FF:10663-109C6: Difference between revisions
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|top_motifs= | |top_motifs=TOPORS:4.28708651435;PITX1..3:4.10554169973;FOXP1:3.91252758068;PAX4:3.23293686208;ALX1:3.1595784344;AIRE:2.62620344742;ZBTB16:2.19014776549;CDX1,2,4:2.16851063033;POU1F1:1.94991437435;FOXD3:1.89284913102;POU3F1..4:1.428417362;PRRX1,2:1.42047896505;ARID5B:1.33040395342;STAT5{A,B}:1.31122686624;PBX1:1.25236894232;HOXA9_MEIS1:1.23113285029;POU2F1..3:1.21162951698;GATA4:1.20587732193;LHX3,4:1.20283262918;DBP:1.16755421189;IKZF2:1.16704663582;OCT4_SOX2{dimer}:1.11224612899;E2F1..5:1.0650869204;FOXL1:1.01831699331;POU6F1:1.00962970603;FOXM1:0.971881575305;BREu{core}:0.960543990279;ZNF143:0.955909660247;NRF1:0.946100071114;GTF2A1,2:0.930954265512;YY1:0.904225701666;bHLH_family:0.897914121777;ATF4:0.890923878997;NKX6-1,2:0.890860062408;EGR1..3:0.872868333643;SOX{8,9,10}:0.853675659394;ATF5_CREB3:0.852442499938;T:0.851483528515;POU5F1:0.825488574021;PAX3,7:0.811157796855;PRDM1:0.795247588841;GFI1:0.785442502873;CUX2:0.77357141769;HOX{A5,B5}:0.760659508098;NKX3-1:0.735040933985;FOXQ1:0.717722318239;CRX:0.716776185181;ZIC1..3:0.698685143751;DMAP1_NCOR{1,2}_SMARC:0.693401947675;RFX1:0.670149405162;ZNF384:0.670001672158;HOX{A6,A7,B6,B7}:0.63667189593;NR6A1:0.629760274873;TFDP1:0.623509608485;UFEwm:0.615994744082;NFY{A,B,C}:0.597211138322;ELK1,4_GABP{A,B1}:0.587349329435;FOX{D1,D2}:0.572214406963;REST:0.542239948355;ZNF423:0.500574739434;ATF6:0.493738031145;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.472762251233;RFX2..5_RFXANK_RFXAP:0.429937272715;TEF:0.390683020294;GTF2I:0.357866835346;ZBTB6:0.331585075629;AHR_ARNT_ARNT2:0.312381854086;BPTF:0.301882050731;MZF1:0.290373376251;MTE{core}:0.277854104316;PATZ1:0.273671804639;SOX17:0.270798527285;FOXN1:0.265548819956;SOX5:0.26005895125;STAT1,3:0.246028537711;TLX1..3_NFIC{dimer}:0.240760450747;KLF4:0.221798165056;RORA:0.213068201388;HMGA1,2:0.205016104808;RBPJ:0.196383991467;HOX{A4,D4}:0.180366591597;EVI1:0.165008486029;RXR{A,B,G}:0.153083958166;ONECUT1,2:0.150618907396;MYB:0.106491564503;ZFP161:0.101115851218;FOXP3:0.080929302599;CDC5L:0.0682928076445;PAX1,9:0.0583801119655;PAX8:0.0321502442075;CREB1:0.0149642468047;NHLH1,2:0.0100354468635;PDX1:-0.00413069588585;SREBF1,2:-0.0188535150433;MED-1{core}:-0.023628653039;NFE2L1:-0.0658157046;TBP:-0.0912980753635;NKX2-1,4:-0.107530122676;PAX2:-0.115140036721;ATF2:-0.131572777871;MEF2{A,B,C,D}:-0.143284832999;RREB1:-0.169131804949;PAX5:-0.192809140033;EN1,2:-0.209430633413;GZF1:-0.224965481141;MAZ:-0.225984888685;FOX{I1,J2}:-0.226935990638;ADNP_IRX_SIX_ZHX:-0.233425172143;NKX2-2,8:-0.233911207316;NKX2-3_NKX2-5:-0.23403881967;SP1:-0.253363249001;TFAP2B:-0.280800340622;JUN:-0.284123812175;XBP1:-0.293920412606;NFIX:-0.319269583175;GFI1B:-0.348614215783;SPIB:-0.352536260487;CEBPA,B_DDIT3:-0.360153184307;ALX4:-0.361933693215;XCPE1{core}:-0.380446765549;HNF1A:-0.383787664034;NANOG:-0.385364542078;PAX6:-0.388994760632;GATA6:-0.416749624415;MYFfamily:-0.450917473887;FOXO1,3,4:-0.460