FF:11592-120G8: Difference between revisions
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|top_motifs= | |top_motifs=GZF1:2.21197814115;ZNF238:1.62188894313;TFAP4:1.44052493399;EN1,2:1.40077843482;AIRE:1.34989737571;FOXD3:1.34814192483;HOX{A6,A7,B6,B7}:1.31318910393;RXR{A,B,G}:1.2325599794;GFI1B:1.18123302003;MYBL2:1.15863630467;TEF:1.14172726566;bHLH_family:1.128365355;PAX5:1.11520105489;HOX{A5,B5}:1.10468791194;GATA4:1.08960733919;NKX2-2,8:1.05473393256;NFIX:1.05303688907;EBF1:1.04920705143;NKX2-1,4:1.03470973168;GLI1..3:1.02969545827;CDX1,2,4:1.01202246084;KLF4:0.981893429466;DBP:0.97921161847;NFATC1..3:0.976880250909;UFEwm:0.947960195871;ALX4:0.89977236346;ESR1:0.894074680495;PATZ1:0.885822942189;TLX1..3_NFIC{dimer}:0.865271861095;NR3C1:0.861995357449;NKX6-1,2:0.859213559361;GTF2I:0.803127112971;FOXO1,3,4:0.762181931362;TAL1_TCF{3,4,12}:0.750410652317;HOX{A4,D4}:0.729017387666;EVI1:0.726029384634;NKX3-1:0.703064161764;SRF:0.689752349438;NR1H4:0.678853311379;FOXM1:0.67769742585;SPZ1:0.660696573254;MAZ:0.651118268623;GTF2A1,2:0.619393724211;STAT2,4,6:0.603734785497;STAT5{A,B}:0.594569487961;TEAD1:0.571184814789;ZNF384:0.55540461078;SREBF1,2:0.548176168122;LHX3,4:0.539029801927;MYFfamily:0.534957508256;SOX17:0.527917139001;NHLH1,2:0.524137205846;ZIC1..3:0.494616237397;HAND1,2:0.492511933019;FOXP3:0.492260543129;ZNF148:0.485974087931;HLF:0.468187078112;NANOG{mouse}:0.45735397701;HNF4A_NR2F1,2:0.450744674032;MZF1:0.449210789572;ARID5B:0.429733784822;AHR_ARNT_ARNT2:0.39340147462;PAX6:0.382492362034;POU3F1..4:0.375288880766;TP53:0.368852860208;ATF6:0.35601312703;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.350943418795;RBPJ:0.336620286968;ONECUT1,2:0.332014472416;VSX1,2:0.331976073078;HIC1:0.328164197844;ZBTB6:0.322796217873;EGR1..3:0.320195646931;MED-1{core}:0.310329749002;CEBPA,B_DDIT3:0.309047893062;HMGA1,2:0.304060262616;RREB1:0.302570057541;PRRX1,2:0.293614912227;TFCP2:0.291260520531;ALX1:0.290020422821;DMAP1_NCOR{1,2}_SMARC:0.2871809855;MTE{core}:0.271070531927;CDC5L:0.260069165948;XBP1:0.254118869138;AR:0.238455268263;RORA:0.229635854396;GCM1,2:0.223134091078;TFAP2{A,C}:0.217152458323;POU6F1:0.21348432246;HSF1,2:0.20682221185;PRDM1:0.197455762955;TLX2:0.188883754113;PBX1:0.159986480743;SOX5:0.120982518614;TFAP2B:0.108199182566;MTF1:0.104206829983;NFE2L2:0.101779852935;ZBTB16:0.0814669567751;ZFP161:0.0772625388247;BPTF:0.0719975710646;IRF1,2:0.07009794458;RFX2..5_RFXANK_RFXAP:0.062988890342;FOXL1:0.0402035296384;ZNF423:0.0369196130483;HNF1A:0.0319773673601;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