FF:10513-107D9: Difference between revisions
From FANTOM5_SSTAR
(Created page with "{{f5samples
|id=FF:10513-107D9
|name=colon carcinoma cell line:CACO-2, biol_rep1
|sample_id=10513
|rna_tube_id=107D9
|rna_box=107
|rna_position=D9
|sample_cell_lot=
|s...") |
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{{f5samples | {{f5samples | ||
|id=FF:10513-107D9 | |id=FF:10513-107D9 | ||
|name=colon carcinoma cell line:CACO-2 | |name=colon carcinoma cell line:CACO-2 | ||
|sample_id=10513 | |sample_id=10513 | ||
|rna_tube_id=107D9 | |rna_tube_id=107D9 | ||
| Line 7: | Line 7: | ||
|rna_position=D9 | |rna_position=D9 | ||
|sample_cell_lot= | |sample_cell_lot= | ||
|sample_cell_catalog=RCB0988 | |sample_cell_catalog=RCB0988 | ||
|sample_company=RIKEN Bioresource centre | |sample_company=RIKEN Bioresource centre | ||
|rna_lot_number= | |rna_lot_number= | ||
| Line 20: | Line 20: | ||
|sample_ethnicity=unknown | |sample_ethnicity=unknown | ||
|rna_rin= | |rna_rin= | ||
|rna_od260/230=2. | |rna_od260/230=2.06 | ||
|rna_od260/280=2. | |rna_od260/280=2.1 | ||
|sample_cell_type=unclassifiable | |sample_cell_type=unclassifiable | ||
|sample_cell_line=CACO-2 | |sample_cell_line=CACO-2 | ||
|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=35. | |rna_weight_ug=35.5765 | ||
|rna_concentration=1.42306 | |rna_concentration=1.42306 | ||
|sample_note= | |sample_note= | ||
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|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:162,DOID:299,DOID:305,DOID:3119,DOID:4 | |ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:162,DOID:299,DOID:305,DOID:3119,DOID:4 | ||
|sample_description= | |sample_description= | ||
|fonse_cell_line=FF:0101120,FF:0101532 | |fonse_cell_line=FF:0101120,FF:0101532 | ||
|fonse_cell_line_closure=FF:0101120,FF:0101532 | |fonse_cell_line_closure=FF:0101120,FF:0101532 | ||
| Line 67: | Line 66: | ||
|fonse_treatment= | |fonse_treatment= | ||
|fonse_treatment_closure= | |fonse_treatment_closure= | ||
|top_motifs= | |||
}} | }} | ||
Revision as of 17:27, 27 February 2012
| Name: | colon carcinoma cell line:CACO-2 |
|---|---|
| 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: CNhs11280
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: CNhs11280
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.667 |
| 10 | 10 | 0.533 |
| 100 | 100 | 0.278 |
| 101 | 101 | 0.635 |
| 102 | 102 | 0.372 |
| 103 | 103 | 0.892 |
| 104 | 104 | 0.629 |
| 105 | 105 | 0.777 |
| 106 | 106 | 0.0788 |
| 107 | 107 | 0.498 |
| 108 | 108 | 0.636 |
| 109 | 109 | 0.453 |
| 11 | 11 | 0.42 |
| 110 | 110 | 0.402 |
| 111 | 111 | 0.881 |
| 112 | 112 | 0.102 |
| 113 | 113 | 0.54 |
| 114 | 114 | 0.289 |
| 115 | 115 | 0.583 |
| 116 | 116 | 0.327 |
| 117 | 117 | 0.81 |
| 118 | 118 | 0.478 |
| 119 | 119 | 0.916 |
| 12 | 12 | 0.978 |
| 120 | 120 | 0.796 |
| 121 | 121 | 0.392 |
| 122 | 122 | 0.121 |
| 123 | 123 | 0.41 |
| 124 | 124 | 0.287 |
| 125 | 125 | 0.31 |
| 126 | 126 | 0.55 |
| 127 | 127 | 0.413 |
| 128 | 128 | 0.0522 |
| 129 | 129 | 0.979 |
| 13 | 13 | 0.00503 |
| 130 | 130 | 0.0705 |
| 131 | 131 | 0.165 |
| 132 | 132 | 0.613 |
| 133 | 133 | 0.0428 |
| 134 | 134 | 0.455 |
| 135 | 135 | 0.204 |
| 136 | 136 | 0.00648 |
| 137 | 137 | 0.0964 |
| 138 | 138 | 0.0331 |
| 139 | 139 | 0.0302 |
| 14 | 14 | 0.408 |
