FF:11594-120H1: Difference between revisions
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{{f5samples | {{f5samples | ||
|ancestors_in_anatomy_facet=UBERON: | |ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002113,UBERON:0002100,UBERON:0000483,UBERON:0001851,UBERON:0002384,UBERON:0000926,UBERON:0000080,UBERON:0000479,UBERON:0000058,UBERON:0000064,UBERON:0000466,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000025,UBERON:0006555,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0003914,UBERON:0005103,UBERON:0000083,UBERON:0002050,UBERON:0005423,UBERON:0002553,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0003103,UBERON:0009569,UBERON:0005291,UBERON:0004211,UBERON:0009773,UBERON:0000489,UBERON:0000353,UBERON:0005177,UBERON:0003891,UBERON:0003104,UBERON:0005172,UBERON:0000464,UBERON:0003567,UBERON:0009201,UBERON:0005256,UBERON:0003918,UBERON:0003838,UBERON:0003586,UBERON:0006598,UBERON:0003886,UBERON:0004819,UBERON:0005173,UBERON:0005169,UBERON:0001231,UBERON:0004810,UBERON:0002532,UBERON:0006553,UBERON:0002321,UBERON:0000074,UBERON:0001225,UBERON:0001285,UBERON:0005215,UBERON:0001229,UBERON:0002303,UBERON:0001008,UBERON:0003074,UBERON:0002417,UBERON:0008987,UBERON:0007684,UBERON:0000916,UBERON:0003887,UBERON:0002319,UBERON:0002120,UBERON:0009142,UBERON:0003081,UBERON:0003064,UBERON:0001230,UBERON:0004875,UBERON:0003220,UBERON:0005749,UBERON:0006603,UBERON:0004876,UBERON:0004199,UBERON:0004208,UBERON:0005095,UBERON:0005721,UBERON:0005754,UBERON:0003060,UBERON:0004209,UBERON:0004198,UBERON:0007687,UBERON:0007297 | ||
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL: | |ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000723,CL:0000048,CL:0000988,CL:0000548,CL:0000034,CL:0000012,CL:0002320,CL:0000063,CL:0000066,CL:0002371,CL:0000219,CL:0000183,CL:0000630,CL:0000004,CL:0000134,CL:0000255,CL:0000669,CL:0000650,CL:1000618,CL:1001318,CL:1000497,CL:0002518,CL:0002681,CL:1000507,CL:0002584,CL:1000494,CL:1000612,CL:1000449,CL:1000746,CL:0002173,CL:1000500 | ||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
|comment=Previously: Renal Glomerular Endothelial Cells, donor2 | |comment=Previously: Renal Glomerular Endothelial Cells, donor2 | ||
Revision as of 17:13, 8 June 2012
| Name: | Renal Glomerular Endothelial Cells, donor2 |
|---|---|
| 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: CNhs12086
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: CNhs12086
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.413 |
| 10 | 10 | 0.849 |
| 100 | 100 | 0.497 |
| 101 | 101 | 0.174 |
| 102 | 102 | 0.577 |
| 103 | 103 | 0.628 |
| 104 | 104 | 0.994 |
| 105 | 105 | 0.811 |
| 106 | 106 | 0.226 |
| 107 | 107 | 0.0438 |
| 108 | 108 | 0.295 |
| 109 | 109 | 0.092 |
| 11 | 11 | 0.0254 |
| 110 | 110 | 0.0192 |
| 111 | 111 | 0.275 |
| 112 | 112 | 0.259 |
| 113 | 113 | 0.829 |
| 114 | 114 | 0.333 |
| 115 | 115 | 0.564 |
| 116 | 116 | 0.447 |
| 117 | 117 | 0.52 |
| 118 | 118 | 0.275 |
| 119 | 119 | 0.31 |
| 12 | 12 | 0.319 |
| 120 | 120 | 0.0215 |
| 121 | 121 | 0.761 |
| 122 | 122 | 0.994 |
| 123 | 123 | 0.0704 |
| 124 | 124 | 0.185 |
| 125 | 125 | 0.833 |
