FF:10813-111B3: Difference between revisions
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|top_motifs= | |top_motifs=FOXL1:2.85083557332;ESR1:2.57837804792;ALX4:2.30780162748;ATF6:2.06650059581;UFEwm:2.06203702592;NKX3-1:2.04055349488;TAL1_TCF{3,4,12}:1.95013468742;HMGA1,2:1.67845845482;HMX1:1.65887577055;ZIC1..3:1.62483626172;EVI1:1.60916709832;GLI1..3:1.59881704758;ZNF384:1.54557953245;NANOG{mouse}:1.53814063805;AIRE:1.48973284488;MAFB:1.36185833217;MYBL2:1.34100461052;LHX3,4:1.23061466907;ZNF238:1.22637027111;KLF4:1.18935129869;TFAP4:1.1565812017;XBP1:1.08536030641;NKX2-1,4:1.06669993401;TEAD1:1.06268207147;FOXD3:1.05823815993;GFI1:1.05458212822;HIF1A:1.04588406923;MTE{core}:1.03151382909;ARID5B:0.949309316;SRF:0.930946516613;RXR{A,B,G}:0.887668581294;GATA4:0.867329448223;PAX4:0.850397693545;CDC5L:0.845607261253;GZF1:0.843841467517;PATZ1:0.840218268402;HOX{A4,D4}:0.839807428784;TFAP2B:0.825471453154;PAX8:0.81398964152;ZNF423:0.807161881664;PRDM1:0.791092072598;FOX{I1,J2}:0.778421851399;TFAP2{A,C}:0.776281282147;TFCP2:0.744019398259;SPZ1:0.707281267488;RBPJ:0.697925456843;MAZ:0.695864343756;HIC1:0.687702374271;TOPORS:0.678123086311;TP53:0.676385571365;ZBTB6:0.646553643211;SOX17:0.644626670008;SOX5:0.622523210527;PAX1,9:0.596508206938;GTF2I:0.596268318447;GFI1B:0.590867092648;TBX4,5:0.574354688451;TLX1..3_NFIC{dimer}:0.534577436735;HSF1,2:0.528046177318;NFATC1..3:0.52510771277;MZF1:0.521750448031;BPTF:0.510409752214;HES1:0.505107122076;IKZF1:0.500470982882;GTF2A1,2:0.497918535963;EGR1..3:0.474362120975;RXRA_VDR{dimer}:0.473476877756;EBF1:0.459454331609;PDX1:0.439043011089;NR6A1:0.429433024607;NR3C1:0.416378681456;POU5F1:0.390683629018;RREB1:0.358003335398;ATF4:0.351680698083;TBP:0.321441997385;STAT5{A,B}:0.316656122983;HOX{A5,B5}:0.31084479881;CREB1:0.310644791036;SP1:0.306973076665;TFDP1:0.295391205557;MTF1:0.293154917027;RFX1:0.280206100961;NFE2L1:0.2755224331;XCPE1{core}:0.269728774803;STAT2,4,6:0.233390374405;NFIL3:0.202610822639;EN1,2:0.188231663586;POU3F1..4:0.182517336843;MYFfamily:0.162778103038;FOXN1:0.155417209484;TEF:0.152451374208;HOX{A6,A7,B6,B7}:0.152192257582;MEF2{A,B,C,D}:0.124221103475;MED-1{core}:0.114140740312;LEF1_TCF7_TCF7L1,2:0.0645275660858;GCM1,2:0.0562334659695;AHR_ARNT_ARNT2:0.0536941767389;IKZF2:0.0492791297399;FOX{F1,F2,J1}:0.0233557897748;HLF:0.0146410327042;FOXO1,3,4:-0.0311856730083;HAND1,2:-0.0362547286455;BACH2:-0.052518344878;REST:-0.0555736516005;bHLH_family:-0.0728347673725;NFIX:-0.0788092901104;CEBPA,B_DDIT3:-0.0896700931254;PAX5:-0.0931107044963;NFE2:-0.0955817279592