FF:10778-110G4: Difference between revisions
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Revision as of 14:00, 4 April 2012
| Name: | hepatic mesenchymal tumor cell line:LI90 |
|---|---|
| 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: CNhs11868
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: CNhs11868
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.797 |
| 10 | 10 | 0.69 |
| 100 | 100 | 0.499 |
| 101 | 101 | 0.631 |
| 102 | 102 | 0.133 |
| 103 | 103 | 0.449 |
| 104 | 104 | 0.564 |
| 105 | 105 | 0.28 |
| 106 | 106 | 0.00377 |
| 107 | 107 | 0.00916 |
| 108 | 108 | 0.423 |
| 109 | 109 | 0.813 |
| 11 | 11 | 0.575 |
| 110 | 110 | 0.468 |
| 111 | 111 | 0.604 |
| 112 | 112 | 0.429 |
| 113 | 113 | 0.553 |
| 114 | 114 | 0.214 |
| 115 | 115 | 0.239 |
| 116 | 116 | 0.0206 |
| 117 | 117 | 0.261 |
| 118 | 118 | 0.757 |
| 119 | 119 | 0.0893 |
| 12 | 12 | 0.138 |
| 120 | 120 | 0.402 |
| 121 | 121 | 0.443 |
| 122 | 122 | 0.142 |
| 123 | 123 | 0.941 |
| 124 | 124 | 0.655 |
| 125 | 125 | 0.875 |
| 126 | 126 | 0.632 |
| 127 | 127 | 0.938 |
| 128 | 128 | 0.0527 |
| 129 | 129 | 0.352 |
| 13 | 13 | 0.0822 |
| 130 | 130 | 0.508 |
| 131 | 131 | 0.188 |
| 132 | 132 | 0.517 |
| 133 | 133 | 0.932 |
| 134 | 134 | 0.637 |
| 135 | 135 | 0.429 |
| 136 | 136 | 0.379 |
| 137 | 137 | 0.473 |
| 138 | 138 | 0.736 |
| 139 | 139 | 0.034 |
| 14 | 14 | 0.311 |
| 140 | 140 | 0.476 |
| 141 | 141 | 0.566 |
| 142 | 142 | 0.712 |
| 143 | 143 | 0.75 |
| 144 | 144 | 0.509 |
| 145 | 145 | 0.812 |
| 146 | 146 | 0.269 |
| 147 | 147 | 0.135 |
| 148 | 148 | 0.938 |
| 149 | 149 | 0.00502 |
| 15 | 15 | 0.692 |
| 150 | 150 | 0.0609 |
| 151 | 151 | 0.468 |
| 152 | 152 | 0.0338 |
| 153 | 153 | 0.63 |
| 154 | 154 | 0.354 |
| 155 | 155 | 0.0467 |
| 156 | 156 | 0.415 |
| 157 | 157 | 0.532 |
| 158 | 158 | 0.13 |
| 159 | 159 | 0.461 |
| 16 | 16 | 0.0937 |
| 160 | 160 | 0.655 |
| 161 | 161 | 0.978 |
| 162 | 162 | 0.864 |
| 163 | 163 | 0.551 |
| 164 | 164 | 0.0466 |
| 165 | 165 | 0.591 |
| 166 | 166 | 0.037 |
| 167 | 167 | 0.911 |
| 168 | 168 | 0.482 |
| 169 | 169 | 0.405 |
| 17 | 17 | 0.271 |
| 18 | 18 | 0.24 |
| 19 | 19 | 0.0761 |
| 2 | 2 | 0.161 |
| 20 | 20 | 0.403 |
| 21 | 21 | 0.421 |
| 22 | 22 | 0.637 |
| 23 | 23 | 0.005 |
| 24 | 24 | 0.316 |
| 25 | 25 | 0.139 |
| 26 | 26 | 0.498 |
| 27 | 27 | 0.974 |
| 28 | 28 | 0.416 |
| 29 | 29 | 0.465 |
| 3 | 3 | 0.545 |
| 30 | 30 | 0.724 |
| 31 | 31 | 0.392 |
| 32 | 32 | 2.84197e-14 |
| 33 | 33 | 0.183 |
| 34 | 34 | 0.674 |
| 35 | 35 | 0.921 |
| 36 | 36 | 0.0814 |
| 37 | 37 | 0.781 |
| 38 | 38 | 0.81 |
| 39 | 39 | 0.523 |
| 4 | 4 | 0.679 |
| 40 | 40 | 0.181 |
| 41 | 41 | 0.955 |
| 42 | 42 | 0.64 |
| 43 | 43 | 0.479 |
| 44 | 44 | 0.704 |
| 45 | 45 | 0.937 |
| 46 | 46 | 0.183 |
| 47 | 47 | 0.672 |
| 48 | 48 | 0.672 |
| 49 | 49 | 0.426 |
| 5 | 5 | 0.172 |
| 50 | 50 | 0.636 |
| 51 | 51 | 0.94 |
| 52 | 52 | 0.263 |
| 53 | 53 | 0.858 |
| 54 | 54 | 0.401 |
| 55 | 55 | 0.168 |
| 56 | 56 | 0.853 |
| 57 | 57 | 0.226 |
| 58 | 58 | 0.538 |
| 59 | 59 | 0.389 |
| 6 | 6 | 0.462 |
| 60 | 60 | 0.225 |
| 61 | 61 | 0.399 |
| 62 | 62 | 0.617 |
| 63 | 63 | 0.19 |
| 64 | 64 | 0.938 |
| 65 | 65 | 0.323 |
