FF:10424-106D1: Difference between revisions
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{{f5samples | {{f5samples | ||
|ancestors_in_anatomy_facet= | |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002106,UBERON:0000945,UBERON:0002100,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000064,UBERON:0000077,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0004457,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0004923,UBERON:0004921,UBERON:0005423,UBERON:0002553,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0009569,UBERON:0005291,UBERON:0010039,UBERON:0002323,UBERON:0005177,UBERON:0000042,UBERON:0003104,UBERON:0004177,UBERON:0005057,UBERON:0005172,UBERON:0000464,UBERON:0004458,UBERON:0001048,UBERON:0000925,UBERON:0004854,UBERON:0009034,UBERON:0006598,UBERON:0003886,UBERON:0002095,UBERON:0004782,UBERON:0004185,UBERON:0005173,UBERON:0003281,UBERON:0002532,UBERON:0001555,UBERON:0005409,UBERON:0002390,UBERON:0002417,UBERON:0007026,UBERON:0001041,UBERON:0002193,UBERON:0000916,UBERON:0002405,UBERON:0003887,UBERON:0009664,UBERON:0009142,UBERON:0003081,UBERON:0002296,UBERON:0005602,UBERON:0001179,UBERON:0006595,UBERON:0006603,UBERON:0004872,UBERON:0006293,UBERON:0003061 | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
|ancestors_in_disease_facet=DOID: | |ancestors_in_disease_facet=DOID:4,DOID:0050686,DOID:162,DOID:2531,DOID:0060058,DOID:14566,DOID:0060083 | ||
|comment= | |comment= | ||
|created_by= | |created_by= | ||
Revision as of 16:13, 8 June 2012
| Name: | splenic lymphoma with villous lymphocytes cell line:SLVL |
|---|---|
| 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
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| Download raw sequence, BAM & CTSS | ||||||||||||
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Relative expression to median (log10)
Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
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: CNhs10741
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: CNhs10741
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.00799 |
| 10 | 10 | 0.0144 |
| 100 | 100 | 0.495 |
| 101 | 101 | 0.195 |
| 102 | 102 | 0.624 |
| 103 | 103 | 0.0876 |
| 104 | 104 | 0.433 |
| 105 | 105 | 0.675 |
| 106 | 106 | 0.957 |
| 107 | 107 | 0.717 |
| 108 | 108 | 0.747 |
| 109 | 109 | 0.0777 |
| 11 | 11 | 0.167 |
| 110 | 110 | 0.114 |
| 111 | 111 | 0.0149 |
| 112 | 112 | 0.104 |
| 113 | 113 | 0.671 |
| 114 | 114 | 0.207 |
| 115 | 115 | 0.623 |
| 116 | 116 | 0.627 |
| 117 | 117 | 0.0188 |
| 118 | 118 | 0.128 |
| 119 | 119 | 0.102 |
| 12 | 12 | 0.852 |
| 120 | 120 | 0.55 |
| 121 | 121 | 0.363 |
| 122 | 122 | 0.371 |
| 123 | 123 | 1.30856e-4 |
| 124 | 124 | 0.0615 |
| 125 | 125 | 0.67 |
| 126 | 126 | 0.117 |
| 127 | 127 | 0.509 |
| 128 | 128 | 0.347 |
| 129 | 129 | 0.39 |
| 13 | 13 | 0.0635 |
| 130 | 130 | 0.995 |
| 131 | 131 | 0.221 |
| 132 | 132 | 0.572 |
| 133 | 133 | 0.587 |
| 134 | 134 | 0.612 |
| 135 | 135 | 0.571 |
| 136 | 136 | 0.281 |
| 137 | 137 | 0.171 |
| 138 | 138 | 0.857 |
| 139 | 139 | 0.218 |
| 14 | 14 | 0.692 |
| 140 | 140 | 0.193 |
| 141 | 141 | 0.0628 |
| 142 | 142 | 0.65 |
| 143 | 143 | 0.304 |
| 144 | 144 | 0.516 |
| 145 | 145 | 0.179 |
| 146 | 146 | 0.426 |
| 147 | 147 | 0.0525 |
| 148 | 148 | 0.115 |
| 149 | 149 | 0.529 |
| 15 | 15 | 0.0523 |
| 150 | 150 | 0.972 |
| 151 | 151 | 0.924 |
| 152 | 152 | 0.0633 |
| 153 | 153 | 0.207 |
| 154 | 154 | 0.905 |
| 155 | 155 | 0.0875 |
| 156 | 156 | 0.959 |
| 157 | 157 | 0.247 |
| 158 | 158 | 0.315 |
| 159 | 159 | 0.337 |
| 16 | 16 | 0.785 |
| 160 | 160 | 0.136 |
| 161 | 161 | 0.00795 |
| 162 | 162 | 0.975 |
| 163 | 163 | 0.761 |
| 164 | 164 | 0.208 |
| 165 | 165 | 0.788 |
| 166 | 166 | 0.265 |
| 167 | 167 | 0.396 |
| 168 | 168 | 0.844 |
| 169 | 169 | 0.722 |
| 17 | 17 | 0.546 |
| 18 | 18 | 0.466 |
| 19 | 19 | 0.949 |
| 2 | 2 | 0.498 |
| 20 | 20 | 0.369 |
| 21 | 21 | 0.161 |
