FF:10444-106F3: Difference between revisions
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{{f5samples | {{f5samples | ||
|id=FF:10444-106F3 | |id=FF:10444-106F3 | ||
|name=glioblastoma cell line:A172 | |name=glioblastoma cell line:A172 | ||
|sample_id=10444 | |sample_id=10444 | ||
|rna_tube_id=106F3 | |rna_tube_id=106F3 | ||
| Line 7: | Line 7: | ||
|rna_position=F3 | |rna_position=F3 | ||
|sample_cell_lot= | |sample_cell_lot= | ||
|sample_cell_catalog=RCB2530 | |sample_cell_catalog=RCB2530 | ||
|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=1.62 | ||
|rna_od260/280=2. | |rna_od260/280=2.11 | ||
|sample_cell_type=glioblast | |sample_cell_type=glioblast | ||
|sample_cell_line=A172 | |sample_cell_line=A172 | ||
|sample_collaboration=Yukio Nakamura (RIKEN BRC) | |sample_collaboration=Yukio Nakamura (RIKEN BRC) | ||
|sample_experimental_condition= | |sample_experimental_condition= | ||
| Line 32: | Line 32: | ||
|rna_concentration=1.48705 | |rna_concentration=1.48705 | ||
|sample_note= | |sample_note= | ||
|profile_hcage= | |profile_hcage=CNhs11248,LSID757,release008,COMPLETED | ||
|profile_cagescan=NCig10059,,, | |profile_cagescan=NCig10059,,, | ||
|profile_srnaseq=,,, | |profile_srnaseq=,,, | ||
| Line 40: | Line 40: | ||
|ancestors_in_disease_facet=DOID:0050686,DOID:14566,DOID:162,DOID:3093,DOID:4 | |ancestors_in_disease_facet=DOID:0050686,DOID:14566,DOID:162,DOID:3093,DOID:4 | ||
|sample_description= | |sample_description= | ||
|fonse_cell_line=FF:0100255 | |fonse_cell_line=FF:0100255 | ||
|fonse_cell_line_closure=FF:0100255 | |fonse_cell_line_closure=FF:0100255 | ||
| Line 67: | Line 66: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|top_motifs= | |||
}} | }} | ||
Revision as of 17:37, 27 February 2012
| Name: | glioblastoma cell line:A172 |
|---|---|
| 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: CNhs11248
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: CNhs11248
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.611 |
| 10 | 10 | 0.277 |
| 100 | 100 | 0.944 |
| 101 | 101 | 0.422 |
| 102 | 102 | 0.484 |
| 103 | 103 | 0.624 |
| 104 | 104 | 0.624 |
| 105 | 105 | 0.771 |
| 106 | 106 | 3.11104e-4 |
| 107 | 107 | 0.38 |
| 108 | 108 | 0.561 |
| 109 | 109 | 0.378 |
| 11 | 11 | 0.321 |
| 110 | 110 | 0.698 |
| 111 | 111 | 0.374 |
| 112 | 112 | 0.0136 |
| 113 | 113 | 0.207 |
| 114 | 114 | 0.209 |
| 115 | 115 | 0.35 |
| 116 | 116 | 0.952 |
| 117 | 117 | 0.929 |
| 118 | 118 | 0.963 |
| 119 | 119 | 0.819 |
| 12 | 12 | 0.274 |
| 120 | 120 | 0.693 |
| 121 | 121 | 0.763 |
| 122 | 122 | 0.809 |
| 123 | 123 | 0.31 |
| 124 | 124 | 0.214 |
| 125 | 125 | 0.96 |
| 126 | 126 | 0.11 |
| 127 | 127 | 0.528 |
| 128 | 128 | 0.00968 |
| 129 | 129 | 0.434 |
| 13 | 13 | 0.0968 |
| 130 | 130 | 0.0775 |
| 131 | 131 | 0.229 |
| 132 | 132 | 0.632 |
| 133 | 133 | 0.402 |
| 134 | 134 | 0.478 |
| 135 | 135 | 0.0744 |
| 136 | 136 | 0.117 |
| 137 | 137 | 0.0176 |
| 138 | 138 | 0.211 |
| 139 | 139 | 0.00206 |
| 14 | 14 | 0.852 |
| 140 | 140 | 0.707 |
| 141 | 141 | 0.549 |
| 142 | 142 | 0.0452 |
| 143 | 143 | 0.445 |
| 144 | 144 | 0.622 |
| 145 | 145 | 0.624 |
| 146 | 146 | 0.671 |
| 147 | 147 | 0.46 |
| 148 | 148 | 0.204 |
| 149 | 149 | 0.257 |
| 15 | 15 | 0.67 |