| 66 | 66 | 0.172 |
| 67 | 67 | 0.191 |
| 68 | 68 | 0.794 |
| 69 | 69 | 0.619 |
| 7 | 7 | 0.277 |
| 70 | 70 | 0.263 |
| 71 | 71 | 0.919 |
| 72 | 72 | 0.435 |
| 73 | 73 | 0.0756 |
| 74 | 74 | 0.0839 |
| 75 | 75 | 0.249 |
| 76 | 76 | 0.991 |
| 77 | 77 | 0.0684 |
| 78 | 78 | 0.988 |
| 79 | 79 | 0.0015 |
| 8 | 8 | 0.29 |
| 80 | 80 | 0.204 |
| 81 | 81 | 0.854 |
| 82 | 82 | 0.0927 |
| 83 | 83 | 0.592 |
| 84 | 84 | 0.789 |
| 85 | 85 | 9.40643e-4 |
| 86 | 86 | 0.916 |
| 87 | 87 | 0.832 |
| 88 | 88 | 0.608 |
| 89 | 89 | 0.352 |
| 9 | 9 | 0.778 |
| 90 | 90 | 0.452 |
| 91 | 91 | 0.538 |
| 92 | 92 | 0.0146 |
| 93 | 93 | 0.915 |
| 94 | 94 | 0.197 |
| 95 | 95 | 0.737 |
| 96 | 96 | 0.684 |
| 97 | 97 | 0.26 |
| 98 | 98 | 0.246 |
| 99 | 99 | 0.0192 |
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: CNhs11868
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
DOID:3350 mesenchymal cell neoplasm
DOID:3571 liver cancer
EFO:0002091 biological replicate
FF:0000003 cell line sample
FF:0000210 human sample
FF:0103519 LI90 cell sample
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)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000040 (monoblast)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000235 (macrophage)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000559 (promonocyte)
0000566 (angioblastic mesenchymal cell)
0000576 (monocyte)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000864 (tissue-resident macrophage)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002194 (monopoietic cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
DOID: Disease
3118 (hepatobiliary disease)
4 (disease)
409 (liver disease)
7 (disease of anatomical entity)
77 (gastrointestinal system disease)
UBERON: Anatomy
0000015 (anatomical boundary)
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000119 (cell layer)
0000353 (parenchyma)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001009 (circulatory system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001280 (liver parenchyma)
0001281 (hepatic sinusoid)
0001434 (skeletal system)
0001474 (bone element)
0001555 (digestive tract)
0001981 (blood vessel)
0002049 (vasculature)
0002050 (embryonic structure)
0002100 (trunk)
0002107 (liver)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002330 (exocrine system)
0002365 (exocrine gland)
0002368 (endocrine gland)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002530 (gland)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003104 (mesenchyme)
0003497 (abdomen blood vessel)
0003513 (trunk blood vessel)
0003835 (abdominal segment blood vessel)
0003894 (liver primordium)
0003909 (sinusoid)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004647 (liver lobule)
0004765 (skeletal element)
0004872 (splanchnic layer of lateral plate mesoderm)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006235 (foregut-midgut junction)
0006925 (digestive gland)
0006965 (vascular cord)
0007026 (primitive gut)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)
0008835 (hepatic diverticulum)
0008836 (liver bud)
0009142 (entire embryonic mesenchyme)
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
