FF:10618-108G6: Difference between revisions
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{{f5samples | {{f5samples | ||
|id= | |id=FF:10618-108G6 | ||
|name= | |name=choriocarcinoma cell line:T3M-3 | ||
|sample_id= | |sample_id=10618 | ||
|rna_tube_id= | |rna_tube_id=108G6 | ||
|rna_box= | |rna_box=108 | ||
|rna_position= | |rna_position=G6 | ||
|sample_cell_lot= | |sample_cell_lot= | ||
|sample_cell_catalog= | |sample_cell_catalog=RCB1018 | ||
|sample_company= | |sample_company=RIKEN Bioresource centre | ||
|rna_lot_number= | |rna_lot_number= | ||
|rna_catalog_number= | |rna_catalog_number= | ||
|sample_species= | |sample_species=Human (Homo sapiens) | ||
|sample_strain= | |sample_strain= | ||
|sample_dev_stage= | |sample_dev_stage= | ||
|sample_tissue= | |sample_tissue=chorioamniotic membrane | ||
|sample_donor(cell lot)= | |sample_donor(cell lot)= | ||
|sample_sex= | |sample_sex=unknown | ||
|sample_age= | |sample_age=fetal | ||
|sample_ethnicity= | |sample_ethnicity=J | ||
|rna_rin= | |rna_rin= | ||
|rna_od260/230= | |rna_od260/230=2.12 | ||
|rna_od260/280= | |rna_od260/280=2.04 | ||
|sample_cell_type= | |sample_cell_type=trophoblast cell | ||
|sample_cell_line= | |sample_cell_line=T3M-3 | ||
|sample_collaboration= | |sample_collaboration=Yukio Nakamura (RIKEN BRC) | ||
|sample_experimental_condition= | |sample_experimental_condition= | ||
|sample_disease= | |sample_disease=choriocarcinoma | ||
|rna_sample_type= | |rna_sample_type=total RNA | ||
|rna_extraction_protocol= | |rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0 | ||
|rna_weight_ug= | |rna_weight_ug=181.29 | ||
|rna_concentration= | |rna_concentration=2.4172 | ||
|sample_note= | |sample_note= | ||
|profile_hcage=,,, | |profile_hcage=CNhs11820,LSID829,release010,COMPLETED | ||
|profile_cagescan=,,, | |profile_cagescan=,,, | ||
|profile_srnaseq=,,, | |profile_srnaseq=,,, | ||
| Line 40: | Line 40: | ||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
|sample_description= | |sample_description= | ||
|fonse_cell_line=FF:0101575 | |fonse_cell_line=FF:0101575 | ||
|fonse_cell_line_closure=FF:0101575 | |fonse_cell_line_closure=FF:0101575 | ||
| 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: | choriocarcinoma cell line:T3M-3 |
|---|---|
| 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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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: CNhs11820
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: CNhs11820
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.803 |
| 10 | 10 | 0.937 |
| 100 | 100 | 0.0656 |
| 101 | 101 | 0.706 |
| 102 | 102 | 0.518 |
| 103 | 103 | 0.101 |
| 104 | 104 | 0.17 |
| 105 | 105 | 0.55 |
| 106 | 106 | 0.0194 |
| 107 | 107 | 0.672 |
| 108 | 108 | 0.716 |
| 109 | 109 | 0.0812 |
| 11 | 11 | 0.824 |
| 110 | 110 | 0.271 |
| 111 | 111 | 0.672 |
| 112 | 112 | 0.247 |
| 113 | 113 | 0.14 |
| 114 | 114 | 0.314 |
| 115 | 115 | 0.886 |
| 116 | 116 | 0.569 |
| 117 | 117 | 0.271 |
| 118 | 118 | 0.366 |
| 119 | 119 | 0.875 |
| 12 | 12 | 0.773 |
| 120 | 120 | 0.735 |
| 121 | 121 | 0.955 |
| 122 | 122 | 0.811 |