| 150 | 150 | 0.834 |
| 151 | 151 | 0.534 |
| 152 | 152 | 0.33 |
| 153 | 153 | 0.166 |
| 154 | 154 | 0.456 |
| 155 | 155 | 0.262 |
| 156 | 156 | 0.707 |
| 157 | 157 | 0.757 |
| 158 | 158 | 0.685 |
| 159 | 159 | 0.651 |
| 16 | 16 | 0.172 |
| 160 | 160 | 0.349 |
| 161 | 161 | 0.589 |
| 162 | 162 | 0.892 |
| 163 | 163 | 0.108 |
| 164 | 164 | 0.271 |
| 165 | 165 | 0.55 |
| 166 | 166 | 0.604 |
| 167 | 167 | 0.252 |
| 168 | 168 | 0.552 |
| 169 | 169 | 0.43 |
| 17 | 17 | 0.541 |
| 18 | 18 | 0.353 |
| 19 | 19 | 0.373 |
| 2 | 2 | 0.61 |
| 20 | 20 | 0.827 |
| 21 | 21 | 0.599 |
| 22 | 22 | 0.733 |
| 23 | 23 | 0.37 |
| 24 | 24 | 0.633 |
| 25 | 25 | 0.26 |
| 26 | 26 | 0.442 |
| 27 | 27 | 0.132 |
| 28 | 28 | 0.326 |
| 29 | 29 | 0.331 |
| 3 | 3 | 0.371 |
| 30 | 30 | 0.66 |
| 31 | 31 | 0.962 |
| 32 | 32 | 0.00542 |
| 33 | 33 | 0.448 |
| 34 | 34 | 0.328 |
| 35 | 35 | 0.116 |
| 36 | 36 | 0.0219 |
| 37 | 37 | 0.517 |
| 38 | 38 | 0.593 |
| 39 | 39 | 0.235 |
| 4 | 4 | 0.832 |
| 40 | 40 | 0.128 |
| 41 | 41 | 0.424 |
| 42 | 42 | 0.925 |
| 43 | 43 | 0.109 |
| 44 | 44 | 0.189 |
| 45 | 45 | 0.911 |
| 46 | 46 | 0.239 |
| 47 | 47 | 0.837 |
| 48 | 48 | 0.735 |
| 49 | 49 | 0.0642 |
| 5 | 5 | 0.0718 |
| 50 | 50 | 0.936 |
| 51 | 51 | 0.671 |
| 52 | 52 | 0.107 |
| 53 | 53 | 0.873 |
| 54 | 54 | 0.958 |
| 55 | 55 | 0.798 |
| 56 | 56 | 0.545 |
| 57 | 57 | 0.622 |
| 58 | 58 | 0.0507 |
| 59 | 59 | 0.16 |
| 6 | 6 | 0.229 |
| 60 | 60 | 0.00448 |
| 61 | 61 | 0.806 |
| 62 | 62 | 0.0944 |
| 63 | 63 | 0.229 |
| 64 | 64 | 0.374 |
| 65 | 65 | 0.0847 |
| 66 | 66 | 6.33585e-4 |
| 67 | 67 | 0.807 |
| 68 | 68 | 0.741 |
| 69 | 69 | 0.459 |
| 7 | 7 | 0.0322 |
| 70 | 70 | 0.00331 |
| 71 | 71 | 0.476 |
| 72 | 72 | 0.26 |
| 73 | 73 | 0.314 |
| 74 | 74 | 0.888 |
| 75 | 75 | 0.219 |
| 76 | 76 | 0.0569 |
| 77 | 77 | 0.345 |
| 78 | 78 | 0.466 |
| 79 | 79 | 0.0943 |
| 8 | 8 | 0.799 |
| 80 | 80 | 0.773 |
| 81 | 81 | 0.483 |
| 82 | 82 | 0.381 |
| 83 | 83 | 0.851 |
| 84 | 84 | 0.701 |
| 85 | 85 | 0.00462 |
| 86 | 86 | 0.419 |
| 87 | 87 | 0.711 |
| 88 | 88 | 0.555 |
| 89 | 89 | 0.0335 |
| 9 | 9 | 0.114 |
| 90 | 90 | 0.761 |
| 91 | 91 | 0.0888 |
| 92 | 92 | 0.178 |
| 93 | 93 | 0.754 |
| 94 | 94 | 0.364 |
| 95 | 95 | 0.0995 |
| 96 | 96 | 0.167 |
| 97 | 97 | 0.0954 |
| 98 | 98 | 0.00431 |
| 99 | 99 | 0.583 |
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: CNhs11248
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)
0000030 (glioblast)
0000055 (non-terminally differentiated cell)
0000095 (neuron associated cell)
0000123 (neuron associated cell (sensu Vertebrata))
0000125 (glial cell)
0000126 (macroglial cell)
0000127 (astrocyte)
0000128 (oligodendrocyte)
0000133 (neurectodermal cell)
0000219 (motile cell)
0000221 (ectodermal cell)
0000243 (glial cell (sensu Vertebrata))
0000255 (eukaryotic cell)
0000333 (migratory neural crest cell)
0000339 (glioblast (sensu Vertebrata))
0000548 (animal cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002453 (oligodendrocyte precursor cell)
DOID: Disease
0050686 (organ system cancer)
14566 (disease of cellular proliferation)
162 (cancer)
3093 (nervous system cancer)
4 (disease)
UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
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
