FF:10084-102B3: Difference between revisions
From FANTOM5_SSTAR
(Created page with "{{f5samples
|id=FF:10084-102B3
|name=brain, adult, donor1
|sample_id=10084
|rna_tube_id=102B3
|rna_box=102
|rna_position=B3
|sample_cell_lot=NA
|sample_cell_catalog=NA...") |
No edit summary |
||
| Line 9: | Line 9: | ||
|sample_cell_catalog=NA | |sample_cell_catalog=NA | ||
|sample_company=Clontech | |sample_company=Clontech | ||
|rna_lot_number= 8101369A-4 | |rna_lot_number=8101369A-4 | ||
|rna_catalog_number=Cat: 636643 Lot: 8101369A-4 | |rna_catalog_number=Cat: 636643 Lot: 8101369A-4 | ||
|sample_species=Human (Homo sapiens) | |sample_species=Human (Homo sapiens) | ||
| Line 15: | Line 15: | ||
|sample_dev_stage=18 years old adult | |sample_dev_stage=18 years old adult | ||
|sample_tissue=brain | |sample_tissue=brain | ||
|sample_donor(cell lot)=1 | |sample_donor(cell lot)=1 | ||
|sample_sex=male | |sample_sex=male | ||
|sample_age= | |sample_age= | ||
| Line 29: | Line 29: | ||
|rna_sample_type=total RNA | |rna_sample_type=total RNA | ||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0 | |rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0 | ||
|rna_weight_ug=10 | |rna_weight_ug=10 | ||
|rna_concentration= | |rna_concentration=1 | ||
|sample_note= | |sample_note= | ||
|profile_hcage=CNhs11796,LSID820,release009,COMPLETED | |profile_hcage=CNhs11796,LSID820,release009,COMPLETED | ||
| Line 40: | Line 40: | ||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
|sample_description= | |sample_description= | ||
|fonse_cell_line= | |fonse_cell_line= | ||
|fonse_cell_line_closure= | |fonse_cell_line_closure= | ||
| Line 67: | Line 66: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|top_motifs= | |||
}} | }} | ||
Revision as of 17:11, 27 February 2012
| Name: | brain, adult, donor1 |
|---|---|
| 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: CNhs11796
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: CNhs11796
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.0371 |
| 10 | 10 | 0.0171 |
| 100 | 100 | 0.35 |
| 101 | 101 | 0.866 |
| 102 | 102 | 0.669 |
| 103 | 103 | 0.0894 |
| 104 | 104 | 0.173 |
| 105 | 105 | 0.356 |
| 106 | 106 | 0.148 |
| 107 | 107 | 0.192 |
| 108 | 108 | 0.887 |
| 109 | 109 | 0.00905 |
| 11 | 11 | 0.0223 |
| 110 | 110 | 0.0273 |
| 111 | 111 | 0.158 |
| 112 | 112 | 0.443 |
| 113 | 113 | 0.535 |
| 114 | 114 | 0.106 |
| 115 | 115 | 0.654 |
| 116 | 116 | 0.382 |
| 117 | 117 | 0.00522 |
| 118 | 118 | 0.107 |
| 119 | 119 | 0.405 |
| 12 | 12 | 0.719 |
| 120 | 120 | 0.139 |
| 121 | 121 | 0.612 |
| 122 | 122 | 0.509 |
| 123 | 123 | 0.854 |
| 124 | 124 | 0.0284 |
| 125 | 125 | 0.325 |
| 126 | 126 | 0.0163 |
| 127 | 127 | 0.371 |
| 128 | 128 | 0.391 |
| 129 | 129 | 0.881 |
| 13 | 13 | 4.29961e-4 |
| 130 | 130 | 0.282 |
| 131 | 131 | 0.155 |
| 132 | 132 | 0.316 |
| 133 | 133 | 0.00461 |
| 134 | 134 | 0.605 |
| 135 | 135 | 0.265 |