;NKX2-2,8:-0.101190928639;DBP:-0.108953691867;FOX{D1,D2}:-0.110623532483;FOXP1:-0.139340517777;ATF5_CREB3:-0.150587947247;JUN:-0.151658505024;ONECUT1,2:-0.152334667726;DMAP1_NCOR{1,2}_SMARC:-0.153434076908;NKX6-1,2:-0.160475674893;SOX2:-0.167178600981;FOS_FOS{B,L1}_JUN{B,D}:-0.183652111871;NFE2L2:-0.183900559148;ZNF143:-0.194245179748;MYB:-0.196174425614;NHLH1,2:-0.20521535664;NR1H4:-0.207001332967;FOSL2:-0.215701850265;NKX3-2:-0.239279086437;IRF1,2:-0.251234157442;FOXA2:-0.263531536984;YY1:-0.289405454364;RUNX1..3:-0.291284398264;ATF2:-0.291321306374;PPARG:-0.296371896459;SMAD1..7,9:-0.305410014057;NRF1:-0.365298545838;E2F1..5:-0.368891111944;PAX3,7:-0.372580490681;T:-0.393881680893;NKX2-3_NKX2-5:-0.414196704408;RFX2..5_RFXANK_RFXAP:-0.44528237641;NFKB1_REL_RELA:-0.461563516954;NFY{A,B,C}:-0.466567671286;HNF4A_NR2F1,2:-0.46755473184;FOXP3:-0.475691969481;ELK1,4_GABP{A,B1}:-0.475927907204;ZBTB16:-0.484812870104;HNF1A:-0.491949673417;LMO2:-0.492515683569;POU2F1..3:-0.500843081322;ZFP161:-0.501754395443;EP300:-0.504075255635;TGIF1:-0.520552623795;ZNF148:-0.53320079155;AR:-0.535974099714;RORA:-0.538705585002;SPIB:-0.595524336092;FOXQ1:-0.621797168106;SREBF1,2:-0.63050852164;SNAI1..3:-0.634685258973;FOXM1:-0.652001824617;PBX1:-0.669064208492;TLX2:-0.674523129284;PITX1..3:-0.680281844175;BREu{core}:-0.718063847301;ADNP_IRX_SIX_ZHX:-0.745491123551;SPI1:-0.771326365754;POU6F1:-0.777143244247;CDX1,2,4:-0.786120901891;IRF7:-0.817750800682;HOXA9_MEIS1:-0.826666382582;ALX1:-0.83038599834;ELF1,2,4:-0.871965933611;PRRX1,2:-0.87575280093;ETS1,2:-0.913933306434;HBP1_HMGB_SSRP1_UBTF:-0.984461679606;NR5A1,2:-0.984788470283;ZEB1:-0.985274906712;STAT1,3:-0.986466840568;SOX{8,9,10}:-1.0055443138;OCT4_SOX2{dimer}:-1.07665096183;ESRRA:-1.0766918085;GATA6:-1.10206930669;VSX1,2:-1.11980966381;PAX2:-1.14648383678;PAX6:-1.19872917513;POU1F1:-1.22608304816;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.23461465424;CUX2:-1.28332205549;CRX:-1.40953954776;NANOG:-1.45643892468;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.45740799303;MYOD1:-1.83929551811 | ||
|comment= | |comment= | ||
|created_by= | |created_by= | ||
Revision as of 18:03, 14 March 2012
| Name: | normal embryonic palatal mesenchymal cell line:HEPM |
|---|---|
| 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: CNhs11894
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: CNhs11894
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.219 |
| 10 | 10 | 0.667 |
| 100 | 100 | 0.754 |
| 101 | 101 | 0.73 |
| 102 | 102 | 0.338 |
| 103 | 103 | 0.36 |
