FF:11798-124C7: Difference between revisions
From FANTOM5_SSTAR
No edit summary |
No edit summary |
||
| Line 66: | Line 66: | ||
|fonse_treatment=EFO:0000369,FF:0000409,FF:0011121,FF:11798-124C7 | |fonse_treatment=EFO:0000369,FF:0000409,FF:0011121,FF:11798-124C7 | ||
|fonse_treatment_closure=EFO:0000369,FF:0000409,FF:0011121,FF:11798-124C7 | |fonse_treatment_closure=EFO:0000369,FF:0000409,FF:0011121,FF:11798-124C7 | ||
|top_motifs= | |top_motifs=PAX3,7:3.43646403234;CREB1:3.32319686439;RUNX1..3:3.16826767223;FOX{D1,D2}:3.14110359386;FOX{F1,F2,J1}:3.02565303924;ELF1,2,4:2.82985874546;RFX2..5_RFXANK_RFXAP:2.80130852863;BPTF:2.67758779671;ATF5_CREB3:2.6463737606;RORA:2.63388669165;FOXO1,3,4:2.61538900582;FOX{I1,J2}:2.527770664;T:2.46007338018;PDX1:2.45509725982;RFX1:2.38315866695;ATF4:2.37044378143;CDX1,2,4:2.10968215143;ETS1,2:2.04452079794;HMX1:2.03822856359;PBX1:1.9955501591;DMAP1_NCOR{1,2}_SMARC:1.98790891375;FOXN1:1.73542631063;TLX2:1.72457042486;LEF1_TCF7_TCF7L1,2:1.5793869432;ATF2:1.53941423817;SPI1:1.40805877266;IRF1,2:1.40375549166;GATA6:1.38630339268;PAX2:1.38162717139;JUN:1.37045148774;ELK1,4_GABP{A,B1}:1.34835197774;TGIF1:1.28310940652;ATF6:1.15538386565;SPIB:1.00161227386;NFIL3:0.986039899856;NFIX:0.9771640857;PAX6:0.947917251302;PAX4:0.939856802861;NFATC1..3:0.931901450588;NANOG{mouse}:0.88952980529;SOX2:0.818840564937;BREu{core}:0.762806703635;NFKB1_REL_RELA:0.730810488778;ZBTB16:0.704879763974;MAFB:0.596267554478;NKX2-1,4:0.51244279308;IRF7:0.50444966963;ZEB1:0.458902158108;STAT1,3:0.433368494807;TBX4,5:0.428892647367;HIF1A:0.401079212537;FOXQ1:0.398410422354;AHR_ARNT_ARNT2:0.356111006263;SNAI1..3:0.339105746931;SREBF1,2:0.329226501629;CRX:0.324355459717;HES1:0.286966941227;HOX{A6,A7,B6,B7}:0.281351280921;MYOD1:0.246480096578;FOXP1:0.241718840424;NFE2L1:0.236043909621;LMO2:0.235311470142;FOXA2:0.215062142898;NR5A1,2:0.213923255314;IKZF2:0.197996803965;YY1:0.189293283233;EP300:0.179321492524;POU2F1..3:0.15903017633;TAL1_TCF{3,4,12}:0.151082446164;NKX6-1,2:0.144926723267;POU1F1:0.0978752013162;SOX5:0.0914267814927;CUX2:0.0322537124233;STAT5{A,B}:-0.0244336338183;NKX2-2,8:-0.0375873882132;MYB:-0.04763610552;AR:-0.0632911951945;NFY{A,B,C}:-0.0678683504341;NANOG:-0.0717100001762;PITX1..3:-0.0960740017043;SPZ1:-0.0976885926818;FOSL2:-0.10435786936;OCT4_SOX2{dimer}:-0.142574208002;PAX5:-0.176854535284;NRF1:-0.180992244926;ZNF384:-0.186921681951;STAT2,4,6:-0.280490799338;EGR1..3:-0.295185326743;E2F1..5:-0.301288514554;NFE2L2:-0.342502249877;BACH2:-0.347955874358;RBPJ:-0.350415459757;HLF:-0.368822085862;FOS_FOS{B,L1}_JUN{B,D}:-0.380773407461;ALX1:-0.385215366666;CEBPA,B_DDIT3:-0.396480034125;ZNF143:-0.43547112643;HNF4A_NR2F1,2:-0.43816711346;NFE2:-0.43872344239;EVI1:-0.44861370594;ZNF148:-0.4537338142;HMGA1,2:-0.457829839172;HBP1_HMGB_SSRP1_UBTF:-0.465369832656;VSX1,2:-0.469422796534;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.472041666011;GFI1:-0.473420626082;DBP:-0.520005947728;HNF1A:-0.521547246747;NKX3-1:-0.525862104132;HAND1,2:-0.546377