| 126 | 126 | 0.675 |
| 127 | 127 | 0.984 |
| 128 | 128 | 0.45 |
| 129 | 129 | 0.0691 |
| 13 | 13 | 0.247 |
| 130 | 130 | 0.991 |
| 131 | 131 | 0.0956 |
| 132 | 132 | 0.108 |
| 133 | 133 | 0.498 |
| 134 | 134 | 0.867 |
| 135 | 135 | 0.0567 |
| 136 | 136 | 0.101 |
| 137 | 137 | 0.447 |
| 138 | 138 | 0.992 |
| 139 | 139 | 0.793 |
| 14 | 14 | 0.981 |
| 140 | 140 | 0.3 |
| 141 | 141 | 0.518 |
| 142 | 142 | 0.908 |
| 143 | 143 | 0.0872 |
| 144 | 144 | 0.407 |
| 145 | 145 | 0.291 |
| 146 | 146 | 0.35 |
| 147 | 147 | 0.163 |
| 148 | 148 | 0.328 |
| 149 | 149 | 0.036 |
| 15 | 15 | 0.676 |
| 150 | 150 | 0.233 |
| 151 | 151 | 0.661 |
| 152 | 152 | 0.0631 |
| 153 | 153 | 0.066 |
| 154 | 154 | 0.321 |
| 155 | 155 | 0.836 |
| 156 | 156 | 0.194 |
| 157 | 157 | 0.508 |
| 158 | 158 | 0.453 |
| 159 | 159 | 0.327 |
| 16 | 16 | 0.65 |
| 160 | 160 | 0.00593 |
| 161 | 161 | 0.701 |
| 162 | 162 | 0.248 |
| 163 | 163 | 0.701 |
| 164 | 164 | 0.419 |
| 165 | 165 | 0.369 |
| 166 | 166 | 0.0765 |
| 167 | 167 | 0.202 |
| 168 | 168 | 0.343 |
| 169 | 169 | 0.0334 |
| 17 | 17 | 0.112 |
| 18 | 18 | 0.853 |
| 19 | 19 | 0.161 |
| 2 | 2 | 0.351 |
| 20 | 20 | 0.611 |
| 21 | 21 | 0.663 |
| 22 | 22 | 0.097 |
| 23 | 23 | 0.23 |
| 24 | 24 | 0.708 |
| 25 | 25 | 0.72 |
| 26 | 26 | 0.168 |
| 27 | 27 | 0.114 |
| 28 | 28 | 0.254 |
| 29 | 29 | 0.502 |
| 3 | 3 | 0.567 |
| 30 | 30 | 0.826 |
| 31 | 31 | 0.911 |
| 32 | 32 | 0.866 |
| 33 | 33 | 0.348 |
| 34 | 34 | 0.0424 |
| 35 | 35 | 0.873 |
| 36 | 36 | 0.0768 |
| 37 | 37 | 0.166 |
| 38 | 38 | 0.237 |
| 39 | 39 | 0.284 |
| 4 | 4 | 0.927 |
| 40 | 40 | 0.00422 |
| 41 | 41 | 0.0456 |
| 42 | 42 | 0.668 |
| 43 | 43 | 0.417 |
| 44 | 44 | 0.281 |
| 45 | 45 | 0.274 |
| 46 | 46 | 0.162 |
| 47 | 47 | 0.228 |
| 48 | 48 | 0.0374 |
| 49 | 49 | 0.796 |
| 5 | 5 | 0.967 |
| 50 | 50 | 0.452 |
| 51 | 51 | 0.37 |
| 52 | 52 | 0.696 |
| 53 | 53 | 0.779 |
| 54 | 54 | 0.536 |
| 55 | 55 | 0.759 |
| 56 | 56 | 0.478 |
| 57 | 57 | 0.31 |
| 58 | 58 | 0.412 |
| 59 | 59 | 0.0236 |
| 6 | 6 | 0.458 |
| 60 | 60 | 0.785 |
| 61 | 61 | 0.562 |
| 62 | 62 | 0.859 |
| 63 | 63 | 0.261 |
| 64 | 64 | 0.161 |
| 65 | 65 | 0.103 |
| 66 | 66 | 0.526 |
| 67 | 67 | 0.373 |
| 68 | 68 | 0.0802 |
| 69 | 69 | 0.343 |
| 7 | 7 | 0.724 |
| 70 | 70 | 0.681 |
| 71 | 71 | 0.336 |
| 72 | 72 | 0.454 |
| 73 | 73 | 0.00962 |
| 74 | 74 | 0.478 |
| 75 | 75 | 0.157 |
| 76 | 76 | 0.434 |
| 77 | 77 | 0.0311 |
| 78 | 78 | 0.551 |
| 79 | 79 | 0.101 |
| 8 | 8 | 0.0159 |
| 80 | 80 | 0.764 |
| 81 | 81 | 0.596 |
| 82 | 82 | 0.609 |
| 83 | 83 | 0.949 |
| 84 | 84 | 0.112 |
| 85 | 85 | 0.371 |
| 86 | 86 | 0.95 |
| 87 | 87 | 0.096 |
| 88 | 88 | 0.757 |
| 89 | 89 | 0.157 |
| 9 | 9 | 0.311 |
| 90 | 90 | 0.191 |
| 91 | 91 | 0.38 |
| 92 | 92 | 0.441 |
| 93 | 93 | 0.292 |
| 94 | 94 | 0.832 |
| 95 | 95 | 0.0139 |
| 96 | 96 | 0.521 |
| 97 | 97 | 0.977 |
| 98 | 98 | 0.279 |
| 99 | 99 | 0.00786 |
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: CNhs12086
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000002 in vivo cell sample
FF:0000154 human renal mesangial cell sample
FF:0000210 human 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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000034 (stem cell)
