FF:11545-120B6: Difference between revisions
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|top_motifs= | |top_motifs=ATF4:2.54732666716;TLX2:2.38077513384;HIF1A:2.14879002645;ATF5_CREB3:2.07863516143;CREB1:2.05924196146;FOX{D1,D2}:2.03702916215;FOXN1:2.03570387137;NFKB1_REL_RELA:1.9948624467;RUNX1..3:1.89821364273;ELF1,2,4:1.79463055673;ALX1:1.71295082874;MYB:1.69439530242;GATA6:1.67392892469;RFX1:1.64745009604;DMAP1_NCOR{1,2}_SMARC:1.62603846271;RFX2..5_RFXANK_RFXAP:1.61732979698;TGIF1:1.55964917202;POU2F1..3:1.51377023999;FOX{I1,J2}:1.50446758929;NANOG{mouse}:1.48589495839;SPIB:1.46459662558;ETS1,2:1.38216852422;PAX2:1.34392956598;JUN:1.26440084563;PBX1:1.26193272389;XBP1:1.14241059887;SPI1:1.14082984467;SOX2:1.03841561379;NFATC1..3:1.00533076516;HMX1:0.955726804531;IRF1,2:0.90862044968;ATF2:0.857838296982;STAT5{A,B}:0.850561222097;RXRA_VDR{dimer}:0.833117563951;PAX8:0.763385163929;RORA:0.756267649754;NFE2:0.737998519235;NFIX:0.734850511507;STAT1,3:0.724647235531;BPTF:0.692430739688;MEF2{A,B,C,D}:0.687122582529;FOXO1,3,4:0.672998266209;NFIL3:0.662783760588;ATF6:0.660656544426;FOSL2:0.621297642119;FOX{F1,F2,J1}:0.576278265481;VSX1,2:0.530044684767;STAT2,4,6:0.523481141841;NFE2L1:0.515394056362;BREu{core}:0.510849684752;ESRRA:0.506736601447;EP300:0.47539578864;PDX1:0.465344730811;RXR{A,B,G}:0.437296596232;TBP:0.411981994412;FOXP3:0.385910050112;MAFB:0.385049509916;FOS_FOS{B,L1}_JUN{B,D}:0.35410913263;SOX5:0.349619573505;HSF1,2:0.329282572845;TBX4,5:0.314808407418;PRRX1,2:0.30703911153;CDX1,2,4:0.285959390664;RBPJ:0.278157343086;T:0.255464055382;BACH2:0.249135763994;MYOD1:0.229265147414;CRX:0.223271936652;EGR1..3:0.215321371572;EBF1:0.201026635118;HAND1,2:0.198963443574;YY1:0.196993892364;ZEB1:0.188449134523;FOXQ1:0.164141949717;AR:0.163384206199;TFAP2{A,C}:0.138205256407;FOXA2:0.134312991752;NR5A1,2:0.134094122776;SREBF1,2:0.124761910482;CUX2:0.102463867123;OCT4_SOX2{dimer}:0.0951139159841;ZNF148:0.0872770913357;LEF1_TCF7_TCF7L1,2:0.0730629562144;SMAD1..7,9:0.0588500251618;NANOG:0.055308423923;CEBPA,B_DDIT3:0.0402266916329;ESR1:0.0318636761943;PAX3,7:0.0272462359809;NR6A1:0.0169781646478;ZNF238:0.0139758376198;bHLH_family:0.00984585102344;HLF:-0.023668844218;TFAP4:-0.0299097300609;MTE{core}:-0.0379232882686;ZIC1..3:-0.0428205021312;ELK1,4_GABP{A,B1}:-0.0432597111338;AHR_ARNT_ARNT2:-0.0524192833953;HBP1_HMGB_SSRP1_UBTF:-0.0530256880237;E2F1..5:-0.0817815458997;AIRE:-0.0956659055775;HOXA9_MEIS1:-0.137609824853;PAX5:-0.14289914514;MZF1:-0.154144500525;NKX2-3_NKX2-5:-0.182282772441;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.197045854073;SRF:-0.203252630015;LMO2:-0.236396915261;NFY{A,B,C}:-0.236759968099;PAX6:-0.254326609471;SOX{8,9,10}:-0.256420555367;NHLH1,2:-0.279771848717;ZBTB16:-0.280032744079;IRF7:-0.294462885763;PATZ1:-0.294950878101;MYFfamily:-0.386001196985;MAZ:-0.416044400733;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.420302134194;