| 104 | 104 | 0.846 |
| 105 | 105 | 0.262 |
| 106 | 106 | 0.482 |
| 107 | 107 | 0.418 |
| 108 | 108 | 0.737 |
| 109 | 109 | 0.234 |
| 11 | 11 | 0.911 |
| 110 | 110 | 0.509 |
| 111 | 111 | 0.214 |
| 112 | 112 | 0.678 |
| 113 | 113 | 0.557 |
| 114 | 114 | 0.631 |
| 115 | 115 | 2.33578e-4 |
| 116 | 116 | 0.355 |
| 117 | 117 | 0.244 |
| 118 | 118 | 0.694 |
| 119 | 119 | 0.287 |
| 12 | 12 | 0.262 |
| 120 | 120 | 0.271 |
| 121 | 121 | 0.396 |
| 122 | 122 | 0.0126 |
| 123 | 123 | 0.0496 |
| 124 | 124 | 0.631 |
| 125 | 125 | 0.399 |
| 126 | 126 | 0.294 |
| 127 | 127 | 0.477 |
| 128 | 128 | 0.604 |
| 129 | 129 | 0.18 |
| 13 | 13 | 0.247 |
| 130 | 130 | 0.879 |
| 131 | 131 | 0.891 |
| 132 | 132 | 0.032 |
| 133 | 133 | 0.812 |
| 134 | 134 | 0.177 |
| 135 | 135 | 0.0779 |
| 136 | 136 | 0.732 |
| 137 | 137 | 0.119 |
| 138 | 138 | 0.539 |
| 139 | 139 | 0.364 |
| 14 | 14 | 0.107 |
| 140 | 140 | 0.0941 |
| 141 | 141 | 0.291 |
| 142 | 142 | 0.271 |
| 143 | 143 | 0.596 |
| 144 | 144 | 0.231 |
| 145 | 145 | 0.576 |
| 146 | 146 | 0.145 |
| 147 | 147 | 0.239 |
| 148 | 148 | 0.152 |
| 149 | 149 | 0.313 |
| 15 | 15 | 0.0594 |
| 150 | 150 | 0.581 |
| 151 | 151 | 0.274 |
| 152 | 152 | 0.037 |
| 153 | 153 | 0.614 |
| 154 | 154 | 0.814 |
| 155 | 155 | 0.731 |
| 156 | 156 | 0.33 |
| 157 | 157 | 0.319 |
| 158 | 158 | 0.0211 |
| 159 | 159 | 0.603 |
| 16 | 16 | 0.169 |
| 160 | 160 | 0.915 |
| 161 | 161 | 0.575 |
| 162 | 162 | 0.918 |
| 163 | 163 | 0.225 |
| 164 | 164 | 0.526 |
| 165 | 165 | 0.245 |
| 166 | 166 | 0.017 |
| 167 | 167 | 0.631 |
| 168 | 168 | 0.171 |
| 169 | 169 | 0.482 |
| 17 | 17 | 0.635 |
| 18 | 18 | 0.983 |
| 19 | 19 | 0.0214 |
| 2 | 2 | 0.998 |
| 20 | 20 | 0.809 |
| 21 | 21 | 0.634 |
| 22 | 22 | 0.766 |
| 23 | 23 | 0.611 |
| 24 | 24 | 0.215 |
| 25 | 25 | 0.188 |
| 26 | 26 | 0.658 |
| 27 | 27 | 0.57 |
| 28 | 28 | 0.213 |
| 29 | 29 | 0.609 |
| 3 | 3 | 0.392 |
| 30 | 30 | 0.901 |
| 31 | 31 | 0.74 |
| 32 | 32 | 9.46976e-17 |
| 33 | 33 | 1 |
| 34 | 34 | 0.209 |
| 35 | 35 | 0.619 |
| 36 | 36 | 0.0747 |
| 37 | 37 | 0.426 |
| 38 | 38 | 0.151 |
| 39 | 39 | 0.736 |
| 4 | 4 | 0.299 |
| 40 | 40 | 0.0289 |
| 41 | 41 | 0.149 |
| 42 | 42 | 0.324 |
| 43 | 43 | 0.393 |
| 44 | 44 | 0.192 |
| 45 | 45 | 0.255 |
| 46 | 46 | 0.649 |
| 47 | 47 | 0.175 |
| 48 | 48 | 0.512 |
| 49 | 49 | 0.175 |
| 5 | 5 | 0.489 |
| 50 | 50 | 0.938 |
| 51 | 51 | 0.59 |
| 52 | 52 | 0.831 |
| 53 | 53 | 0.123 |
| 54 | 54 | 0.995 |
| 55 | 55 | 0.271 |
| 56 | 56 | 0.541 |
| 57 | 57 | 0.549 |
| 58 | 58 | 0.0815 |
| 59 | 59 | 0.991 |
| 6 | 6 | 0.507 |
| 60 | 60 | 0.58 |
