FF:10813-111B3: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
| Line 41: | Line 41: | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|has_quality= | |has_quality= | ||
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/normal%2520embryonic%2520palatal%2520mesenchymal%2520cell%2520line%253aHEPM.CNhs11894.10813-111B3.hg19.nobarcode.bam | |||
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/normal%2520embryonic%2520palatal%2520mesenchymal%2520cell%2520line%253aHEPM.CNhs11894.10813-111B3.hg19.ctss.bed.gz | |||
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/normal%2520embryonic%2520palatal%2520mesenchymal%2520cell%2520line%253aHEPM.CNhs11894.10813-111B3.hg19.nobarcode.rdna.fa.gz | |||
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/normal%2520embryonic%2520palatal%2520mesenchymal%2520cell%2520line%253aHEPM.CNhs11894.10813-111B3.hg38.nobarcode.bam | |||
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/normal%2520embryonic%2520palatal%2520mesenchymal%2520cell%2520line%253aHEPM.CNhs11894.10813-111B3.hg38.nobarcode.ctss.bed.gz | |||
|id=FF:10813-111B3 | |id=FF:10813-111B3 | ||
|is_a=CL:0000134;;EFO:0002091;;FF:0000210;;FF:0100669;;UBERON:0005705 | |is_a=CL:0000134;;EFO:0002091;;FF:0000210;;FF:0100669;;UBERON:0005705 | ||
Revision as of 14:58, 17 May 2017
| Name: | normal embryonic palatal mesenchymal cell line:HEPM |
|---|---|
| Species: | Human (Homo sapiens) |
| Library ID: | CNhs11894 |
| Sample type: | cell lines |
| Genomic View: | UCSC |
| RefEX: | Specific genes |
| CAGEd-oPOSSUM: | link |
| Additional information | ||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample information
RNA information
|
| CAGE Accession numbers | ||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
| Download raw sequence, BAM & CTSS | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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
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: CNhs11894
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: CNhs11894
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.219 |
| 10 | 10 | 0.667 |
| 100 | 100 | 0.754 |
| 101 | 101 | 0.73 |
| 102 | 102 | 0.338 |
| 103 | 103 | 0.36 |
| 104 | 104 | 0.846 |
| 105 | 105 | 0.262 |
| 106 | 106 | 0.482 |
| 107 | 107 | 0.418 |
| 108 | 108 | 0.737 |
| 109 | 109 | 0.234 |
| 11 | 11 | 0.911 |
| 110 | 110 | 0.509 |
| 111 | 111 | 0.214 |
| 112 | 112 | 0.678 |
| 113 | 113 | 0.557 |
| 114 | 114 | 0.631 |
| 115 | 115 | 2.33578e-4 |
| 116 | 116 | 0.355 |
| 117 | 117 | 0.244 |
| 118 | 118 | 0.694 |
| 119 | 119 | 0.287 |
| 12 | 12 | 0.262 |
| 120 | 120 | 0.271 |
| 121 | 121 | 0.396 |
| 122 | 122 | 0.0126 |
| 123 | 123 | 0.0496 |
| 124 | 124 | 0.631 |
| 125 | 125 | 0.399 |
| 126 | 126 | 0.294 |
| 127 | 127 | 0.477 |
| 128 | 128 | 0.604 |
| 129 | 129 | 0.18 |
| 13 | 13 | 0.247 |
| 130 | 130 | 0.879 |
| 131 | 131 | 0.891 |
| 132 | 132 | 0.032 |
| 133 | 133 | 0.812 |
| 134 | 134 | 0.177 |
| 135 | 135 | 0.0779 |
| 136 | 136 | 0.732 |
| 137 | 137 | 0.119 |
| 138 | 138 | 0.539 |
| 139 | 139 | 0.364 |
| 14 | 14 | 0.107 |
| 140 | 140 | 0.0941 |
| 141 | 141 | 0.291 |
| 142 | 142 | 0.271 |
| 143 | 143 | 0.596 |
| 144 | 144 | 0.231 |
| 145 | 145 | 0.576 |
| 146 | 146 | 0.145 |
| 147 | 147 | 0.239 |
| 148 | 148 | 0.152 |
| 149 | 149 | 0.313 |
| 15 | 15 | 0.0594 |
| 150 | 150 | 0.581 |
| 151 | 151 | 0.274 |
| 152 | 152 | 0.037 |
| 153 | 153 | 0.614 |
| 154 | 154 | 0.814 |
| 155 | 155 | 0.731 |
| 156 | 156 | 0.33 |
| 157 | 157 | 0.319 |
| 158 | 158 | 0.0211 |
| 159 | 159 | 0.603 |
| 16 | 16 | 0.169 |
| 160 | 160 | 0.915 |
| 161 | 161 | 0.575 |
| 162 | 162 | 0.918 |
| 163 | 163 | 0.225 |
| 164 | 164 | 0.526 |
| 165 | 165 | 0.245 |
| 166 | 166 | 0.017 |
| 167 | 167 | 0.631 |
| 168 | 168 | 0.171 |
| 169 | 169 | 0.482 |
| 17 | 17 | 0.635 |
| 18 | 18 | 0.983 |
| 19 | 19 | 0.0214 |
| 2 | 2 | 0.998 |
| 20 | 20 | 0.809 |
| 21 | 21 | 0.634 |
| 22 | 22 | 0.766 |
| 23 | 23 | 0.611 |
| 24 | 24 | 0.215 |
