FF:10423-106C9: Difference between revisions
From FANTOM5_SSTAR
(Created page with "{{f5samples
|id=FF:10423-106C9
|name=choriocarcinoma cell line:BeWo, biol_rep1
|sample_id=10423
|rna_tube_id=106C9
|rna_box=106
|rna_position=C9
|sample_cell_lot=
|sam...") |
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{{f5samples | {{f5samples | ||
|id=FF:10423-106C9 | |id=FF:10423-106C9 | ||
|name=choriocarcinoma cell line:BeWo | |name=choriocarcinoma cell line:BeWo | ||
|sample_id=10423 | |sample_id=10423 | ||
|rna_tube_id=106C9 | |rna_tube_id=106C9 | ||
| Line 7: | Line 7: | ||
|rna_position=C9 | |rna_position=C9 | ||
|sample_cell_lot= | |sample_cell_lot= | ||
|sample_cell_catalog=RCB1644 | |sample_cell_catalog=RCB1644 | ||
|sample_company=RIKEN Bioresource centre | |sample_company=RIKEN Bioresource centre | ||
|rna_lot_number= | |rna_lot_number= | ||
| Line 19: | Line 19: | ||
|sample_age=fetal | |sample_age=fetal | ||
|sample_ethnicity= | |sample_ethnicity= | ||
|rna_rin=9. | |rna_rin=9.9 | ||
|rna_od260/230=1. | |rna_od260/230=1.53 | ||
|rna_od260/280=2. | |rna_od260/280=2.07 | ||
|sample_cell_type=trophoblast cell | |sample_cell_type=trophoblast cell | ||
|sample_cell_line=BeWo | |sample_cell_line=BeWo | ||
|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=72. | |rna_weight_ug=72.6381 | ||
|rna_concentration=1.61418 | |rna_concentration=1.61418 | ||
|sample_note=machine failed, remainder reloaded, low amount | |sample_note=machine failed, remainder reloaded, low amount | ||
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|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:2994,DOID:3095,DOID:4 | |ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:2994,DOID:3095,DOID:4 | ||
|sample_description= | |sample_description= | ||
|fonse_cell_line=FF:0101575 | |fonse_cell_line=FF:0101575 | ||
|fonse_cell_line_closure=FF:0101575 | |fonse_cell_line_closure=FF:0101575 | ||
| 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: | choriocarcinoma cell line:BeWo |
|---|---|
| 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: CNhs10740
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: CNhs10740
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.458 |
| 10 | 10 | 0.661 |
| 100 | 100 | 0.0392 |
| 101 | 101 | 0.346 |
| 102 | 102 | 0.0646 |
| 103 | 103 | 0.103 |
| 104 | 104 | 0.111 |
| 105 | 105 | 0.741 |
| 106 | 106 | 0.338 |
| 107 | 107 | 0.685 |
| 108 | 108 | 0.506 |
| 109 | 109 | 0.0743 |
| 11 | 11 | 0.696 |
| 110 | 110 | 0.335 |
| 111 | 111 | 0.814 |
| 112 | 112 | 0.381 |
| 113 | 113 | 0.0144 |
| 114 | 114 | 0.268 |
| 115 | 115 | 0.816 |
| 116 | 116 | 0.636 |
| 117 | 117 | 0.0184 |
| 118 | 118 | 0.23 |
| 119 | 119 | 0.796 |
| 12 | 12 | 0.95 |
| 120 | 120 | 0.689 |
| 121 | 121 | 0.635 |
| 122 | 122 | 0.886 |
| 123 | 123 | 0.36 |
| 124 | 124 | 0.978 |
| 125 | 125 | 0.867 |
| 126 | 126 | 0.718 |
| 127 | 127 | 0.407 |
| 128 | 128 | 0.512 |
| 129 | 129 | 0.903 |
| 13 | 13 | 7.14923e-5 |
| 130 | 130 | 0.343 |
| 131 | 131 | 0.182 |
| 132 | 132 | 0.952 |
| 133 | 133 | 2.25913e-4 |