| 123 | 123 | 0.0186 |
| 124 | 124 | 0.956 |
| 125 | 125 | 0.649 |
| 126 | 126 | 0.991 |
| 127 | 127 | 0.621 |
| 128 | 128 | 0.168 |
| 129 | 129 | 0.643 |
| 13 | 13 | 0.00889 |
| 130 | 130 | 0.923 |
| 131 | 131 | 0.238 |
| 132 | 132 | 0.907 |
| 133 | 133 | 6.42448e-4 |
| 134 | 134 | 0.767 |
| 135 | 135 | 0.0195 |
| 136 | 136 | 0.0347 |
| 137 | 137 | 0.0302 |
| 138 | 138 | 0.92 |
| 139 | 139 | 0.565 |
| 14 | 14 | 0.861 |
| 140 | 140 | 0.569 |
| 141 | 141 | 0.123 |
| 142 | 142 | 0.25 |
| 143 | 143 | 0.0291 |
| 144 | 144 | 0.0419 |
| 145 | 145 | 0.891 |
| 146 | 146 | 0.937 |
| 147 | 147 | 0.312 |
| 148 | 148 | 0.109 |
| 149 | 149 | 0.528 |
| 15 | 15 | 0.743 |
| 150 | 150 | 0.258 |
| 151 | 151 | 0.198 |
| 152 | 152 | 0.899 |
| 153 | 153 | 0.439 |
| 154 | 154 | 0.856 |
| 155 | 155 | 0.307 |
| 156 | 156 | 0.625 |
| 157 | 157 | 0.802 |
| 158 | 158 | 0.597 |
| 159 | 159 | 0.914 |
| 16 | 16 | 0.65 |
| 160 | 160 | 0.752 |
| 161 | 161 | 0.529 |
| 162 | 162 | 0.394 |
| 163 | 163 | 0.359 |
| 164 | 164 | 0.796 |
| 165 | 165 | 0.181 |
| 166 | 166 | 0.0142 |
| 167 | 167 | 0.611 |
| 168 | 168 | 0.0341 |
| 169 | 169 | 0.913 |
| 17 | 17 | 0.445 |
| 18 | 18 | 0.77 |
| 19 | 19 | 0.384 |
| 2 | 2 | 0.34 |
| 20 | 20 | 0.356 |
| 21 | 21 | 0.6 |
| 22 | 22 | 0.692 |
| 23 | 23 | 0.127 |
| 24 | 24 | 0.85 |
| 25 | 25 | 0.478 |
| 26 | 26 | 0.976 |
| 27 | 27 | 0.473 |
| 28 | 28 | 0.918 |
| 29 | 29 | 0.606 |
| 3 | 3 | 0.987 |
| 30 | 30 | 0.722 |
| 31 | 31 | 0.417 |
| 32 | 32 | 0.142 |
| 33 | 33 | 0.936 |
| 34 | 34 | 0.59 |
| 35 | 35 | 0.214 |
| 36 | 36 | 0.0646 |
| 37 | 37 | 0.707 |
| 38 | 38 | 0.528 |
| 39 | 39 | 0.124 |
| 4 | 4 | 0.375 |
| 40 | 40 | 0.0359 |
| 41 | 41 | 0.0475 |
| 42 | 42 | 0.481 |
| 43 | 43 | 0.384 |
| 44 | 44 | 0.915 |
| 45 | 45 | 0.937 |
| 46 | 46 | 0.501 |
| 47 | 47 | 0.482 |
| 48 | 48 | 0.525 |
| 49 | 49 | 0.637 |
| 5 | 5 | 0.468 |
| 50 | 50 | 0.514 |
| 51 | 51 | 0.919 |
| 52 | 52 | 0.708 |
| 53 | 53 | 0.627 |
| 54 | 54 | 0.948 |
| 55 | 55 | 0.943 |
| 56 | 56 | 0.664 |
| 57 | 57 | 0.0418 |
| 58 | 58 | 0.994 |
| 59 | 59 | 0.0799 |
| 6 | 6 | 0.102 |
| 60 | 60 | 0.363 |
| 61 | 61 | 0.404 |
| 62 | 62 | 0.598 |
| 63 | 63 | 0.655 |
| 64 | 64 | 0.457 |
| 65 | 65 | 0.763 |
| 66 | 66 | 0.0519 |
| 67 | 67 | 0.611 |
| 68 | 68 | 0.1 |
| 69 | 69 | 0.604 |
| 7 | 7 | 0.205 |
| 70 | 70 | 0.142 |
| 71 | 71 | 0.147 |
| 72 | 72 | 0.119 |
| 73 | 73 | 0.974 |
| 74 | 74 | 0.225 |
| 75 | 75 | 0.976 |
| 76 | 76 | 0.468 |
| 77 | 77 | 0.781 |
| 78 | 78 | 0.274 |
| 79 | 79 | 0.151 |
| 8 | 8 | 0.526 |
| 80 | 80 | 0.0908 |
| 81 | 81 | 0.456 |
| 82 | 82 | 0.57 |
| 83 | 83 | 0.216 |
| 84 | 84 | 0.953 |
| 85 | 85 | 0.0814 |
| 86 | 86 | 0.246 |
| 87 | 87 | 0.561 |
| 88 | 88 | 0.641 |
| 89 | 89 | 0.0542 |
| 9 | 9 | 0.148 |
| 90 | 90 | 0.709 |
| 91 | 91 | 0.0684 |
| 92 | 92 | 0.285 |
| 93 | 93 | 0.815 |
| 94 | 94 | 0.825 |
| 95 | 95 | 0.068 |
| 96 | 96 | 0.366 |
| 97 | 97 | 0.444 |
| 98 | 98 | 0.66 |
| 99 | 99 | 0.662 |
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: CNhs11820
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
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
