FF:10409-106B4: Difference between revisions
From FANTOM5_SSTAR
(Created page with "{{f5samples
|id=FF:10409-106B4
|name=chronic myelogenous leukemia cell line:KU812, biol_rep1
|sample_id=10409
|rna_tube_id=106B4
|rna_box=106
|rna_position=B4
|sample_c...") |
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{{f5samples | {{f5samples | ||
|id=FF:10409-106B4 | |id=FF:10409-106B4 | ||
|name=chronic myelogenous leukemia cell line:KU812 | |name=chronic myelogenous leukemia cell line:KU812 | ||
|sample_id=10409 | |sample_id=10409 | ||
|rna_tube_id=106B4 | |rna_tube_id=106B4 | ||
| Line 7: | Line 7: | ||
|rna_position=B4 | |rna_position=B4 | ||
|sample_cell_lot= | |sample_cell_lot= | ||
|sample_cell_catalog=RCB0495 | |sample_cell_catalog=RCB0495 | ||
|sample_company=RIKEN Bioresource centre | |sample_company=RIKEN Bioresource centre | ||
|rna_lot_number= | |rna_lot_number= | ||
| Line 20: | Line 20: | ||
|sample_ethnicity=unknown | |sample_ethnicity=unknown | ||
|rna_rin= | |rna_rin= | ||
|rna_od260/230=1. | |rna_od260/230=1.85 | ||
|rna_od260/280=2. | |rna_od260/280=2.06 | ||
|sample_cell_type=basophil progenitor cell | |sample_cell_type=basophil progenitor cell | ||
|sample_cell_line=KU812 | |sample_cell_line=KU812 | ||
|sample_collaboration=Yukio Nakamura (RIKEN BRC) | |sample_collaboration=Yukio Nakamura (RIKEN BRC) | ||
|sample_experimental_condition= | |sample_experimental_condition= | ||
| Line 29: | Line 29: | ||
|rna_sample_type=total RNA | |rna_sample_type=total RNA | ||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | |rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | ||
|rna_weight_ug=59. | |rna_weight_ug=59.6555 | ||
|rna_concentration=2.38622 | |rna_concentration=2.38622 | ||
|sample_note=machine failed, remainder reloaded, low amount | |sample_note=machine failed, remainder reloaded, low amount | ||
| Line 40: | Line 40: | ||
|ancestors_in_disease_facet=DOID:0050686,DOID:0060083,DOID:1036,DOID:1240,DOID:14566,DOID:162,DOID:2531,DOID:4,DOID:8692 | |ancestors_in_disease_facet=DOID:0050686,DOID:0060083,DOID:1036,DOID:1240,DOID:14566,DOID:162,DOID:2531,DOID:4,DOID:8692 | ||
|sample_description= | |sample_description= | ||
|fonse_cell_line=FF:0101035 | |fonse_cell_line=FF:0101035 | ||
|fonse_cell_line_closure=FF:0101035 | |fonse_cell_line_closure=FF:0101035 | ||
| Line 67: | Line 66: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|top_motifs= | |||
}} | }} | ||
Revision as of 17:27, 27 February 2012
| Name: | chronic myelogenous leukemia cell line:KU812 |
|---|---|
| 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: CNhs10727
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: CNhs10727
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.165 |
| 10 | 10 | 0.0148 |
| 100 | 100 | 0.704 |
| 101 | 101 | 0.236 |
| 102 | 102 | 0.528 |
| 103 | 103 | 0.721 |
| 104 | 104 | 0.559 |
| 105 | 105 | 0.492 |
| 106 | 106 | 0.217 |
| 107 | 107 | 0.502 |
| 108 | 108 | 0.374 |
| 109 | 109 | 0.0433 |
| 11 | 11 | 0.155 |
| 110 | 110 | 0.157 |
| 111 | 111 | 0.0557 |
| 112 | 112 | 0.0705 |
| 113 | 113 | 0.694 |
| 114 | 114 | 0.49 |
| 115 | 115 | 0.0834 |
| 116 | 116 | 0.974 |
| 117 | 117 | 0.0672 |
| 118 | 118 | 0.961 |
| 119 | 119 | 0.307 |
| 12 | 12 | 0.933 |
| 120 | 120 | 0.676 |
| 121 | 121 | 0.566 |
| 122 | 122 | 0.911 |
| 123 | 123 | 0.655 |
| 124 | 124 | 0.0181 |
| 125 | 125 | 0.567 |
| 126 | 126 | 0.32 |
| 127 | 127 | 0.494 |
| 128 | 128 | 0.25 |
| 129 | 129 | 0.865 |