| 136 | 136 | 0.00794 |
| 137 | 137 | 0.359 |
| 138 | 138 | 0.821 |
| 139 | 139 | 0.17 |
| 14 | 14 | 0.93 |
| 140 | 140 | 0.375 |
| 141 | 141 | 0.302 |
| 142 | 142 | 0.898 |
| 143 | 143 | 0.0086 |
| 144 | 144 | 0.964 |
| 145 | 145 | 0.12 |
| 146 | 146 | 0.386 |
| 147 | 147 | 0.851 |
| 148 | 148 | 0.187 |
| 149 | 149 | 0.736 |
| 15 | 15 | 0.0475 |
| 150 | 150 | 0.136 |
| 151 | 151 | 0.767 |
| 152 | 152 | 0.227 |
| 153 | 153 | 0.499 |
| 154 | 154 | 0.499 |
| 155 | 155 | 0.483 |
| 156 | 156 | 0.893 |
| 157 | 157 | 0.264 |
| 158 | 158 | 0.395 |
| 159 | 159 | 0.435 |
| 16 | 16 | 0.0675 |
| 160 | 160 | 0.269 |
| 161 | 161 | 0.188 |
| 162 | 162 | 0.889 |
| 163 | 163 | 0.738 |
| 164 | 164 | 0.0155 |
| 165 | 165 | 0.0534 |
| 166 | 166 | 0.988 |
| 167 | 167 | 0.344 |
| 168 | 168 | 0.631 |
| 169 | 169 | 0.0131 |
| 17 | 17 | 0.192 |
| 18 | 18 | 0.168 |
| 19 | 19 | 0.343 |
| 2 | 2 | 0.777 |
| 20 | 20 | 0.0709 |
| 21 | 21 | 0.0781 |
| 22 | 22 | 0.316 |
| 23 | 23 | 0.503 |
| 24 | 24 | 0.05 |
| 25 | 25 | 0.311 |
| 26 | 26 | 5.47113e-5 |
| 27 | 27 | 0.924 |
| 28 | 28 | 0.551 |
| 29 | 29 | 0.00338 |
| 3 | 3 | 0.0106 |
| 30 | 30 | 0.512 |
| 31 | 31 | 0.926 |
| 32 | 32 | 0.079 |
| 33 | 33 | 0.0473 |
| 34 | 34 | 0.962 |
| 35 | 35 | 0.565 |
| 36 | 36 | 0.121 |
| 37 | 37 | 0.0441 |
| 38 | 38 | 0.364 |
| 39 | 39 | 0.309 |
| 4 | 4 | 0.914 |
| 40 | 40 | 0.095 |
| 41 | 41 | 0.313 |
| 42 | 42 | 0.0937 |
| 43 | 43 | 0.0968 |
| 44 | 44 | 0.471 |
| 45 | 45 | 0.895 |
| 46 | 46 | 0.069 |
| 47 | 47 | 0.0878 |
| 48 | 48 | 0.0606 |
| 49 | 49 | 0.183 |
| 5 | 5 | 0.361 |
| 50 | 50 | 0.325 |
| 51 | 51 | 0.531 |
| 52 | 52 | 0.878 |
| 53 | 53 | 0.67 |
| 54 | 54 | 0.567 |
| 55 | 55 | 0.444 |
| 56 | 56 | 0.54 |
| 57 | 57 | 0.231 |
| 58 | 58 | 0.293 |
| 59 | 59 | 0.245 |
| 6 | 6 | 0.524 |
| 60 | 60 | 0.0993 |
| 61 | 61 | 0.0443 |
| 62 | 62 | 0.164 |
| 63 | 63 | 0.225 |
| 64 | 64 | 0.247 |
| 65 | 65 | 0.443 |
| 66 | 66 | 0.115 |
| 67 | 67 | 0.297 |
| 68 | 68 | 0.583 |
| 69 | 69 | 0.689 |
| 7 | 7 | 0.0267 |
| 70 | 70 | 0.0355 |
| 71 | 71 | 0.00431 |
| 72 | 72 | 0.299 |
| 73 | 73 | 0.0621 |
| 74 | 74 | 0.517 |
| 75 | 75 | 0.0201 |
| 76 | 76 | 0.244 |
| 77 | 77 | 0.432 |
| 78 | 78 | 0.00174 |
| 79 | 79 | 0.457 |
| 8 | 8 | 0.0964 |
| 80 | 80 | 0.611 |
| 81 | 81 | 0.578 |
| 82 | 82 | 0.566 |
| 83 | 83 | 0.0681 |
| 84 | 84 | 0.744 |
| 85 | 85 | 0.542 |
| 86 | 86 | 0.172 |
| 87 | 87 | 0.0191 |
| 88 | 88 | 0.892 |
| 89 | 89 | 0.63 |
| 9 | 9 | 0.461 |
| 90 | 90 | 0.0207 |
| 91 | 91 | 0.391 |
| 92 | 92 | 0.555 |
| 93 | 93 | 0.841 |
| 94 | 94 | 0.05 |
| 95 | 95 | 0.0212 |
| 96 | 96 | 0.942 |
| 97 | 97 | 0.73 |
| 98 | 98 | 0.316 |
| 99 | 99 | 0.941 |
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: CNhs11796
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
UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)
0007023 (adult organism)
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