.0300093725616;ADNP_IRX_SIX_ZHX:0.0116549144419;CUX2:0.0109436616582;HIF1A:-0.00915077464957;TBX4,5:-0.0179678751338;FOX{D1,D2}:-0.0222650953706;NKX2-3_NKX2-5:-0.0229774903031;PAX8:-0.0443262485534;T:-0.045701283917;PAX1,9:-0.0545405851249;PDX1:-0.057307910281;SP1:-0.0615539073301;HES1:-0.0636691292097;PAX4:-0.0650580482779;BREu{core}:-0.0793350298958;YY1:-0.0893117617363;STAT1,3:-0.0936904375936;FOXA2:-0.101596143658;CRX:-0.11187915377;FOXQ1:-0.11783311083;IKZF1:-0.140301771638;TBP:-0.143306036219;SMAD1..7,9:-0.14951713267;FOSL2:-0.1498422539;EP300:-0.17353348358;NFE2:-0.179098208413;RXRA_VDR{dimer}:-0.185282788319;MEF2{A,B,C,D}:-0.186130477305;JUN:-0.197886327292;RUNX1..3:-0.198562774301;POU5F1:-0.206368158359;XCPE1{core}:-0.213156309651;FOS_FOS{B,L1}_JUN{B,D}:-0.216669380624;TOPORS:-0.221571406418;BACH2:-0.229199810958;NFE2L1:-0.230820056041;TFDP1:-0.238911055678;NKX3-2:-0.244337667711;TGIF1:-0.249335690806;RFX1:-0.271334901139;IRF7:-0.282975636041;MAFB:-0.309342716386;NFKB1_REL_RELA:-0.336110597862;HOXA9_MEIS1:-0.340581112802;NR5A1,2:-0.34235384489;LEF1_TCF7_TCF7L1,2:-0.381369471182;REST:-0.382667637588;ATF2:-0.384542072144;HMX1:-0.423513768981;ZNF143:-0.432019538603;NRF1:-0.453949357153;ATF4:-0.478634046422;FOX{F1,F2,J1}:-0.486986426835;MYB:-0.502032058874;SPI1:-0.517237450613;NFIL3:-0.525576137075;HBP1_HMGB_SSRP1_UBTF:-0.539728177546;NANOG:-0.539846452767;PAX3,7:-0.541627940983;LMO2:-0.542898450635;ATF5_CREB3:-0.545097546874;GFI1:-0.551239803429;PAX2:-0.554972582618;NR6A1:-0.579319990972;ESRRA:-0.583091702985;CREB1:-0.590779856787;GATA6:-0.62821615936;ETS1,2:-0.629748232459;SOX2:-0.72898933133;SPIB:-0.744162974754;IKZF2:-0.767403250151;ELF1,2,4:-0.782914214004;ELK1,4_GABP{A,B1}:-0.806394817849;POU2F1..3:-0.841187847833;OCT4_SOX2{dimer}:-0.882615264239;FOXN1:-0.884470199315;SNAI1..3:-0.885877133158;E2F1..5:-0.925914172846;POU1F1:-0.953822137185;ZEB1:-0.969855101795;MYOD1:-1.00897609268;FOXP1:-1.02250324954;SOX{8,9,10}:-1.10735365048;NFY{A,B,C}:-1.22535482893;PITX1..3:-1.31380019058;FOX{I1,J2}:-1.59993546557;PPARG:-2.28972683593 | ||
|comment=Previously: Smooth Muscle Cells - Bronchial, donor2 | |comment=Previously: Smooth Muscle Cells - Bronchial, donor2 | ||
|created_by= | |created_by= | ||
Revision as of 17:51, 14 March 2012
| Name: | Smooth Muscle Cells - Bronchial, donor2 |
|---|---|
| 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: CNhs12348
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: CNhs12348
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.646 |
| 10 | 10 | 0.566 |