| 13 | 13 | 0.00505 |
| 130 | 130 | 0.00929 |
| 131 | 131 | 0.423 |
| 132 | 132 | 0.407 |
| 133 | 133 | 0.18 |
| 134 | 134 | 0.841 |
| 135 | 135 | 0.514 |
| 136 | 136 | 0.0478 |
| 137 | 137 | 0.694 |
| 138 | 138 | 0.626 |
| 139 | 139 | 0.537 |
| 14 | 14 | 0.298 |
| 140 | 140 | 0.828 |
| 141 | 141 | 0.308 |
| 142 | 142 | 0.458 |
| 143 | 143 | 0.208 |
| 144 | 144 | 0.609 |
| 145 | 145 | 0.537 |
| 146 | 146 | 0.358 |
| 147 | 147 | 0.101 |
| 148 | 148 | 0.848 |
| 149 | 149 | 0.141 |
| 15 | 15 | 0.484 |
| 150 | 150 | 0.978 |
| 151 | 151 | 0.524 |
| 152 | 152 | 0.0466 |
| 153 | 153 | 0.847 |
| 154 | 154 | 0.989 |
| 155 | 155 | 0.0894 |
| 156 | 156 | 0.64 |
| 157 | 157 | 0.741 |
| 158 | 158 | 0.88 |
| 159 | 159 | 0.364 |
| 16 | 16 | 0.312 |
| 160 | 160 | 0.343 |
| 161 | 161 | 0.403 |
| 162 | 162 | 0.907 |
| 163 | 163 | 0.238 |
| 164 | 164 | 0.12 |
| 165 | 165 | 0.797 |
| 166 | 166 | 0.336 |
| 167 | 167 | 0.433 |
| 168 | 168 | 0.779 |
| 169 | 169 | 0.674 |
| 17 | 17 | 0.741 |
| 18 | 18 | 0.269 |
| 19 | 19 | 0.801 |
| 2 | 2 | 0.225 |
| 20 | 20 | 0.164 |
| 21 | 21 | 0.927 |
| 22 | 22 | 0.845 |
| 23 | 23 | 0.0146 |
| 24 | 24 | 0.554 |
| 25 | 25 | 0.185 |
| 26 | 26 | 0.504 |
| 27 | 27 | 0.499 |
| 28 | 28 | 0.492 |
| 29 | 29 | 0.0438 |
| 3 | 3 | 0.303 |
| 30 | 30 | 0.0201 |
| 31 | 31 | 0.175 |
| 32 | 32 | 0.0119 |
| 33 | 33 | 0.116 |
| 34 | 34 | 0.607 |
| 35 | 35 | 0.632 |
| 36 | 36 | 0.0225 |
| 37 | 37 | 0.479 |
| 38 | 38 | 0.863 |
| 39 | 39 | 0.489 |
| 4 | 4 | 0.0214 |
| 40 | 40 | 0.182 |
| 41 | 41 | 0.899 |
| 42 | 42 | 0.373 |
| 43 | 43 | 0.481 |
| 44 | 44 | 0.575 |
| 45 | 45 | 0.74 |
| 46 | 46 | 0.553 |
| 47 | 47 | 0.0966 |
| 48 | 48 | 0.191 |
| 49 | 49 | 0.084 |
| 5 | 5 | 0.57 |
| 50 | 50 | 0.998 |
| 51 | 51 | 0.638 |
| 52 | 52 | 0.265 |
| 53 | 53 | 0.164 |
| 54 | 54 | 0.586 |
| 55 | 55 | 0.351 |
| 56 | 56 | 0.98 |
| 57 | 57 | 0.487 |
| 58 | 58 | 0.169 |
| 59 | 59 | 0.878 |
| 6 | 6 | 0.959 |
| 60 | 60 | 0.753 |
| 61 | 61 | 0.342 |
| 62 | 62 | 0.29 |
| 63 | 63 | 0.981 |
| 64 | 64 | 0.427 |
| 65 | 65 | 0.328 |
| 66 | 66 | 2.6691e-9 |
| 67 | 67 | 0.802 |
| 68 | 68 | 0.257 |
| 69 | 69 | 0.866 |
| 7 | 7 | 0.0267 |
| 70 | 70 | 0.383 |
| 71 | 71 | 0.0707 |
| 72 | 72 | 0.865 |
| 73 | 73 | 0.453 |
| 74 | 74 | 0.542 |
| 75 | 75 | 0.0456 |
| 76 | 76 | 0.235 |
| 77 | 77 | 0.187 |
| 78 | 78 | 0.0323 |
| 79 | 79 | 0.0851 |
| 8 | 8 | 0.89 |
| 80 | 80 | 0.435 |
| 81 | 81 | 0.943 |
| 82 | 82 | 0.819 |
| 83 | 83 | 0.401 |
| 84 | 84 | 0.893 |
| 85 | 85 | 0.183 |
| 86 | 86 | 0.987 |
| 87 | 87 | 0.199 |
| 88 | 88 | 0.503 |
| 89 | 89 | 0.391 |
| 9 | 9 | 0.873 |
| 90 | 90 | 0.304 |
| 91 | 91 | 0.12 |
| 92 | 92 | 0.261 |
| 93 | 93 | 0.89 |
| 94 | 94 | 0.568 |
| 95 | 95 | 0.0322 |
| 96 | 96 | 0.941 |
| 97 | 97 | 0.341 |
| 98 | 98 | 0.322 |
| 99 | 99 | 0.471 |
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: CNhs10727
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)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000763 (myeloid cell)
0000837 (hematopoietic multipotent progenitor cell)
0000988 (hematopoietic cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
DOID: Disease
0050686 (organ system cancer)
0060083 (immune system cancer)
1036 (chronic leukemia)
1240 (leukemia)
14566 (disease of cellular proliferation)
162 (cancer)
2531 (hematologic cancer)
4 (disease)
8692 (myeloid leukemia)
UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)
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