867351;GLI1..3:-0.569132199696;FOXD3:-0.569512547522;SOX{8,9,10}:-0.573395665957;PRRX1,2:-0.584008000704;NHLH1,2:-0.589846628864;PPARG:-0.616871459654;FOXP3:-0.646244769943;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.651547638785;FOXM1:-0.672403050381;SRF:-0.708331210097;MYFfamily:-0.710186721795;SMAD1..7,9:-0.72882784479;GCM1,2:-0.762432716522;ALX4:-0.792249546473;RXRA_VDR{dimer}:-0.837303444988;MEF2{A,B,C,D}:-0.852024752159;bHLH_family:-0.856381462885;RREB1:-0.857365044134;ESRRA:-0.891856582929;PAX8:-0.896682013602;MED-1{core}:-0.896985587783;ZFP161:-0.966391696124;XBP1:-0.969114090622;ZBTB6:-0.992894524748;HOX{A5,B5}:-1.00088280716;GFI1B:-1.01409649271;MZF1:-1.02587734818;AIRE:-1.05037047904;ADNP_IRX_SIX_ZHX:-1.05445040854;MTF1:-1.08397549683;SOX17:-1.10781518851;MYBL2:-1.11138734613;ZNF238:-1.11313176793;MAZ:-1.12503734383;POU5F1:-1.1284837882;TFAP4:-1.17999025753;TP53:-1.19074419478;TFDP1:-1.19881599937;ARID5B:-1.21611334128;PATZ1:-1.22220195378;HSF1,2:-1.22428173235;REST:-1.23366373359;TBP:-1.28121246381;MTE{core}:-1.28396833869;NR6A1:-1.31287656256;PRDM1:-1.32004619767;LHX3,4:-1.33044569932;GATA4:-1.36862951741;TOPORS:-1.40332123276;NR1H4:-1.41235995309;TFAP2B:-1.43601217776;TFCP2:-1.4548962279;HOXA9_MEIS1:-1.45599317374;HIC1:-1.45620991113;ZNF423:-1.45845433903;UFEwm:-1.47122490442;SP1:-1.50612863425;NKX2-3_NKX2-5:-1.51925843616;NR3C1:-1.58139896862;GTF2A1,2:-1.6254867612;GTF2I:-1.63606793303;POU3F1..4:-1.66613650233;CDC5L:-1.67927205083;XCPE1{core}:-1.68911975966;ONECUT1,2:-1.72140268104;TLX1..3_NFIC{dimer}:-1.72541766449;FOXL1:-1.74548545937;TEAD1:-1.74629351694;EN1,2:-1.82091793165;ZIC1..3:-1.86740326929;GZF1:-1.86926787413;HOX{A4,D4}:-1.87298027188;EBF1:-1.89515212703;ESR1:-1.89771799247;KLF4:-1.93344921373;RXR{A,B,G}:-1.94174841754;TFAP2{A,C}:-1.98697081226;POU6F1:-2.03937369179;PAX1,9:-2.10786788615;TEF:-2.39387833024;NKX3-2:-2.52156413546;IKZF1:-2.99418364174 | ||
|comment=Changed from previous label. TODO: full classification | |comment=Changed from previous label. TODO: full classification | ||
|created_by= | |created_by= | ||
Revision as of 17:39, 14 March 2012
| Name: | CD4+CD25-CD45RA- memory conventional T cells, donor2 |
|---|---|
| Species: | Human (Homo sapiens) |
| Library ID: | {{{library_id}}} |
| Sample type: | {{{sample_category}}} |
| Genomic View: | UCSC |
| CAGEd-oPOSSUM: | link |
| Additional information | ||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample information
RNA information
|
| Download raw sequence, BAM & CTSS | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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: CNhs13237
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: CNhs13237
| Novel motif | Logo | P-value |
|---|---|---|
| 1 | 1 | 0.553 |
| 10 | 10 | 0.0187 |
| 100 | 100 | 0.9 |
| 101 | 101 | 0.344 |
| 102 | 102 | 0.988 |
| 103 | 103 | 0.535 |
| 104 | 104 | 0.63 |
| 105 | 105 | 0.241 |
| 106 | 106 | 0.505 |
| 107 | 107 | 0.0101 |
| 108 | 108 | 0.516 |
| 109 | 109 | 0.157 |