| 100 | 100 | 0.641 |
| 101 | 101 | 0.803 |
| 102 | 102 | 0.0402 |
| 103 | 103 | 0.108 |
| 104 | 104 | 0.475 |
| 105 | 105 | 0.936 |
| 106 | 106 | 0.174 |
| 107 | 107 | 0.00636 |
| 108 | 108 | 0.101 |
| 109 | 109 | 0.572 |
| 11 | 11 | 0.828 |
| 110 | 110 | 0.268 |
| 111 | 111 | 0.724 |
| 112 | 112 | 0.941 |
| 113 | 113 | 0.417 |
| 114 | 114 | 0.693 |
| 115 | 115 | 0.148 |
| 116 | 116 | 0.0618 |
| 117 | 117 | 0.479 |
| 118 | 118 | 0.402 |
| 119 | 119 | 0.423 |
| 12 | 12 | 0.457 |
| 120 | 120 | 0.11 |
| 121 | 121 | 0.268 |
| 122 | 122 | 0.145 |
| 123 | 123 | 1.08628e-4 |
| 124 | 124 | 0.856 |
| 125 | 125 | 0.218 |
| 126 | 126 | 0.548 |
| 127 | 127 | 0.847 |
| 128 | 128 | 0.0687 |
| 129 | 129 | 0.368 |
| 13 | 13 | 0.178 |
| 130 | 130 | 0.707 |
| 131 | 131 | 0.413 |
| 132 | 132 | 0.804 |
| 133 | 133 | 0.148 |
| 134 | 134 | 0.682 |
| 135 | 135 | 0.945 |
| 136 | 136 | 0.944 |
| 137 | 137 | 0.0318 |
| 138 | 138 | 0.932 |
| 139 | 139 | 0.59 |
| 14 | 14 | 0.229 |
| 140 | 140 | 0.159 |
| 141 | 141 | 0.305 |
| 142 | 142 | 0.856 |
| 143 | 143 | 0.988 |
| 144 | 144 | 0.335 |
| 145 | 145 | 0.805 |
| 146 | 146 | 0.691 |
| 147 | 147 | 0.231 |
| 148 | 148 | 0.541 |
| 149 | 149 | 0.0754 |
| 15 | 15 | 0.865 |
| 150 | 150 | 0.578 |
| 151 | 151 | 0.876 |
| 152 | 152 | 0.644 |
| 153 | 153 | 0.219 |
| 154 | 154 | 0.279 |
| 155 | 155 | 0.033 |
| 156 | 156 | 0.221 |
| 157 | 157 | 0.0954 |
| 158 | 158 | 0.191 |
| 159 | 159 | 0.422 |
| 16 | 16 | 0.0883 |
| 160 | 160 | 0.498 |
| 161 | 161 | 0.619 |
| 162 | 162 | 0.0962 |
| 163 | 163 | 0.893 |
| 164 | 164 | 0.204 |
| 165 | 165 | 0.872 |
| 166 | 166 | 0.0518 |
| 167 | 167 | 0.274 |
| 168 | 168 | 0.809 |
| 169 | 169 | 0.149 |
| 17 | 17 | 0.705 |
| 18 | 18 | 0.0772 |
| 19 | 19 | 0.00482 |
| 2 | 2 | 0.286 |
| 20 | 20 | 0.423 |
| 21 | 21 | 0.206 |
| 22 | 22 | 0.136 |
| 23 | 23 | 0.0233 |
| 24 | 24 | 0.396 |
| 25 | 25 | 0.0989 |
| 26 | 26 | 0.442 |
| 27 | 27 | 0.666 |
| 28 | 28 | 0.119 |
| 29 | 29 | 0.804 |
| 3 | 3 | 0.962 |
| 30 | 30 | 0.415 |
| 31 | 31 | 0.188 |
| 32 | 32 | 2.46237e-7 |
| 33 | 33 | 0.597 |
| 34 | 34 | 0.409 |
| 35 | 35 | 0.789 |
| 36 | 36 | 0.0383 |
| 37 | 37 | 0.756 |
| 38 | 38 | 0.426 |
| 39 | 39 | 0.462 |
| 4 | 4 | 0.116 |
| 40 | 40 | 0.0235 |
| 41 | 41 | 0.193 |
| 42 | 42 | 0.416 |
| 43 | 43 | 0.406 |
| 44 | 44 | 0.295 |
| 45 | 45 | 0.682 |
| 46 | 46 | 0.429 |
| 47 | 47 | 0.424 |
| 48 | 48 | 0.471 |
| 49 | 49 | 0.795 |
| 5 | 5 | 0.873 |
| 50 | 50 | 0.935 |
| 51 | 51 | 0.614 |
| 52 | 52 | 0.419 |
| 53 | 53 | 0.0214 |
| 54 | 54 | 0.25 |
| 55 | 55 | 0.252 |
| 56 | 56 | 0.349 |
| 57 | 57 | 0.626 |