| 22 | 22 | 0.986 |
| 23 | 23 | 0.325 |
| 24 | 24 | 0.174 |
| 25 | 25 | 0.188 |
| 26 | 26 | 0.0839 |
| 27 | 27 | 0.742 |
| 28 | 28 | 0.696 |
| 29 | 29 | 0.0206 |
| 3 | 3 | 0.0885 |
| 30 | 30 | 0.0791 |
| 31 | 31 | 0.765 |
| 32 | 32 | 0.733 |
| 33 | 33 | 0.741 |
| 34 | 34 | 0.632 |
| 35 | 35 | 0.126 |
| 36 | 36 | 0.0175 |
| 37 | 37 | 0.329 |
| 38 | 38 | 0.335 |
| 39 | 39 | 0.547 |
| 4 | 4 | 0.665 |
| 40 | 40 | 0.387 |
| 41 | 41 | 0.653 |
| 42 | 42 | 0.114 |
| 43 | 43 | 0.282 |
| 44 | 44 | 0.167 |
| 45 | 45 | 0.409 |
| 46 | 46 | 0.19 |
| 47 | 47 | 0.0486 |
| 48 | 48 | 0.0903 |
| 49 | 49 | 0.16 |
| 5 | 5 | 0.644 |
| 50 | 50 | 0.952 |
| 51 | 51 | 0.671 |
| 52 | 52 | 0.428 |
| 53 | 53 | 0.35 |
| 54 | 54 | 0.767 |
| 55 | 55 | 0.957 |
| 56 | 56 | 0.75 |
| 57 | 57 | 0.081 |
| 58 | 58 | 0.136 |
| 59 | 59 | 0.662 |
| 6 | 6 | 0.886 |
| 60 | 60 | 0.814 |
| 61 | 61 | 0.0826 |
| 62 | 62 | 0.122 |
| 63 | 63 | 0.548 |
| 64 | 64 | 0.267 |
| 65 | 65 | 0.799 |
| 66 | 66 | 0.1 |
| 67 | 67 | 0.584 |
| 68 | 68 | 0.335 |
| 69 | 69 | 0.794 |
| 7 | 7 | 0.108 |
| 70 | 70 | 0.443 |
| 71 | 71 | 0.0238 |
| 72 | 72 | 0.264 |
| 73 | 73 | 0.96 |
| 74 | 74 | 0.551 |
| 75 | 75 | 0.00566 |
| 76 | 76 | 0.26 |
| 77 | 77 | 0.846 |
| 78 | 78 | 0.319 |
| 79 | 79 | 0.541 |
| 8 | 8 | 0.173 |
| 80 | 80 | 0.376 |
| 81 | 81 | 0.0625 |
| 82 | 82 | 0.867 |
| 83 | 83 | 0.64 |
| 84 | 84 | 0.215 |
| 85 | 85 | 0.877 |
| 86 | 86 | 0.24 |
| 87 | 87 | 0.319 |
| 88 | 88 | 0.794 |
| 89 | 89 | 0.668 |
| 9 | 9 | 0.639 |
| 90 | 90 | 0.0153 |
| 91 | 91 | 0.89 |
| 92 | 92 | 0.838 |
| 93 | 93 | 0.877 |
| 94 | 94 | 0.493 |
| 95 | 95 | 0.0446 |
| 96 | 96 | 0.24 |
| 97 | 97 | 0.271 |
| 98 | 98 | 0.374 |
| 99 | 99 | 0.23 |
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: CNhs10741
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000003 cell line sample
FF:0000210 human sample
FF:0100104 lymphoma cell line sample
UBERON:0002106 spleen
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
4 (disease)
0050686 (organ system cancer)
162 (cancer)
2531 (hematologic cancer)
0060058 (lymphoma)
14566 (disease of cellular proliferation)
0060083 (immune system cancer)
UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002106 (spleen)
0000945 (stomach)
0002100 (trunk)
0000926 (mesoderm)
0000479 (tissue)
0001007 (digestive system)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0004457 (cavity lining)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0005423 (developing anatomical structure)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0009569 (subdivision of trunk)
0005291 (embryonic tissue)
0010039 (food storage organ)
0002323 (body cavity)
0005177 (trunk region element)
0000042 (serous membrane)
0003104 (mesenchyme)
0004177 (hemopoietic organ)
0005057 (immune organ)
0005172 (abdomen element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0001048 (primordium)
0000925 (endoderm)
0004854 (gastrointestinal system mesentery)
0009034 (stomach region)
0006598 (presumptive structure)
0003886 (body cavity precursor)
0002095 (mesentery)
0004782 (gastrointestinal system serosa)
0004185 (endodermal part of digestive tract)
0005173 (abdominal segment element)
0003281 (mesentery of stomach)
0002532 (epiblast (generic))
0001555 (digestive tract)
0005409 (gastrointestinal system)
0002390 (hematopoietic system)
0002417 (abdominal segment of trunk)
0007026 (primitive gut)
0001041 (foregut)
0002193 (hemolymphoid system)
0000916 (abdomen)
0002405 (immune system)
0003887 (intraembryonic coelom)
0009664 (gut mesentery)
0009142 (entire embryonic mesenchyme)
0003081 (lateral plate mesoderm)
0002296 (dorsal mesentery)
0005602 (dorsal mesogastrium)
0001179 (peritoneal cavity)
0006595 (presumptive endoderm)
0006603 (presumptive mesoderm)
0004872 (splanchnic layer of lateral plate mesoderm)
0006293 (spleen primordium)
0003061 (blood island)
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
