FF:10697-109G4: Difference between revisions
From FANTOM5_SSTAR
(Created page with "{{f5samples
|id=FF:10697-109G4
|name=peripheral neuroectodermal tumor cell line:KU-SN, biol_rep1
|sample_id=10697
|rna_tube_id=109G4
|rna_box=109
|rna_position=G4
|samp...") |
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{{f5samples | {{f5samples | ||
|id=FF:10697-109G4 | |id=FF:10697-109G4 | ||
|name=peripheral neuroectodermal tumor cell line:KU-SN | |name=peripheral neuroectodermal tumor cell line:KU-SN | ||
|sample_id=10697 | |sample_id=10697 | ||
|rna_tube_id=109G4 | |rna_tube_id=109G4 | ||
| Line 7: | Line 7: | ||
|rna_position=G4 | |rna_position=G4 | ||
|sample_cell_lot= | |sample_cell_lot= | ||
|sample_cell_catalog=RCB1317 | |sample_cell_catalog=RCB1317 | ||
|sample_company=RIKEN Bioresource centre | |sample_company=RIKEN Bioresource centre | ||
|rna_lot_number= | |rna_lot_number= | ||
| Line 20: | Line 20: | ||
|sample_ethnicity=J | |sample_ethnicity=J | ||
|rna_rin= | |rna_rin= | ||
|rna_od260/230=2. | |rna_od260/230=2.15 | ||
|rna_od260/280=2. | |rna_od260/280=2.05 | ||
|sample_cell_type=unclassifiable | |sample_cell_type=unclassifiable | ||
|sample_cell_line=KU-SN | |sample_cell_line=KU-SN | ||
|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=160. | |rna_weight_ug=160.2915 | ||
|rna_concentration=2.13722 | |rna_concentration=2.13722 | ||
|sample_note= | |sample_note= | ||
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|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:171,DOID:2994,DOID:3095,DOID:4 | |ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:171,DOID:2994,DOID:3095,DOID:4 | ||
|sample_description= | |sample_description= | ||
|fonse_cell_line=FF:10697-109G4 | |fonse_cell_line=FF:10697-109G4 | ||
|fonse_cell_line_closure=FF:10697-109G4 | |fonse_cell_line_closure=FF:10697-109G4 | ||
| Line 67: | Line 66: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|top_motifs= | |||
}} | }} | ||
Revision as of 17:50, 27 February 2012
| Name: | peripheral neuroectodermal tumor cell line:KU-SN |
|---|---|
| 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: CNhs11830
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: CNhs11830
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.412 |
| 10 | 10 | 0.396 |
| 100 | 100 | 0.168 |
| 101 | 101 | 0.921 |
| 102 | 102 | 0.948 |
| 103 | 103 | 0.0492 |
| 104 | 104 | 0.456 |
| 105 | 105 | 0.26 |
| 106 | 106 | 0.00265 |
| 107 | 107 | 0.00518 |
| 108 | 108 | 0.613 |
| 109 | 109 | 0.0867 |
| 11 | 11 | 0.66 |
| 110 | 110 | 0.798 |
| 111 | 111 | 0.762 |
| 112 | 112 | 0.298 |
| 113 | 113 | 0.28 |
| 114 | 114 | 0.301 |
| 115 | 115 | 0.792 |
| 116 | 116 | 0.923 |
| 117 | 117 | 0.808 |
| 118 | 118 | 0.887 |
| 119 | 119 | 0.741 |
| 12 | 12 | 0.118 |
| 120 | 120 | 0.405 |
| 121 | 121 | 0.0359 |
| 122 | 122 | 0.0968 |
| 123 | 123 | 0.0208 |
| 124 | 124 | 0.396 |
| 125 | 125 | 0.829 |
| 126 | 126 | 0.466 |
| 127 | 127 | 0.315 |
| 128 | 128 | 0.105 |
| 129 | 129 | 0.208 |
| 13 | 13 | 0.876 |
| 130 | 130 | 0.934 |
| 131 | 131 | 0.389 |
| 132 | 132 | 0.397 |
| 133 | 133 | 0.882 |