| 58 | 58 | 0.222 |
| 59 | 59 | 0.19 |
| 6 | 6 | 0.572 |
| 60 | 60 | 0.785 |
| 61 | 61 | 0.459 |
| 62 | 62 | 0.739 |
| 63 | 63 | 0.861 |
| 64 | 64 | 0.458 |
| 65 | 65 | 0.321 |
| 66 | 66 | 0.52 |
| 67 | 67 | 0.788 |
| 68 | 68 | 0.575 |
| 69 | 69 | 0.407 |
| 7 | 7 | 0.196 |
| 70 | 70 | 0.0623 |
| 71 | 71 | 0.758 |
| 72 | 72 | 0.428 |
| 73 | 73 | 0.802 |
| 74 | 74 | 0.284 |
| 75 | 75 | 0.267 |
| 76 | 76 | 0.71 |
| 77 | 77 | 0.772 |
| 78 | 78 | 0.257 |
| 79 | 79 | 0.135 |
| 8 | 8 | 0.5 |
| 80 | 80 | 0.321 |
| 81 | 81 | 0.291 |
| 82 | 82 | 0.667 |
| 83 | 83 | 0.274 |
| 84 | 84 | 0.184 |
| 85 | 85 | 0.0213 |
| 86 | 86 | 0.767 |
| 87 | 87 | 0.15 |
| 88 | 88 | 0.289 |
| 89 | 89 | 0.355 |
| 9 | 9 | 0.222 |
| 90 | 90 | 0.789 |
| 91 | 91 | 0.478 |
| 92 | 92 | 0.0199 |
| 93 | 93 | 0.579 |
| 94 | 94 | 0.176 |
| 95 | 95 | 0.47 |
| 96 | 96 | 0.741 |
| 97 | 97 | 0.313 |
| 98 | 98 | 0.584 |
| 99 | 99 | 0.00281 |
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: CNhs12348
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000002 in vivo cell sample
FF:0000152 human renal cortical epithelial 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
CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000056 (myoblast)
0000183 (contractile cell)
0000187 (muscle cell)
0000192 (smooth muscle cell)
0000211 (electrically active cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000355 (multi-potent skeletal muscle stem cell)
0000393 (electrically responsive cell)
0000514 (smooth muscle myoblast)
0000548 (animal cell)
0000680 (muscle precursor cell)
0000723 (somatic stem cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002598 (bronchial smooth muscle cell)
UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000119 (cell layer)
0000383 (musculature of body)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000915 (thoracic segment of trunk)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0001004 (respiratory system)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0001558 (lower respiratory tract)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002185 (bronchus)
0002204 (musculoskeletal system)
0002224 (thoracic cavity)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003082 (myotome)
0003104 (mesenchyme)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004290 (dermomyotome)
0005178 (thoracic cavity element)
0005181 (thoracic segment organ)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0007023 (adult organism)
0007196 (tracheobronchial tree)
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
