FF:10477-106I9: Difference between revisions
From FANTOM5_SSTAR
(Created page with "{{f5samples
|id=FF:10477-106I9
|name=rhabdomyosarcoma cell line:RMS-YM, biol_rep1
|sample_id=10477
|rna_tube_id=106I9
|rna_box=106
|rna_position=I9
|sample_cell_lot=
|...") |
No edit summary |
||
| Line 1: | Line 1: | ||
{{f5samples | {{f5samples | ||
|id=FF:10477-106I9 | |id=FF:10477-106I9 | ||
|name=rhabdomyosarcoma cell line:RMS-YM | |name=rhabdomyosarcoma cell line:RMS-YM | ||
|sample_id=10477 | |sample_id=10477 | ||
|rna_tube_id=106I9 | |rna_tube_id=106I9 | ||
| Line 7: | Line 7: | ||
|rna_position=I9 | |rna_position=I9 | ||
|sample_cell_lot= | |sample_cell_lot= | ||
|sample_cell_catalog=RCB1695 | |sample_cell_catalog=RCB1695 | ||
|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=1. | |rna_od260/230=1.69 | ||
|rna_od260/280=1. | |rna_od260/280=1.96 | ||
|sample_cell_type=skeletal muscle cell | |sample_cell_type=skeletal muscle cell | ||
|sample_cell_line=RMS-YM | |sample_cell_line=RMS-YM | ||
|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=82. | |rna_weight_ug=82.474 | ||
|rna_concentration=3.29896 | |rna_concentration=3.29896 | ||
|sample_note= | |sample_note= | ||
| Line 40: | Line 40: | ||
|ancestors_in_disease_facet=DOID:0050687,DOID:1115,DOID:14566,DOID:162,DOID:4 | |ancestors_in_disease_facet=DOID:0050687,DOID:1115,DOID:14566,DOID:162,DOID:4 | ||
|sample_description= | |sample_description= | ||
|fonse_cell_line=FF:0100400 | |fonse_cell_line=FF:0100400 | ||
|fonse_cell_line_closure=FF:0100400 | |fonse_cell_line_closure=FF:0100400 | ||
| Line 67: | Line 66: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|top_motifs= | |||
}} | }} | ||
Revision as of 17:51, 27 February 2012
| Name: | rhabdomyosarcoma cell line:RMS-YM |
|---|---|
| Species: | Human (Homo sapiens) |
| Library ID: | {{{library_id}}} |
| Sample type: | {{{sample_category}}} |
| Genomic View: | UCSC |
| CAGEd-oPOSSUM: | link |
| Additional information | ||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample information
RNA information
|
| Download raw sequence, BAM & CTSS | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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: CNhs11269
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: CNhs11269
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.369 |
| 10 | 10 | 0.44 |
| 100 | 100 | 0.753 |
| 101 | 101 | 0.969 |
| 102 | 102 | 0.82 |
| 103 | 103 | 0.0726 |
| 104 | 104 | 0.844 |
| 105 | 105 | 0.935 |
| 106 | 106 | 0.00439 |
| 107 | 107 | 0.692 |
| 108 | 108 | 0.829 |
| 109 | 109 | 0.0181 |
| 11 | 11 | 0.0628 |
| 110 | 110 | 0.934 |
| 111 | 111 | 0.557 |
| 112 | 112 | 3.74919e-4 |
| 113 | 113 | 0.00322 |
| 114 | 114 | 0.0131 |
| 115 | 115 | 0.276 |
| 116 | 116 | 0.781 |
| 117 | 117 | 0.829 |
| 118 | 118 | 0.253 |
| 119 | 119 | 0.219 |
| 12 | 12 | 0.297 |
| 120 | 120 | 0.864 |
| 121 | 121 | 0.569 |
| 122 | 122 | 0.171 |
| 123 | 123 | 0.611 |
| 124 | 124 | 0.534 |
| 125 | 125 | 0.317 |
| 126 | 126 | 0.203 |
| 127 | 127 | 0.32 |
| 128 | 128 | 0.139 |