| 140 | 140 | 0.741 |
| 141 | 141 | 0.847 |
| 142 | 142 | 0.723 |
| 143 | 143 | 0.0983 |
| 144 | 144 | 0.409 |
| 145 | 145 | 0.508 |
| 146 | 146 | 0.798 |
| 147 | 147 | 0.512 |
| 148 | 148 | 0.405 |
| 149 | 149 | 0.641 |
| 15 | 15 | 0.729 |
| 150 | 150 | 0.494 |
| 151 | 151 | 0.208 |
| 152 | 152 | 0.375 |
| 153 | 153 | 0.594 |
| 154 | 154 | 0.0989 |
| 155 | 155 | 0.349 |
| 156 | 156 | 0.616 |
| 157 | 157 | 0.336 |
| 158 | 158 | 0.363 |
| 159 | 159 | 0.693 |
| 16 | 16 | 0.724 |
| 160 | 160 | 0.328 |
| 161 | 161 | 0.807 |
| 162 | 162 | 0.956 |
| 163 | 163 | 0.201 |
| 164 | 164 | 0.303 |
| 165 | 165 | 0.818 |
| 166 | 166 | 0.0431 |
| 167 | 167 | 0.812 |
| 168 | 168 | 0.24 |
| 169 | 169 | 0.488 |
| 17 | 17 | 0.791 |
| 18 | 18 | 0.0277 |
| 19 | 19 | 0.149 |
| 2 | 2 | 0.241 |
| 20 | 20 | 0.418 |
| 21 | 21 | 0.225 |
| 22 | 22 | 0.604 |
| 23 | 23 | 0.0224 |
| 24 | 24 | 0.622 |
| 25 | 25 | 0.886 |
| 26 | 26 | 0.992 |
| 27 | 27 | 0.337 |
| 28 | 28 | 0.876 |
| 29 | 29 | 0.702 |
| 3 | 3 | 0.427 |
| 30 | 30 | 0.654 |
| 31 | 31 | 0.712 |
| 32 | 32 | 0.0128 |
| 33 | 33 | 0.637 |
| 34 | 34 | 0.513 |
| 35 | 35 | 0.391 |
| 36 | 36 | 0.318 |
| 37 | 37 | 0.421 |
| 38 | 38 | 0.815 |
| 39 | 39 | 0.399 |
| 4 | 4 | 0.551 |
| 40 | 40 | 0.0343 |
| 41 | 41 | 0.0492 |
| 42 | 42 | 0.868 |
| 43 | 43 | 0.21 |
| 44 | 44 | 0.596 |
| 45 | 45 | 0.525 |
| 46 | 46 | 0.307 |
| 47 | 47 | 0.542 |
| 48 | 48 | 0.743 |
| 49 | 49 | 0.337 |
| 5 | 5 | 0.623 |
| 50 | 50 | 0.359 |
| 51 | 51 | 0.814 |
| 52 | 52 | 0.932 |
| 53 | 53 | 0.45 |
| 54 | 54 | 0.754 |
| 55 | 55 | 0.566 |
| 56 | 56 | 0.657 |
| 57 | 57 | 0.931 |
| 58 | 58 | 0.637 |
| 59 | 59 | 0.0616 |
| 6 | 6 | 0.84 |
| 60 | 60 | 0.373 |
| 61 | 61 | 0.319 |
| 62 | 62 | 0.25 |
| 63 | 63 | 0.553 |
| 64 | 64 | 0.667 |
| 65 | 65 | 0.0645 |
| 66 | 66 | 2.9958e-4 |
| 67 | 67 | 0.119 |
| 68 | 68 | 0.201 |
| 69 | 69 | 0.387 |
| 7 | 7 | 0.157 |
| 70 | 70 | 0.0944 |
| 71 | 71 | 0.494 |
| 72 | 72 | 0.578 |
| 73 | 73 | 0.604 |
| 74 | 74 | 0.166 |
| 75 | 75 | 0.692 |
| 76 | 76 | 0.947 |
| 77 | 77 | 0.214 |
| 78 | 78 | 0.00764 |
| 79 | 79 | 0.111 |
| 8 | 8 | 0.772 |
| 80 | 80 | 0.22 |
| 81 | 81 | 0.391 |
| 82 | 82 | 0.00826 |
| 83 | 83 | 0.651 |
| 84 | 84 | 0.483 |
| 85 | 85 | 0.0917 |
| 86 | 86 | 0.66 |
| 87 | 87 | 0.0819 |
| 88 | 88 | 0.991 |
| 89 | 89 | 0.0303 |
| 9 | 9 | 0.0469 |
| 90 | 90 | 0.778 |
| 91 | 91 | 0.00516 |
| 92 | 92 | 0.076 |
| 93 | 93 | 0.856 |
| 94 | 94 | 0.025 |
| 95 | 95 | 0.317 |
| 96 | 96 | 0.246 |
| 97 | 97 | 0.924 |
| 98 | 98 | 0.703 |
| 99 | 99 | 0.799 |
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: CNhs11280
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)
0000255 (eukaryotic cell)
0000548 (animal cell)
DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
299 (adenocarcinoma)
305 (carcinoma)
3119 (gastrointestinal system cancer)
4 (disease)
UBERON: Anatomy
0000059 (large intestine)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000160 (intestine)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001007 (digestive system)
0001046 (hindgut)
0001052 (rectum)
0001062 (anatomical entity)
0001155 (colon)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004907 (lower digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)
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