| 11 | 11 | 0.292 |
| 110 | 110 | 0.922 |
| 111 | 111 | 0.937 |
| 112 | 112 | 0.882 |
| 113 | 113 | 0.28 |
| 114 | 114 | 0.637 |
| 115 | 115 | 0.234 |
| 116 | 116 | 0.131 |
| 117 | 117 | 0.00243 |
| 118 | 118 | 0.396 |
| 119 | 119 | 0.378 |
| 12 | 12 | 0.6 |
| 120 | 120 | 1 |
| 121 | 121 | 0.962 |
| 122 | 122 | 0.774 |
| 123 | 123 | 0.0566 |
| 124 | 124 | 0.633 |
| 125 | 125 | 0.669 |
| 126 | 126 | 0.408 |
| 127 | 127 | 0.945 |
| 128 | 128 | 0.662 |
| 129 | 129 | 0.902 |
| 13 | 13 | 0.545 |
| 130 | 130 | 0.37 |
| 131 | 131 | 0.765 |
| 132 | 132 | 0.274 |
| 133 | 133 | 0.655 |
| 134 | 134 | 0.91 |
| 135 | 135 | 0.995 |
| 136 | 136 | 0.856 |
| 137 | 137 | 0.0186 |
| 138 | 138 | 0.459 |
| 139 | 139 | 0.0549 |
| 14 | 14 | 0.61 |
| 140 | 140 | 0.196 |
| 141 | 141 | 0.853 |
| 142 | 142 | 0.622 |
| 143 | 143 | 0.00161 |
| 144 | 144 | 0.944 |
| 145 | 145 | 0.968 |
| 146 | 146 | 0.462 |
| 147 | 147 | 0.0151 |
| 148 | 148 | 0.255 |
| 149 | 149 | 0.528 |
| 15 | 15 | 0.175 |
| 150 | 150 | 0.727 |
| 151 | 151 | 0.674 |
| 152 | 152 | 0.511 |
| 153 | 153 | 0.877 |
| 154 | 154 | 0.459 |
| 155 | 155 | 0.0403 |
| 156 | 156 | 0.321 |
| 157 | 157 | 0.332 |
| 158 | 158 | 0.0163 |
| 159 | 159 | 0.303 |
| 16 | 16 | 0.533 |
| 160 | 160 | 0.185 |
| 161 | 161 | 0.913 |
| 162 | 162 | 0.0438 |
| 163 | 163 | 0.388 |
| 164 | 164 | 0.143 |
| 165 | 165 | 0.517 |
| 166 | 166 | 0.501 |
| 167 | 167 | 0.287 |
| 168 | 168 | 0.531 |
| 169 | 169 | 0.22 |
| 17 | 17 | 0.728 |
| 18 | 18 | 0.863 |
| 19 | 19 | 0.0447 |
| 2 | 2 | 0.425 |
| 20 | 20 | 0.332 |
| 21 | 21 | 0.826 |
| 22 | 22 | 0.402 |
| 23 | 23 | 0.529 |
| 24 | 24 | 0.783 |
| 25 | 25 | 0.0806 |
| 26 | 26 | 0.687 |
| 27 | 27 | 0.627 |
| 28 | 28 | 0.453 |
| 29 | 29 | 0.027 |
| 3 | 3 | 0.303 |
| 30 | 30 | 0.128 |
| 31 | 31 | 0.714 |
| 32 | 32 | 0.033 |
| 33 | 33 | 0.16 |
| 34 | 34 | 0.376 |
| 35 | 35 | 0.235 |
| 36 | 36 | 0.0301 |
| 37 | 37 | 0.193 |
| 38 | 38 | 0.728 |
| 39 | 39 | 0.258 |
| 4 | 4 | 0.706 |
| 40 | 40 | 0.638 |
| 41 | 41 | 0.0926 |
| 42 | 42 | 0.183 |
| 43 | 43 | 0.556 |
| 44 | 44 | 0.771 |
| 45 | 45 | 0.24 |
| 46 | 46 | 0.63 |
| 47 | 47 | 0.305 |
| 48 | 48 | 0.534 |
| 49 | 49 | 0.231 |
| 5 | 5 | 0.343 |
| 50 | 50 | 0.492 |
| 51 | 51 | 0.87 |
| 52 | 52 | 0.399 |
| 53 | 53 | 0.613 |
| 54 | 54 | 0.995 |
| 55 | 55 | 0.725 |
| 56 | 56 | 0.922 |
| 57 | 57 | 0.964 |
| 58 | 58 | 0.151 |
| 59 | 59 | 0.562 |
| 6 | 6 | 0.761 |
| 60 | 60 | 0.551 |
| 61 | 61 | 0.0765 |
| 62 | 62 | 0.182 |
| 63 | 63 | 0.823 |
| 64 | 64 | 0.715 |
| 65 | 65 | 0.701 |
| 66 | 66 | 0.781 |
| 67 | 67 | 0.526 |
| 68 | 68 | 0.823 |
| 69 | 69 | 0.697 |
| 7 | 7 | 0.346 |
| 70 | 70 | 0.0975 |
| 71 | 71 | 0.0904 |
| 72 | 72 | 0.133 |
| 73 | 73 | 0.567 |
| 74 | 74 | 0.682 |
| 75 | 75 | 0.0198 |
| 76 | 76 | 0.156 |
| 77 | 77 | 0.0169 |
| 78 | 78 | 0.823 |
| 79 | 79 | 0.793 |
| 8 | 8 | 0.589 |
| 80 | 80 | 0.0021 |
| 81 | 81 | 0.56 |
| 82 | 82 | 0.313 |
| 83 | 83 | 0.457 |
| 84 | 84 | 0.651 |
| 85 | 85 | 0.699 |
| 86 | 86 | 0.0998 |
| 87 | 87 | 0.866 |
| 88 | 88 | 0.837 |