| 129 | 129 | 0.845 |
| 13 | 13 | 0.776 |
| 130 | 130 | 0.0248 |
| 131 | 131 | 0.959 |
| 132 | 132 | 0.945 |
| 133 | 133 | 0.611 |
| 134 | 134 | 0.562 |
| 135 | 135 | 0.142 |
| 136 | 136 | 0.262 |
| 137 | 137 | 0.0571 |
| 138 | 138 | 0.589 |
| 139 | 139 | 0.0578 |
| 14 | 14 | 0.163 |
| 140 | 140 | 0.408 |
| 141 | 141 | 0.746 |
| 142 | 142 | 0.233 |
| 143 | 143 | 0.0456 |
| 144 | 144 | 0.666 |
| 145 | 145 | 0.923 |
| 146 | 146 | 0.707 |
| 147 | 147 | 0.437 |
| 148 | 148 | 0.115 |
| 149 | 149 | 0.0579 |
| 15 | 15 | 0.204 |
| 150 | 150 | 0.513 |
| 151 | 151 | 0.528 |
| 152 | 152 | 0.00863 |
| 153 | 153 | 0.98 |
| 154 | 154 | 0.663 |
| 155 | 155 | 0.806 |
| 156 | 156 | 0.533 |
| 157 | 157 | 0.492 |
| 158 | 158 | 0.852 |
| 159 | 159 | 0.233 |
| 16 | 16 | 0.105 |
| 160 | 160 | 0.75 |
| 161 | 161 | 0.825 |
| 162 | 162 | 0.571 |
| 163 | 163 | 0.564 |
| 164 | 164 | 0.164 |
| 165 | 165 | 0.323 |
| 166 | 166 | 0.889 |
| 167 | 167 | 0.475 |
| 168 | 168 | 0.632 |
| 169 | 169 | 0.052 |
| 17 | 17 | 0.503 |
| 18 | 18 | 0.623 |
| 19 | 19 | 0.363 |
| 2 | 2 | 0.186 |
| 20 | 20 | 0.981 |
| 21 | 21 | 0.909 |
| 22 | 22 | 0.167 |
| 23 | 23 | 0.0131 |
| 24 | 24 | 0.512 |
| 25 | 25 | 0.579 |
| 26 | 26 | 0.473 |
| 27 | 27 | 0.0377 |
| 28 | 28 | 0.949 |
| 29 | 29 | 0.455 |
| 3 | 3 | 0.418 |
| 30 | 30 | 0.364 |
| 31 | 31 | 0.55 |
| 32 | 32 | 0.0198 |
| 33 | 33 | 0.705 |
| 34 | 34 | 0.604 |
| 35 | 35 | 0.697 |
| 36 | 36 | 0.542 |
| 37 | 37 | 0.0745 |
| 38 | 38 | 0.275 |
| 39 | 39 | 0.726 |
| 4 | 4 | 0.381 |
| 40 | 40 | 0.14 |
| 41 | 41 | 0.337 |
| 42 | 42 | 0.984 |
| 43 | 43 | 0.249 |
| 44 | 44 | 0.0611 |
| 45 | 45 | 0.291 |
| 46 | 46 | 0.103 |
| 47 | 47 | 0.335 |
| 48 | 48 | 0.34 |
| 49 | 49 | 0.81 |
| 5 | 5 | 0.202 |
| 50 | 50 | 0.887 |
| 51 | 51 | 0.948 |
| 52 | 52 | 0.148 |
| 53 | 53 | 0.622 |
| 54 | 54 | 0.98 |
| 55 | 55 | 0.299 |
| 56 | 56 | 0.97 |
| 57 | 57 | 0.623 |
| 58 | 58 | 0.345 |
| 59 | 59 | 0.0199 |
| 6 | 6 | 0.555 |
| 60 | 60 | 0.0375 |
| 61 | 61 | 1 |
| 62 | 62 | 0.278 |
| 63 | 63 | 0.337 |
| 64 | 64 | 0.247 |
| 65 | 65 | 0.0424 |
| 66 | 66 | 0.0109 |
| 67 | 67 | 0.589 |
| 68 | 68 | 0.702 |
| 69 | 69 | 0.251 |
| 7 | 7 | 0.919 |
| 70 | 70 | 0.0304 |
| 71 | 71 | 0.148 |
| 72 | 72 | 0.038 |
| 73 | 73 | 0.00721 |
| 74 | 74 | 0.0994 |
| 75 | 75 | 0.477 |
| 76 | 76 | 0.998 |
| 77 | 77 | 0.0487 |
| 78 | 78 | 0.393 |
| 79 | 79 | 0.593 |
| 8 | 8 | 0.355 |
| 80 | 80 | 0.191 |
| 81 | 81 | 0.38 |
| 82 | 82 | 0.00253 |
| 83 | 83 | 0.357 |
| 84 | 84 | 0.491 |
| 85 | 85 | 0.00309 |
| 86 | 86 | 0.274 |
| 87 | 87 | 0.0149 |
| 88 | 88 | 0.595 |
| 89 | 89 | 0.0443 |
| 9 | 9 | 0.186 |
| 90 | 90 | 0.406 |
| 91 | 91 | 0.189 |
| 92 | 92 | 0.153 |
| 93 | 93 | 0.577 |
| 94 | 94 | 0.518 |
| 95 | 95 | 0.0218 |
| 96 | 96 | 0.203 |
| 97 | 97 | 0.917 |
| 98 | 98 | 0.303 |
| 99 | 99 | 0.779 |
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: CNhs11269
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)
1115 (sarcoma)
14566 (disease of cellular proliferation)
162 (cancer)
4 (disease)
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