556071515;NFIL3:-0.473031795392;NKX3-2:-0.474217119734;NFE2L2:-0.493799066673;RUNX1..3:-0.494301318914;TLX2:-0.500540499191;MTF1:-0.504903551592;NFKB1_REL_RELA:-0.50795941823;TAL1_TCF{3,4,12}:-0.521848785092;FOXA2:-0.534888329017;EBF1:-0.57131422961;TEAD1:-0.574172381404;HIC1:-0.59468816737;IRF1,2:-0.599600122574;HES1:-0.642005863741;ZNF238:-0.642722935946;HNF4A_NR2F1,2:-0.644864579266;SPI1:-0.673847509637;EP300:-0.676519292458;IRF7:-0.676531315097;SRF:-0.696501713941;MAFB:-0.713793839853;TFAP2{A,C}:-0.716136612568;SOX2:-0.717274366863;LMO2:-0.729108902667;NFE2:-0.73143370006;STAT2,4,6:-0.735011912376;TP53:-0.741984286029;AR:-0.75444688592;ELF1,2,4:-0.759466970008;FOS_FOS{B,L1}_JUN{B,D}:-0.766082922391;NANOG{mouse}:-0.773836554888;SNAI1..3:-0.778560796942;HLF:-0.785275154744;ZEB1:-0.81109435967;HBP1_HMGB_SSRP1_UBTF:-0.818093358351;HMX1:-0.85295447092;FOSL2:-0.880942142748;MYOD1:-0.897924152322;SPZ1:-0.902574261879;MYBL2:-0.91407707129;BACH2:-0.927860891287;ETS1,2:-0.931669344735;NR1H4:-0.977957660531;TBX4,5:-0.992779540648;LEF1_TCF7_TCF7L1,2:-1.06206063657;TGIF1:-1.10292293193;HSF1,2:-1.12863038597;GLI1..3:-1.15118102103;ESRRA:-1.19844932787;GCM1,2:-1.20292859407;HIF1A:-1.21133811494;SMAD1..7,9:-1.23029076256;NR3C1:-1.23417167821;HAND1,2:-1.28989515865;PPARG:-1.30946425009;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.36292223969;NR5A1,2:-1.39442946492;IKZF1:-1.45382574991;NFATC1..3:-1.48337395688;FOX{F1,F2,J1}:-1.49365836515;VSX1,2:-1.56133730371;RXRA_VDR{dimer}:-1.63774155407;TFAP4:-1.63869669236;ZNF148:-1.9270647122;TFCP2:-1.93321115773;ESR1:-2.07261836761 | ||
|comment= | |comment= | ||
|created_by= | |created_by= | ||
Revision as of 18:02, 14 March 2012
| Name: | neuroectodermal tumor cell line:FU-RPNT-2 |
|---|---|
| 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: CNhs11753
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: CNhs11753
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.718 |
| 10 | 10 | 0.98 |
| 100 | 100 | 0.418 |
| 101 | 101 | 0.606 |
| 102 | 102 | 0.814 |
| 103 | 103 | 0.0021 |
| 104 | 104 | 0.686 |
| 105 | 105 | 0.36 |
| 106 | 106 | 0.0356 |
| 107 | 107 | 0.0759 |
| 108 | 108 | 0.7 |
| 109 | 109 | 0.125 |
| 11 | 11 | 0.673 |
| 110 | 110 | 0.697 |
| 111 | 111 | 0.912 |
| 112 | 112 | 0.648 |
| 113 | 113 | 0.997 |
| 114 | 114 | 0.068 |
| 115 | 115 | 0.304 |
| 116 | 116 | 0.508 |
| 117 | 117 | 0.953 |
| 118 | 118 | 0.591 |
| 119 | 119 | 0.732 |
| 12 | 12 | 0.55 |
| 120 | 120 | 0.391 |
| 121 | 121 | 0.353 |
| 122 | 122 | 0.121 |
| 123 | 123 | 4.31211e-5 |
| 124 | 124 | 0.499 |
| 125 | 125 | 0.813 |
| 126 | 126 | 0.119 |
| 127 | 127 | 0.127 |
| 128 | 128 | 0.436 |
| 129 | 129 | 0.456 |
| 13 | 13 | 0.289 |
| 130 | 130 | 0.938 |
| 131 | 131 | 0.706 |
| 132 | 132 | 0.379 |
| 133 | 133 | 0.717 |
| 134 | 134 | 0.931 |
| 135 | 135 | 0.0866 |
| 136 | 136 | 0.208 |
| 137 | 137 | 0.21 |
| 138 | 138 | 0.521 |
| 139 | 139 | 0.764 |
| 14 | 14 | 0.688 |
| 140 | 140 | 0.874 |
| 141 | 141 | 0.863 |
| 142 | 142 | 0.535 |
| 143 | 143 | 0.00229 |
| 144 | 144 | 0.481 |