0002320 (connective tissue cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000219 (motile cell)
0000183 (contractile cell)
0000630 (supportive cell)
0000134 (mesenchymal cell)
0000255 (eukaryotic cell)
0000669 (pericyte cell)
0000650 (mesangial cell)
1000618 (juxtaglomerular complex cell)
1001318 (renal interstitial pericyte)
1000497 (kidney cell)
0002518 (kidney epithelial cell)
0002681 (kidney cortical cell)
1000507 (kidney tubule cell)
0002584 (renal cortical epithelial cell)
1000494 (nephron tubule epithelial cell)
1000612 (kidney corpuscule cell)
1000449 (epithelial cell of nephron)
1000746 (glomerular cell)
0002173 (extraglomerular mesangial cell)
1000500 (kidney interstitial cell)
UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0002113 (kidney)
0002100 (trunk)
0000483 (epithelium)
0001851 (cortex)
0002384 (connective tissue)
0000926 (mesoderm)
0000080 (mesonephros)
0000479 (tissue)
0000058 (duct)
0000064 (organ part)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000025 (tube)
0006555 (excretory tube)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0003914 (epithelial tube)
0005103 (mesonephric epithelium)
0000083 (mesonephric tubule)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0000119 (cell layer)
0003103 (compound organ)
0009569 (subdivision of trunk)
0005291 (embryonic tissue)
0004211 (nephron epithelium)
0009773 (renal tubule)
0000489 (cavitated compound organ)
0000353 (parenchyma)
0005177 (trunk region element)
0003891 (stroma)
0003104 (mesenchyme)
0005172 (abdomen element)
0000464 (anatomical space)
0003567 (abdomen connective tissue)
0009201 (nephric duct)
0005256 (trunk mesenchyme)
0003918 (kidney mesenchyme)
0003838 (abdominal segment connective tissue)
0003586 (trunk connective tissue)
0006598 (presumptive structure)
0003886 (body cavity precursor)
0004819 (kidney epithelium)
0005173 (abdominal segment element)
0005169 (interstitial tissue)
0001231 (nephron tubule)
0004810 (nephron tubule epithelium)
0002532 (epiblast (generic))
0006553 (renal duct)
0002321 (extraglomerular mesangium)
0000074 (renal glomerulus)
0001225 (cortex of kidney)
0001285 (nephron)
0005215 (kidney interstitium)
0001229 (renal corpuscle)
0002303 (juxtaglomerular apparatus)
0001008 (renal system)
0003074 (mesonephric duct)
0002417 (abdominal segment of trunk)
0008987 (renal parenchyma)
0007684 (uriniferous tubule)
0000916 (abdomen)
0003887 (intraembryonic coelom)
0002319 (mesangium)
0002120 (pronephros)
0009142 (entire embryonic mesenchyme)
0003081 (lateral plate mesoderm)
0003064 (intermediate mesoderm)
0001230 (glomerular capsule)
0004875 (nephrogenic cord)
0003220 (metanephric mesenchyme)
0005749 (glomerular tuft)
0006603 (presumptive mesoderm)
0004876 (urogenital ridge)
0004199 (S-shaped body)
0004208 (nephrogenic mesenchyme)
0005095 (kidney rudiment)
0005721 (pronephric mesoderm)
0005754 (rostral part of nephrogenic cord)
0003060 (pronephric duct)
0004209 (renal vesicle)
0004198 (comma-shaped body)
0007687 (kidney field)
0007297 (presumptive pronephric mesoderm)
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