| 134 | 134 | 0.931 |
| 135 | 135 | 0.262 |
| 136 | 136 | 0.00486 |
| 137 | 137 | 0.11 |
| 138 | 138 | 0.967 |
| 139 | 139 | 0.373 |
| 14 | 14 | 0.912 |
| 140 | 140 | 0.257 |
| 141 | 141 | 0.171 |
| 142 | 142 | 0.872 |
| 143 | 143 | 0.0416 |
| 144 | 144 | 0.0474 |
| 145 | 145 | 0.389 |
| 146 | 146 | 0.795 |
| 147 | 147 | 0.212 |
| 148 | 148 | 0.22 |
| 149 | 149 | 0.782 |
| 15 | 15 | 0.715 |
| 150 | 150 | 0.943 |
| 151 | 151 | 0.536 |
| 152 | 152 | 0.887 |
| 153 | 153 | 0.5 |
| 154 | 154 | 0.742 |
| 155 | 155 | 0.103 |
| 156 | 156 | 0.376 |
| 157 | 157 | 0.814 |
| 158 | 158 | 0.77 |
| 159 | 159 | 0.786 |
| 16 | 16 | 0.489 |
| 160 | 160 | 0.73 |
| 161 | 161 | 0.283 |
| 162 | 162 | 0.0618 |
| 163 | 163 | 0.266 |
| 164 | 164 | 0.645 |
| 165 | 165 | 0.652 |
| 166 | 166 | 0.0115 |
| 167 | 167 | 0.86 |
| 168 | 168 | 0.286 |
| 169 | 169 | 0.196 |
| 17 | 17 | 0.596 |
| 18 | 18 | 0.749 |
| 19 | 19 | 0.428 |
| 2 | 2 | 0.871 |
| 20 | 20 | 0.748 |
| 21 | 21 | 0.524 |
| 22 | 22 | 0.573 |
| 23 | 23 | 0.439 |
| 24 | 24 | 0.292 |
| 25 | 25 | 0.483 |
| 26 | 26 | 0.415 |
| 27 | 27 | 0.932 |
| 28 | 28 | 0.661 |
| 29 | 29 | 0.298 |
| 3 | 3 | 0.563 |
| 30 | 30 | 0.948 |
| 31 | 31 | 0.92 |
| 32 | 32 | 0.17 |
| 33 | 33 | 0.342 |
| 34 | 34 | 0.524 |
| 35 | 35 | 0.663 |
| 36 | 36 | 0.313 |
| 37 | 37 | 0.488 |
| 38 | 38 | 0.756 |
| 39 | 39 | 0.264 |
| 4 | 4 | 0.624 |
| 40 | 40 | 0.0178 |
| 41 | 41 | 0.0707 |
| 42 | 42 | 0.443 |
| 43 | 43 | 0.816 |
| 44 | 44 | 0.298 |
| 45 | 45 | 0.439 |
| 46 | 46 | 0.954 |
| 47 | 47 | 0.0986 |
| 48 | 48 | 0.219 |
| 49 | 49 | 0.871 |
| 5 | 5 | 0.298 |
| 50 | 50 | 0.311 |
| 51 | 51 | 0.851 |
| 52 | 52 | 0.82 |
| 53 | 53 | 0.339 |
| 54 | 54 | 0.872 |
| 55 | 55 | 0.684 |
| 56 | 56 | 0.883 |
| 57 | 57 | 0.0857 |
| 58 | 58 | 0.466 |
| 59 | 59 | 0.79 |
| 6 | 6 | 0.622 |
| 60 | 60 | 0.748 |
| 61 | 61 | 0.385 |
| 62 | 62 | 0.513 |
| 63 | 63 | 0.801 |
| 64 | 64 | 0.774 |
| 65 | 65 | 0.802 |
| 66 | 66 | 0.00372 |
| 67 | 67 | 0.857 |
| 68 | 68 | 0.0293 |
| 69 | 69 | 0.479 |
| 7 | 7 | 0.138 |
| 70 | 70 | 0.211 |
| 71 | 71 | 0.442 |
| 72 | 72 | 0.893 |
| 73 | 73 | 0.912 |
| 74 | 74 | 0.41 |
| 75 | 75 | 0.0673 |
| 76 | 76 | 0.802 |
| 77 | 77 | 0.613 |
| 78 | 78 | 0.00171 |
| 79 | 79 | 0.247 |
| 8 | 8 | 0.766 |
| 80 | 80 | 0.021 |
| 81 | 81 | 0.967 |
| 82 | 82 | 0.824 |
| 83 | 83 | 0.785 |
| 84 | 84 | 0.675 |
| 85 | 85 | 0.423 |
| 86 | 86 | 0.533 |
| 87 | 87 | 0.024 |
| 88 | 88 | 0.73 |
| 89 | 89 | 0.0772 |
| 9 | 9 | 0.177 |
| 90 | 90 | 0.775 |
| 91 | 91 | 0.0614 |
| 92 | 92 | 0.776 |
| 93 | 93 | 0.644 |
| 94 | 94 | 0.364 |
| 95 | 95 | 0.0112 |
| 96 | 96 | 0.515 |
| 97 | 97 | 0.825 |
| 98 | 98 | 0.741 |
| 99 | 99 | 0.3 |
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: CNhs10740
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)
0000039 (germ line cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000586 (germ cell)
DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
2994 (germ cell cancer)
3095 (germ cell and embryonal cancer)
4 (disease)
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