PPARG:-0.424862942142;HIC1:-0.441256443155;TFAP2B:-0.44368669512;SNAI1..3:-0.446138823828;HNF1A:-0.461195121955;REST:-0.465167181957;HES1:-0.473958120048;HNF4A_NR2F1,2:-0.489979141922;TAL1_TCF{3,4,12}:-0.493564737596;SOX17:-0.496914817887;EN1,2:-0.503644377598;EVI1:-0.516447058228;NKX6-1,2:-0.539141524721;HOX{A5,B5}:-0.542551437025;POU5F1:-0.57063020458;MYBL2:-0.585294180895;ZNF423:-0.58996936446;ARID5B:-0.613818342011;DBP:-0.630630670015;NFE2L2:-0.631187808727;NKX3-1:-0.64787257483;ZNF143:-0.662677282654;IKZF2:-0.681714987494;MED-1{core}:-0.683571944045;GFI1:-0.699065981226;NKX2-2,8:-0.701018474612;SP1:-0.701737582416;POU3F1..4:-0.710980943991;ZFP161:-0.711342741432;PAX4:-0.714526925233;MTF1:-0.715905419359;TLX1..3_NFIC{dimer}:-0.788066782302;GZF1:-0.812449128192;ALX4:-0.8182082134;ZBTB6:-0.848787739367;ONECUT1,2:-0.851762021804;GLI1..3:-0.855521846962;FOXP1:-0.9596694025;GTF2I:-0.972213789751;NRF1:-0.987057120813;HMGA1,2:-0.998296429988;NKX2-1,4:-1.01784244455;TFDP1:-1.02760997142;LHX3,4:-1.04836384778;XCPE1{core}:-1.10057753211;FOXL1:-1.11679447704;TOPORS:-1.17491952505;HOX{A6,A7,B6,B7}:-1.23666840589;TEAD1:-1.24786235154;TEF:-1.26210900602;PRDM1:-1.26316724961;GATA4:-1.26764912728;TFCP2:-1.35024898705;GTF2A1,2:-1.37626970491;GFI1B:-1.37699213619;TP53:-1.42258617817;FOXM1:-1.42661095641;POU1F1:-1.43637513159;GCM1,2:-1.48500290949;RREB1:-1.52093698196;POU6F1:-1.56952039691;UFEwm:-1.56997852358;PAX1,9:-1.63120770976;HOX{A4,D4}:-1.64717613401;CDC5L:-1.67830433934;IKZF1:-1.6960063716;NR3C1:-1.75280198538;PITX1..3:-1.78818083655;KLF4:-1.79956807343;ADNP_IRX_SIX_ZHX:-1.85344939194;ZNF384:-1.90481340648;NKX3-2:-1.95705299402;NR1H4:-2.41264438164;SPZ1:-2.5036745741;FOXD3:-2.98698733164 | ||
|comment= | |comment= | ||
|created_by= | |created_by= | ||
Revision as of 17:38, 14 March 2012
| Name: | CD34+ Progenitors, donor1 |
|---|---|
| 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: CNhs13227
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: CNhs13227
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.672 |
| 10 | 10 | 0.125 |
| 100 | 100 | 0.389 |
| 101 | 101 | 0.627 |
| 102 | 102 | 0.885 |
| 103 | 103 | 0.185 |
| 104 | 104 | 0.424 |
| 105 | 105 | 0.446 |
| 106 | 106 | 0.00505 |
| 107 | 107 | 0.273 |
| 108 | 108 | 0.216 |
| 109 | 109 | 0.321 |
| 11 | 11 | 0.599 |
| 110 | 110 | 0.564 |
| 111 | 111 | 0.14 |
| 112 | 112 | 0.892 |
| 113 | 113 | 0.366 |
| 114 | 114 | 0.606 |
| 115 | 115 | 0.262 |
| 116 | 116 | 0.297 |
| 117 | 117 | 0.0039 |
| 118 | 118 | 0.114 |
| 119 | 119 | 0.372 |
| 12 | 12 | 0.285 |
| 120 | 120 | 0.592 |
| 121 | 121 | 0.529 |
| 122 | 122 | 0.345 |
| 123 | 123 | 0.546 |
| 124 | 124 | 0.903 |
| 125 | 125 | 0.939 |
| 126 | 126 | 0.298 |
| 127 | 127 | 0.798 |
| 128 | 128 | 0.451 |
| 129 | 129 | 0.867 |
| 13 | 13 | 0.153 |
| 130 | 130 | 0.691 |
| 131 | 131 | 0.579 |
| 132 | 132 | 0.0192 |
| 133 | 133 | 0.0297 |
| 134 | 134 | 0.598 |
| 135 | 135 | 0.873 |