| 89 | 89 | 0.0542 |
| 9 | 9 | 0.924 |
| 90 | 90 | 0.142 |
| 91 | 91 | 0.844 |
| 92 | 92 | 0.857 |
| 93 | 93 | 0.516 |
| 94 | 94 | 0.19 |
| 95 | 95 | 0.00552 |
| 96 | 96 | 0.35 |
| 97 | 97 | 0.424 |
| 98 | 98 | 0.233 |
| 99 | 99 | 1.44131e-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: CNhs13237
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000002 in vivo 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)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000051 (common lymphoid progenitor)
0000084 (T cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000624 (CD4-positive, alpha-beta T cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000789 (alpha-beta T cell)
0000790 (immature alpha-beta T cell)
0000791 (mature alpha-beta T cell)
0000805 (immature single positive thymocyte)
0000806 (DN2 thymocyte)
0000807 (DN3 thymocyte)
0000808 (DN4 thymocyte)
0000809 (double-positive, alpha-beta thymocyte)
0000810 (CD4-positive, alpha-beta thymocyte)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000893 (thymocyte)
0000894 (DN1 thymic pro-T cell)
0000895 (naive thymus-derived CD4-positive, alpha-beta T cell)
0000898 (naive T cell)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002419 (mature T cell)
0002420 (immature T cell)
0002425 (early T lineage precursor)
0002427 (resting double-positive thymocyte)
0002428 (double-positive blast)
0002429 (CD69-positive double-positive thymocyte)
0002431 (CD4-positive, CD8-intermediate double-positive thymocyte)
0002432 (CD24-positive, CD4 single-positive thymocyte)
0002433 (CD69-positive, CD4-positive single-positive thymocyte)
0002436 (mature CD4 single-positive thymocyte)
0002489 (double negative thymocyte)
UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0000974 (neck)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001042 (chordate pharynx)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001557 (upper respiratory tract)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002342 (neural crest)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002370 (thymus)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002530 (gland)
0002532 (epiblast (generic))
0003075 (neural plate)
0003104 (mesenchyme)
0003295 (pharyngeal gland)
0003351 (pharyngeal epithelium)
0003408 (gland of gut)
0003929 (gut epithelium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004177 (hemopoietic organ)
0004185 (endodermal part of digestive tract)
0004807 (respiratory system epithelium)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005058 (hemolymphoid system gland)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005428 (vagal neural crest)
0005562 (thymus primordium)
0005911 (endo-epithelium)
0006562 (pharynx)
0006598 (presumptive structure)
0007026 (primitive gut)
0007284 (presumptive neural plate)
0007690 (early pharyngeal endoderm)
0009113 (thymic region)
0009142 (entire embryonic mesenchyme)
0009145 (pharyngeal region of foregut)
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
