174 |
| 77 | 77 | 0.317 |
| 78 | 78 | 0.119 |
| 79 | 79 | 0.843 |
| 8 | 8 | 0.457 |
| 80 | 80 | 0.00174 |
| 81 | 81 | 0.714 |
| 82 | 82 | 0.445 |
| 83 | 83 | 0.904 |
| 84 | 84 | 0.902 |
| 85 | 85 | 0.372 |
| 86 | 86 | 0.587 |
| 87 | 87 | 0.0898 |
| 88 | 88 | 0.498 |
| 89 | 89 | 0.923 |
| 9 | 9 | 0.0955 |
| 90 | 90 | 0.208 |
| 91 | 91 | 0.177 |
| 92 | 92 | 0.993 |
| 93 | 93 | 0.38 |
| 94 | 94 | 0.286 |
| 95 | 95 | 0.229 |
| 96 | 96 | 0.769 |
| 97 | 97 | 0.787 |
| 98 | 98 | 0.511 |
| 99 | 99 | 0.362 |
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: CNhs11745
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000003 cell line sample
FF:0000210 human sample
FF:0102787 clear cell adenocarcinoma cell 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)
0000066 (epithelial cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
120 (female reproductive organ cancer)
14566 (disease of cellular proliferation)
162 (cancer)
193 (reproductive organ cancer)
299 (adenocarcinoma)
305 (carcinoma)
4 (disease)
4468 (clear cell adenocarcinoma)
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