| 61 | 61 | 0.549 |
| 62 | 62 | 0.252 |
| 63 | 63 | 0.945 |
| 64 | 64 | 0.847 |
| 65 | 65 | 0.825 |
| 66 | 66 | 0.0704 |
| 67 | 67 | 0.485 |
| 68 | 68 | 0.957 |
| 69 | 69 | 0.623 |
| 7 | 7 | 0.13 |
| 70 | 70 | 0.298 |
| 71 | 71 | 0.395 |
| 72 | 72 | 0.662 |
| 73 | 73 | 0.324 |
| 74 | 74 | 0.971 |
| 75 | 75 | 0.382 |
| 76 | 76 | 0.998 |
| 77 | 77 | 0.898 |
| 78 | 78 | 0.0345 |
| 79 | 79 | 0.00717 |
| 8 | 8 | 0.556 |
| 80 | 80 | 0.0491 |
| 81 | 81 | 0.961 |
| 82 | 82 | 0.776 |
| 83 | 83 | 0.389 |
| 84 | 84 | 0.96 |
| 85 | 85 | 0.318 |
| 86 | 86 | 0.751 |
| 87 | 87 | 0.84 |
| 88 | 88 | 0.477 |
| 89 | 89 | 0.557 |
| 9 | 9 | 0.738 |
| 90 | 90 | 0.304 |
| 91 | 91 | 0.967 |
| 92 | 92 | 0.804 |
| 93 | 93 | 0.418 |
| 94 | 94 | 0.791 |
| 95 | 95 | 0.967 |
| 96 | 96 | 0.952 |
| 97 | 97 | 0.682 |
| 98 | 98 | 0.0614 |
| 99 | 99 | 0.165 |
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: CNhs11894
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
CL:0000134 mesenchymal cell
EFO:0002091 biological replicate
FF:0000003 cell line sample
FF:0000210 human sample
FF:0100669 embryonic cell line sample
UBERON:0005705 primary palate mesenchyme
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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000075 (subdivision of skeletal system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001444 (subdivision of head)
0001456 (face)
0001474 (bone element)
0001708 (jaw skeleton)
0001709 (upper jaw region)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002244 (premaxilla)
0002329 (somite)
0002342 (neural crest)
0002346 (neurectoderm)
0002384 (connective tissue)
0002397 (maxilla)
0002514 (intramembranous bone)
0002532 (epiblast (generic))
0002539 (pharyngeal arch)
0003059 (presomitic mesoderm)
0003075 (neural plate)
0003077 (paraxial mesoderm)
0003089 (sclerotome)
0003104 (mesenchyme)
0003129 (skull)
0003323 (mesenchyme of upper jaw)
0003457 (head bone)
0003462 (facial bone)
0004066 (frontonasal prominence)
0004068 (medial nasal prominence)
0004089 (midface)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004288 (skeleton)
0004765 (skeletal element)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005620 (primary palate)
0005705 (primary palate mesenchyme)
0006598 (presumptive structure)
0007284 (presumptive neural plate)
0007375 (roof of mouth)
0008001 (irregular bone)
0008193 (pneumatized bone)
0008814 (pharyngeal arch system)
0008816 (embryonic head)
0009142 (entire embryonic mesenchyme)
0009292 (embryonic nasal process)
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
