FF:10493-107B7: Difference between revisions
From FANTOM5_SSTAR
(Created page with "{{f5samples
|id=FF:10493-107B7
|name=mesothelioma cell line:ACC-MESO-1, biol_rep1
|sample_id=10493
|rna_tube_id=107B7
|rna_box=107
|rna_position=B7
|sample_cell_lot=
|...") |
No edit summary |
||
| Line 1: | Line 1: | ||
{{f5samples | {{f5samples | ||
|id=FF:10493-107B7 | |id=FF:10493-107B7 | ||
|name=mesothelioma cell line:ACC-MESO-1 | |name=mesothelioma cell line:ACC-MESO-1 | ||
|sample_id=10493 | |sample_id=10493 | ||
|rna_tube_id=107B7 | |rna_tube_id=107B7 | ||
| Line 7: | Line 7: | ||
|rna_position=B7 | |rna_position=B7 | ||
|sample_cell_lot= | |sample_cell_lot= | ||
|sample_cell_catalog=RCB2292 | |sample_cell_catalog=RCB2292 | ||
|sample_company=RIKEN Bioresource centre | |sample_company=RIKEN Bioresource centre | ||
|rna_lot_number= | |rna_lot_number= | ||
| Line 20: | Line 20: | ||
|sample_ethnicity=J | |sample_ethnicity=J | ||
|rna_rin= | |rna_rin= | ||
|rna_od260/230=2. | |rna_od260/230=2.04 | ||
|rna_od260/280=2. | |rna_od260/280=2.07 | ||
|sample_cell_type=mesothelial cell | |sample_cell_type=mesothelial cell | ||
|sample_cell_line=ACC-MESO-1 | |sample_cell_line=ACC-MESO-1 | ||
|sample_collaboration=Yukio Nakamura (RIKEN BRC) | |sample_collaboration=Yukio Nakamura (RIKEN BRC) | ||
|sample_experimental_condition= | |sample_experimental_condition= | ||
| Line 29: | Line 29: | ||
|rna_sample_type=total RNA | |rna_sample_type=total RNA | ||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | |rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | ||
|rna_weight_ug=50. | |rna_weight_ug=50.6495 | ||
|rna_concentration=2.02598 | |rna_concentration=2.02598 | ||
|sample_note= | |sample_note= | ||
| Line 40: | Line 40: | ||
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:162,DOID:170,DOID:305,DOID:4,DOID:7 | |ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:162,DOID:170,DOID:305,DOID:4,DOID:7 | ||
|sample_description= | |sample_description= | ||
|fonse_cell_line=FF:0101120,FF:0102424 | |fonse_cell_line=FF:0101120,FF:0102424 | ||
|fonse_cell_line_closure=FF:0101120,FF:0102424 | |fonse_cell_line_closure=FF:0101120,FF:0102424 | ||
| Line 67: | Line 66: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|top_motifs= | |||
}} | }} | ||
Revision as of 17:47, 27 February 2012
| Name: | mesothelioma cell line:ACC-MESO-1 |
|---|---|
| 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: CNhs11263
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: CNhs11263
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.741 |
| 10 | 10 | 0.319 |
| 100 | 100 | 0.178 |
| 101 | 101 | 0.0558 |
| 102 | 102 | 0.592 |
| 103 | 103 | 0.327 |
| 104 | 104 | 0.79 |
| 105 | 105 | 0.886 |
| 106 | 106 | 0.00231 |
| 107 | 107 | 0.153 |
| 108 | 108 | 0.269 |
| 109 | 109 | 0.178 |
| 11 | 11 | 0.217 |
| 110 | 110 | 0.928 |
| 111 | 111 | 0.156 |
| 112 | 112 | 0.00776 |
| 113 | 113 | 0.186 |
| 114 | 114 | 0.957 |
| 115 | 115 | 0.561 |
| 116 | 116 | 0.2 |
| 117 | 117 | 0.544 |
| 118 | 118 | 0.0562 |
| 119 | 119 | 0.602 |
| 12 | 12 | 0.584 |
| 120 | 120 | 0.655 |
| 121 | 121 | 0.516 |
| 122 | 122 | 0.177 |
| 123 | 123 | 0.785 |
| 124 | 124 | 0.544 |
| 125 | 125 | 0.167 |
| 126 | 126 | 0.545 |
| 127 | 127 | 0.33 |
| 128 | 128 | 0.0289 |
| 129 | 129 | 0.94 |
| 13 | 13 | 0.212 |
| 130 | 130 | 0.579 |
| 131 | 131 | 0.392 |
| 132 | 132 | 0.658 |
| 133 | 133 | 0.0987 |
| 134 | 134 | 0.183 |
| 135 | 135 | 0.137 |
| 136 | 136 | 0.0292 |
| 137 | 137 | 0.236 |
| 138 | 138 | 0.306 |
| 139 | 139 | 0.458 |
| 14 | 14 | 0.239 |
| 140 | 140 | 0.0559 |
| 141 | 141 | 0.722 |
| 142 | 142 | 0.078 |
| 143 | 143 | 0.658 |
| 144 | 144 | 0.852 |
| 145 | 145 | 0.00483 |