| 134 | 134 | 0.814 |
| 135 | 135 | 0.0332 |
| 136 | 136 | 0.1 |
| 137 | 137 | 0.319 |
| 138 | 138 | 0.898 |
| 139 | 139 | 0.591 |
| 14 | 14 | 0.544 |
| 140 | 140 | 0.575 |
| 141 | 141 | 0.373 |
| 142 | 142 | 0.514 |
| 143 | 143 | 0.364 |
| 144 | 144 | 0.813 |
| 145 | 145 | 0.798 |
| 146 | 146 | 0.746 |
| 147 | 147 | 0.741 |
| 148 | 148 | 0.0972 |
| 149 | 149 | 0.186 |
| 15 | 15 | 0.958 |
| 150 | 150 | 0.334 |
| 151 | 151 | 0.658 |
| 152 | 152 | 0.00175 |
| 153 | 153 | 0.36 |
| 154 | 154 | 0.331 |
| 155 | 155 | 0.949 |
| 156 | 156 | 0.78 |
| 157 | 157 | 0.462 |
| 158 | 158 | 0.318 |
| 159 | 159 | 0.143 |
| 16 | 16 | 0.275 |
| 160 | 160 | 0.535 |
| 161 | 161 | 0.902 |
| 162 | 162 | 0.436 |
| 163 | 163 | 0.696 |
| 164 | 164 | 0.462 |
| 165 | 165 | 0.646 |
| 166 | 166 | 0.832 |
| 167 | 167 | 0.147 |
| 168 | 168 | 0.0988 |
| 169 | 169 | 0.0355 |
| 17 | 17 | 0.499 |
| 18 | 18 | 0.429 |
| 19 | 19 | 0.123 |
| 2 | 2 | 0.0888 |
| 20 | 20 | 0.48 |
| 21 | 21 | 0.95 |
| 22 | 22 | 0.0582 |
| 23 | 23 | 0.0657 |
| 24 | 24 | 0.521 |
| 25 | 25 | 0.613 |
| 26 | 26 | 0.356 |
| 27 | 27 | 0.68 |
| 28 | 28 | 0.933 |
| 29 | 29 | 0.564 |
| 3 | 3 | 0.837 |
| 30 | 30 | 0.0587 |
| 31 | 31 | 0.342 |
| 32 | 32 | 0.015 |
| 33 | 33 | 0.899 |
| 34 | 34 | 0.143 |
| 35 | 35 | 0.351 |
| 36 | 36 | 0.134 |
| 37 | 37 | 0.548 |
| 38 | 38 | 0.513 |
| 39 | 39 | 0.267 |
| 4 | 4 | 0.788 |
| 40 | 40 | 0.34 |
| 41 | 41 | 0.066 |
| 42 | 42 | 0.285 |
| 43 | 43 | 0.74 |
| 44 | 44 | 0.831 |
| 45 | 45 | 0.131 |
| 46 | 46 | 0.825 |
| 47 | 47 | 0.568 |
| 48 | 48 | 0.987 |
| 49 | 49 | 0.912 |
| 5 | 5 | 0.582 |
| 50 | 50 | 0.297 |
| 51 | 51 | 0.846 |
| 52 | 52 | 0.129 |
| 53 | 53 | 0.799 |
| 54 | 54 | 0.32 |
| 55 | 55 | 0.572 |
| 56 | 56 | 0.996 |
| 57 | 57 | 0.146 |
| 58 | 58 | 0.666 |
| 59 | 59 | 0.0549 |
| 6 | 6 | 0.673 |
| 60 | 60 | 0.141 |
| 61 | 61 | 0.915 |
| 62 | 62 | 0.475 |
| 63 | 63 | 0.71 |
| 64 | 64 | 0.705 |
| 65 | 65 | 0.214 |
| 66 | 66 | 0.414 |
| 67 | 67 | 0.0328 |
| 68 | 68 | 0.526 |
| 69 | 69 | 0.289 |
| 7 | 7 | 0.702 |
| 70 | 70 | 0.529 |
| 71 | 71 | 0.934 |
| 72 | 72 | 0.872 |
| 73 | 73 | 0.00684 |
| 74 | 74 | 0.303 |
| 75 | 75 | 0.538 |
| 76 | 76 | 0.429 |
| 77 | 77 | 0.0528 |
| 78 | 78 | 0.334 |
| 79 | 79 | 0.467 |
| 8 | 8 | 0.973 |
| 80 | 80 | 0.0103 |
| 81 | 81 | 0.553 |
| 82 | 82 | 0.514 |
| 83 | 83 | 0.627 |
| 84 | 84 | 0.732 |
| 85 | 85 | 0.0548 |
| 86 | 86 | 0.855 |
| 87 | 87 | 0.0742 |
| 88 | 88 | 0.25 |
| 89 | 89 | 0.229 |
| 9 | 9 | 0.119 |
| 90 | 90 | 0.198 |
| 91 | 91 | 0.155 |
| 92 | 92 | 0.572 |
| 93 | 93 | 0.153 |
| 94 | 94 | 0.892 |
| 95 | 95 | 0.882 |
| 96 | 96 | 0.672 |
| 97 | 97 | 0.811 |
| 98 | 98 | 0.31 |
| 99 | 99 | 0.61 |
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: CNhs11830
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
DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
171 (neuroectodermal tumor)
2994 (germ cell cancer)
3095 (germ cell and embryonal cancer)
4 (disease)
UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0005423 (developing anatomical structure)
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