| 136 | 136 | 0.359 |
| 137 | 137 | 0.00204 |
| 138 | 138 | 0.771 |
| 139 | 139 | 0.413 |
| 14 | 14 | 0.85 |
| 140 | 140 | 0.47 |
| 141 | 141 | 0.821 |
| 142 | 142 | 0.862 |
| 143 | 143 | 0.13 |
| 144 | 144 | 0.721 |
| 145 | 145 | 0.281 |
| 146 | 146 | 0.86 |
| 147 | 147 | 0.0656 |
| 148 | 148 | 0.815 |
| 149 | 149 | 0.866 |
| 15 | 15 | 0.402 |
| 150 | 150 | 0.654 |
| 151 | 151 | 0.562 |
| 152 | 152 | 0.258 |
| 153 | 153 | 0.866 |
| 154 | 154 | 0.811 |
| 155 | 155 | 0.0354 |
| 156 | 156 | 0.307 |
| 157 | 157 | 0.309 |
| 158 | 158 | 0.0586 |
| 159 | 159 | 0.129 |
| 16 | 16 | 0.596 |
| 160 | 160 | 0.476 |
| 161 | 161 | 0.364 |
| 162 | 162 | 0.0798 |
| 163 | 163 | 0.866 |
| 164 | 164 | 0.587 |
| 165 | 165 | 0.35 |
| 166 | 166 | 0.526 |
| 167 | 167 | 0.221 |
| 168 | 168 | 0.755 |
| 169 | 169 | 0.339 |
| 17 | 17 | 0.822 |
| 18 | 18 | 0.723 |
| 19 | 19 | 0.187 |
| 2 | 2 | 0.326 |
| 20 | 20 | 0.35 |
| 21 | 21 | 0.247 |
| 22 | 22 | 0.953 |
| 23 | 23 | 0.952 |
| 24 | 24 | 0.935 |
| 25 | 25 | 0.35 |
| 26 | 26 | 0.968 |
| 27 | 27 | 0.748 |
| 28 | 28 | 0.371 |
| 29 | 29 | 0.134 |
| 3 | 3 | 0.647 |
| 30 | 30 | 0.422 |
| 31 | 31 | 0.662 |
| 32 | 32 | 0.0138 |
| 33 | 33 | 0.291 |
| 34 | 34 | 0.776 |
| 35 | 35 | 0.258 |
| 36 | 36 | 0.156 |
| 37 | 37 | 0.00893 |
| 38 | 38 | 0.784 |
| 39 | 39 | 0.739 |
| 4 | 4 | 0.592 |
| 40 | 40 | 0.69 |
| 41 | 41 | 0.0984 |
| 42 | 42 | 0.436 |
| 43 | 43 | 0.702 |
| 44 | 44 | 0.372 |
| 45 | 45 | 0.938 |
| 46 | 46 | 0.764 |
| 47 | 47 | 0.747 |
| 48 | 48 | 0.918 |
| 49 | 49 | 0.541 |
| 5 | 5 | 0.544 |
| 50 | 50 | 0.985 |
| 51 | 51 | 0.518 |
| 52 | 52 | 0.682 |
| 53 | 53 | 0.672 |
| 54 | 54 | 0.662 |
| 55 | 55 | 0.463 |
| 56 | 56 | 0.978 |
| 57 | 57 | 0.528 |
| 58 | 58 | 0.288 |
| 59 | 59 | 0.563 |
| 6 | 6 | 0.272 |
| 60 | 60 | 0.343 |
| 61 | 61 | 0.0767 |
| 62 | 62 | 0.214 |
| 63 | 63 | 0.634 |
| 64 | 64 | 0.87 |
| 65 | 65 | 0.596 |
| 66 | 66 | 0.912 |
| 67 | 67 | 0.656 |
| 68 | 68 | 0.975 |
| 69 | 69 | 0.215 |
| 7 | 7 | 0.5 |
| 70 | 70 | 0.691 |
| 71 | 71 | 0.166 |
| 72 | 72 | 0.141 |
| 73 | 73 | 0.123 |
| 74 | 74 | 0.528 |
| 75 | 75 | 0.186 |
| 76 | 76 | 0.303 |
| 77 | 77 | 0.0784 |
| 78 | 78 | 0.965 |
| 79 | 79 | 0.0633 |
| 8 | 8 | 0.341 |
| 80 | 80 | 0.0206 |
| 81 | 81 | 0.814 |
| 82 | 82 | 0.107 |
| 83 | 83 | 0.0033 |
| 84 | 84 | 0.322 |
| 85 | 85 | 0.953 |
| 86 | 86 | 0.0284 |
| 87 | 87 | 0.0556 |
| 88 | 88 | 0.518 |
| 89 | 89 | 0.106 |
| 9 | 9 | 0.306 |
| 90 | 90 | 0.983 |
| 91 | 91 | 0.783 |
| 92 | 92 | 0.949 |
| 93 | 93 | 0.511 |
| 94 | 94 | 0.377 |
| 95 | 95 | 0.0022 |
| 96 | 96 | 0.63 |
| 97 | 97 | 0.967 |
| 98 | 98 | 0.487 |
| 99 | 99 | 5.00058e-5 |
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: CNhs13227
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000002 in vivo cell sample
FF:0000026 human CD34-positive hematopoietic stem cell sample
FF:0000210 human sample
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