| 145 | 145 | 0.878 |
| 146 | 146 | 0.965 |
| 147 | 147 | 0.574 |
| 148 | 148 | 0.0674 |
| 149 | 149 | 0.124 |
| 15 | 15 | 0.455 |
| 150 | 150 | 0.364 |
| 151 | 151 | 0.365 |
| 152 | 152 | 0.00809 |
| 153 | 153 | 0.391 |
| 154 | 154 | 0.165 |
| 155 | 155 | 0.618 |
| 156 | 156 | 0.491 |
| 157 | 157 | 0.82 |
| 158 | 158 | 0.267 |
| 159 | 159 | 0.298 |
| 16 | 16 | 0.26 |
| 160 | 160 | 0.901 |
| 161 | 161 | 0.259 |
| 162 | 162 | 0.547 |
| 163 | 163 | 0.794 |
| 164 | 164 | 0.479 |
| 165 | 165 | 0.546 |
| 166 | 166 | 0.701 |
| 167 | 167 | 0.542 |
| 168 | 168 | 0.62 |
| 169 | 169 | 0.0101 |
| 17 | 17 | 0.268 |
| 18 | 18 | 0.168 |
| 19 | 19 | 0.139 |
| 2 | 2 | 0.0808 |
| 20 | 20 | 0.257 |
| 21 | 21 | 0.138 |
| 22 | 22 | 0.0578 |
| 23 | 23 | 0.0101 |
| 24 | 24 | 0.192 |
| 25 | 25 | 0.467 |
| 26 | 26 | 0.813 |
| 27 | 27 | 0.112 |
| 28 | 28 | 0.632 |
| 29 | 29 | 0.845 |
| 3 | 3 | 0.746 |
| 30 | 30 | 0.0893 |
| 31 | 31 | 0.221 |
| 32 | 32 | 0.0653 |
| 33 | 33 | 0.788 |
| 34 | 34 | 0.11 |
| 35 | 35 | 0.982 |
| 36 | 36 | 0.348 |
| 37 | 37 | 0.309 |
| 38 | 38 | 0.465 |
| 39 | 39 | 0.833 |
| 4 | 4 | 0.554 |
| 40 | 40 | 0.755 |
| 41 | 41 | 0.0552 |
| 42 | 42 | 0.58 |
| 43 | 43 | 0.338 |
| 44 | 44 | 0.307 |
| 45 | 45 | 0.152 |
| 46 | 46 | 0.451 |
| 47 | 47 | 0.872 |
| 48 | 48 | 0.915 |
| 49 | 49 | 0.951 |
| 5 | 5 | 0.454 |
| 50 | 50 | 0.845 |
| 51 | 51 | 0.775 |
| 52 | 52 | 0.308 |
| 53 | 53 | 0.148 |
| 54 | 54 | 0.517 |
| 55 | 55 | 0.623 |
| 56 | 56 | 0.752 |
| 57 | 57 | 0.349 |
| 58 | 58 | 0.563 |
| 59 | 59 | 0.0257 |
| 6 | 6 | 0.0783 |
| 60 | 60 | 0.114 |
| 61 | 61 | 0.325 |
| 62 | 62 | 0.205 |
| 63 | 63 | 0.96 |
| 64 | 64 | 0.776 |
| 65 | 65 | 0.286 |
| 66 | 66 | 0.574 |
| 67 | 67 | 0.918 |
| 68 | 68 | 0.714 |
| 69 | 69 | 0.478 |
| 7 | 7 | 0.869 |
| 70 | 70 | 0.35 |
| 71 | 71 | 0.612 |
| 72 | 72 | 0.323 |
| 73 | 73 | 0.0488 |
| 74 | 74 | 0.0854 |
| 75 | 75 | 0.873 |
| 76 | 76 | 0.197 |
| 77 | 77 | 0.132 |
| 78 | 78 | 0.718 |
| 79 | 79 | 0.545 |
| 8 | 8 | 0.706 |
| 80 | 80 | 0.0437 |
| 81 | 81 | 0.844 |
| 82 | 82 | 0.826 |
| 83 | 83 | 0.727 |
| 84 | 84 | 0.281 |
| 85 | 85 | 0.133 |
| 86 | 86 | 0.722 |
| 87 | 87 | 0.453 |
| 88 | 88 | 0.442 |
| 89 | 89 | 0.0195 |
| 9 | 9 | 0.032 |
| 90 | 90 | 0.274 |
| 91 | 91 | 0.671 |
| 92 | 92 | 0.373 |
| 93 | 93 | 0.406 |
| 94 | 94 | 0.587 |
| 95 | 95 | 0.378 |
| 96 | 96 | 0.747 |
| 97 | 97 | 0.822 |
| 98 | 98 | 0.567 |
| 99 | 99 | 0.705 |
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: CNhs11753
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
DOID:171 neuroectodermal tumor
EFO:0002091 biological replicate
FF:0000003 cell line sample
FF:0000210 human sample
UBERON:0002346 neurectoderm
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
DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
171 (neuroectodermal tumor)
2994 (germ cell cancer)
3095 (germ cell and embryonal cancer)
4 (disease)
UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0005423 (developing anatomical structure)
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