| 25 | 25 | 0.188 |
| 26 | 26 | 0.658 |
| 27 | 27 | 0.57 |
| 28 | 28 | 0.213 |
| 29 | 29 | 0.609 |
| 3 | 3 | 0.392 |
| 30 | 30 | 0.901 |
| 31 | 31 | 0.74 |
| 32 | 32 | 9.46976e-17 |
| 33 | 33 | 1 |
| 34 | 34 | 0.209 |
| 35 | 35 | 0.619 |
| 36 | 36 | 0.0747 |
| 37 | 37 | 0.426 |
| 38 | 38 | 0.151 |
| 39 | 39 | 0.736 |
| 4 | 4 | 0.299 |
| 40 | 40 | 0.0289 |
| 41 | 41 | 0.149 |
| 42 | 42 | 0.324 |
| 43 | 43 | 0.393 |
| 44 | 44 | 0.192 |
| 45 | 45 | 0.255 |
| 46 | 46 | 0.649 |
| 47 | 47 | 0.175 |
| 48 | 48 | 0.512 |
| 49 | 49 | 0.175 |
| 5 | 5 | 0.489 |
| 50 | 50 | 0.938 |
| 51 | 51 | 0.59 |
| 52 | 52 | 0.831 |
| 53 | 53 | 0.123 |
| 54 | 54 | 0.995 |
| 55 | 55 | 0.271 |
| 56 | 56 | 0.541 |
| 57 | 57 | 0.549 |
| 58 | 58 | 0.0815 |
| 59 | 59 | 0.991 |
| 6 | 6 | 0.507 |
| 60 | 60 | 0.58 |
| 61 | 61 | 0.549 |
| 62 | 62 | 0.252 |
| 63 | 63 | 0.945 |
| 64 | 64 | 0.847 |
| 65 | 65 | 0.825 |
| 66 | 66 | 0.0704 |
| 67 | 67 | 0.485 |
| 68 | 68 | 0.957 |
| 69 | 69 | 0.623 |
| 7 | 7 | 0.13 |
| 70 | 70 | 0.298 |
| 71 | 71 | 0.395 |
| 72 | 72 | 0.662 |
| 73 | 73 | 0.324 |
| 74 | 74 | 0.971 |
| 75 | 75 | 0.382 |
| 76 | 76 | 0.998 |
| 77 | 77 | 0.898 |
| 78 | 78 | 0.0345 |
| 79 | 79 | 0.00717 |
| 8 | 8 | 0.556 |
| 80 | 80 | 0.0491 |
| 81 | 81 | 0.961 |
| 82 | 82 | 0.776 |
| 83 | 83 | 0.389 |
| 84 | 84 | 0.96 |
| 85 | 85 | 0.318 |
| 86 | 86 | 0.751 |
| 87 | 87 | 0.84 |
| 88 | 88 | 0.477 |
| 89 | 89 | 0.557 |
| 9 | 9 | 0.738 |
| 90 | 90 | 0.304 |
| 91 | 91 | 0.967 |
| 92 | 92 | 0.804 |
| 93 | 93 | 0.418 |
| 94 | 94 | 0.791 |
| 95 | 95 | 0.967 |
| 96 | 96 | 0.952 |
| 97 | 97 | 0.682 |
| 98 | 98 | 0.0614 |
| 99 | 99 | 0.165 |
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: CNhs11894
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
CL:0000134 mesenchymal cell
EFO:0002091 biological replicate
FF:0000210 human sample
FF:0100669 embryonic cell line sample
UBERON:0005705 primary palate mesenchyme
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)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000219 (motile cell)
0000134 (mesenchymal cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0001474 (bone element)
0002384 (connective tissue)
0000033 (head)
0000479 (tissue)
0005705 (primary palate mesenchyme)
0004121 (ectoderm-derived structure)
0004119 (endoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000467 (anatomical system)
0010313 (neural crest-derived structure)
0001062 (anatomical entity)
0000480 (anatomical group)
0000075 (subdivision of skeletal system)
0004765 (skeletal element)
0008193 (pneumatized bone)
0001708 (jaw skeleton)
0010912 (subdivision of skeleton)
0011159 (primary subdivision of cranial skeletal system)
0002514 (intramembranous bone)
0003457 (head bone)
0008907 (dermal bone)
0008001 (irregular bone)
0007213 (mesenchyme derived from head neural crest)
0009891 (facial mesenchyme)
0003104 (mesenchyme)
0007914 (head or neck bone)
0010317 (germ layer / neural crest derived structure)
0007375 (roof of mouth)
0003323 (mesenchyme of upper jaw)
0010258 (mesenchyme from rhombencephalic neural crest)
0005253 (head mesenchyme)
0007842 (membrane bone)
0004089 (midface)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0001456 (face)
0008895 (splanchnocranium)
0002397 (maxilla)
0003113 (dermatocranium)
0011137 (axial skeletal system)
0003277 (skeleton of upper jaw)
0009142 (entire embryonic mesenchyme)
0010323 (cranial skeletal system)
0001709 (upper jaw region)
0002244 (premaxilla)
0005620 (primary palate)
0010364 (dermal skeleton)
0004288 (skeleton)
FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100669 (embryonic cell line sample)
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
CL:0000134 (mesenchymal cell)
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0005062 (neural fold)
UBERON:0007284 (presumptive neural plate)
UBERON:0003099 (cranial neural crest)
UBERON:0003852 (rhombencephalon neural crest)
UBERON:0010316 (germ layer / neural crest)