| 146 | 146 | 0.934 |
| 147 | 147 | 0.664 |
| 148 | 148 | 0.646 |
| 149 | 149 | 0.16 |
| 15 | 15 | 0.227 |
| 150 | 150 | 0.334 |
| 151 | 151 | 0.356 |
| 152 | 152 | 0.352 |
| 153 | 153 | 0.463 |
| 154 | 154 | 0.235 |
| 155 | 155 | 0.214 |
| 156 | 156 | 0.337 |
| 157 | 157 | 0.589 |
| 158 | 158 | 0.784 |
| 159 | 159 | 0.194 |
| 16 | 16 | 0.213 |
| 160 | 160 | 0.174 |
| 161 | 161 | 0.967 |
| 162 | 162 | 0.624 |
| 163 | 163 | 0.919 |
| 164 | 164 | 0.32 |
| 165 | 165 | 0.517 |
| 166 | 166 | 0.662 |
| 167 | 167 | 0.656 |
| 168 | 168 | 0.254 |
| 169 | 169 | 0.888 |
| 17 | 17 | 0.461 |
| 18 | 18 | 0.727 |
| 19 | 19 | 0.177 |
| 2 | 2 | 0.307 |
| 20 | 20 | 0.0251 |
| 21 | 21 | 0.752 |
| 22 | 22 | 0.652 |
| 23 | 23 | 0.22 |
| 24 | 24 | 0.829 |
| 25 | 25 | 0.217 |
| 26 | 26 | 0.353 |
| 27 | 27 | 0.254 |
| 28 | 28 | 0.202 |
| 29 | 29 | 0.391 |
| 3 | 3 | 0.285 |
| 30 | 30 | 0.982 |
| 31 | 31 | 0.314 |
| 32 | 32 | 0.00281 |
| 33 | 33 | 0.85 |
| 34 | 34 | 0.361 |
| 35 | 35 | 0.00132 |
| 36 | 36 | 0.118 |
| 37 | 37 | 0.842 |
| 38 | 38 | 0.33 |
| 39 | 39 | 0.977 |
| 4 | 4 | 0.565 |
| 40 | 40 | 0.0562 |
| 41 | 41 | 0.149 |
| 42 | 42 | 0.0504 |
| 43 | 43 | 0.85 |
| 44 | 44 | 0.108 |
| 45 | 45 | 0.56 |
| 46 | 46 | 0.0698 |
| 47 | 47 | 0.982 |
| 48 | 48 | 0.896 |
| 49 | 49 | 0.445 |
| 5 | 5 | 0.373 |
| 50 | 50 | 0.245 |
| 51 | 51 | 0.237 |
| 52 | 52 | 0.897 |
| 53 | 53 | 0.447 |
| 54 | 54 | 0.251 |
| 55 | 55 | 0.944 |
| 56 | 56 | 0.42 |
| 57 | 57 | 0.656 |
| 58 | 58 | 0.283 |
| 59 | 59 | 0.0327 |
| 6 | 6 | 0.354 |
| 60 | 60 | 0.0839 |
| 61 | 61 | 0.00286 |
| 62 | 62 | 0.0767 |
| 63 | 63 | 0.629 |
| 64 | 64 | 0.68 |
| 65 | 65 | 0.685 |
| 66 | 66 | 4.49061e-7 |
| 67 | 67 | 0.738 |
| 68 | 68 | 0.0729 |
| 69 | 69 | 0.36 |
| 7 | 7 | 0.559 |
| 70 | 70 | 0.816 |
| 71 | 71 | 0.464 |
| 72 | 72 | 0.696 |
| 73 | 73 | 0.227 |
| 74 | 74 | 0.765 |
| 75 | 75 | 0.266 |
| 76 | 76 | 0.245 |
| 77 | 77 | 0.23 |
| 78 | 78 | 0.726 |
| 79 | 79 | 0.13 |
| 8 | 8 | 0.396 |
| 80 | 80 | 0.278 |
| 81 | 81 | 0.331 |
| 82 | 82 | 0.378 |
| 83 | 83 | 0.241 |
| 84 | 84 | 0.431 |
| 85 | 85 | 0.34 |
| 86 | 86 | 0.155 |
| 87 | 87 | 0.15 |
| 88 | 88 | 0.71 |
| 89 | 89 | 0.25 |
| 9 | 9 | 0.089 |
| 90 | 90 | 0.698 |
| 91 | 91 | 0.113 |
| 92 | 92 | 0.945 |
| 93 | 93 | 0.589 |
| 94 | 94 | 0.975 |
| 95 | 95 | 0.338 |
| 96 | 96 | 0.997 |
| 97 | 97 | 0.137 |
| 98 | 98 | 0.0908 |
| 99 | 99 | 0.6 |
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: CNhs11263
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
CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000076 (squamous epithelial cell)
0000077 (mesothelial cell)
0000150 (glandular epithelial cell)
0000151 (secretory cell)
0000163 (endocrine cell)
0000174 (steroid hormone secreting cell)
0000213 (lining cell)
0000215 (barrier cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002078 (meso-epithelial cell)
0002097 (cortical cell of adrenal gland)
0002321 (embryonic cell)
0002371 (somatic cell)
DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
170 (endocrine gland cancer)
305 (carcinoma)
4 (disease)
7 (disease of anatomical entity)
UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000480 (anatomical group)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001062 (anatomical entity)
0001235 (adrenal cortex)
0001851 (cortex)
0002050 (embryonic structure)
0002100 (trunk)
0002342 (neural crest)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002369 (adrenal gland)
0002417 (abdominal segment of trunk)
0002530 (gland)
0002532 (epiblast (generic))
0003075 (neural plate)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007284 (presumptive neural plate)
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
