FF:10085-102B4: Difference between revisions
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|top_motifs= | |top_motifs=PRRX1,2:3.95610482654;AHR_ARNT_ARNT2:3.77680727594;MED-1{core}:3.56145725108;EGR1..3:3.46124850847;MZF1:3.44723065212;NKX2-3_NKX2-5:3.26769367908;ZFP161:3.20444606673;TFAP2B:3.10931915151;REST:3.00295503641;SOX2:2.93857957705;NHLH1,2:2.85412819577;POU3F1..4:2.76152717285;MTE{core}:2.75243066235;RFX1:2.70554459517;BREu{core}:2.64457546405;DBP:2.5465968791;FOXM1:2.46429329709;MTF1:2.45801796611;POU5F1:2.44151334796;RREB1:2.43414252673;RORA:2.38505915199;OCT4_SOX2{dimer}:2.31570933684;ATF2:2.30679020141;GTF2I:2.3035171723;POU6F1:2.28919317512;PATZ1:2.2639514878;ZBTB6:2.19720085871;CUX2:2.15864400641;POU1F1:2.09448664256;SOX{8,9,10}:2.07505196093;PRDM1:2.05069559234;PAX6:2.00509978249;TFDP1:1.89669885023;HOX{A4,D4}:1.88908536381;JUN:1.82886994287;MYFfamily:1.82320943388;GCM1,2:1.81668215982;SMAD1..7,9:1.78853176296;LEF1_TCF7_TCF7L1,2:1.76831634318;HIC1:1.76630883149;NANOG:1.76385169826;MAZ:1.75523744214;SOX17:1.75166968858;ZNF423:1.75127510391;CDC5L:1.74934158331;ZIC1..3:1.74451260722;ADNP_IRX_SIX_ZHX:1.73766085771;GTF2A1,2:1.66160410258;LMO2:1.63331119592;FOXL1:1.55599332602;GFI1B:1.52422570087;T:1.49057279666;TGIF1:1.38618690591;GZF1:1.37724696484;ZNF384:1.34777684247;NKX6-1,2:1.34733695262;SOX5:1.33245337094;HMGA1,2:1.29073716101;PAX5:1.1998650529;LHX3,4:1.17216636243;GFI1:1.14920967933;PAX8:1.12633213486;ARID5B:1.10887576554;RFX2..5_RFXANK_RFXAP:1.04200405147;NRF1:1.04167574767;HAND1,2:1.02641277522;ONECUT1,2:1.01917637243;HOXA9_MEIS1:1.00554049968;MAFB:0.99383469704;VSX1,2:0.993367961794;MYOD1:0.946908703029;FOXP1:0.921964069821;IKZF2:0.842105199019;KLF4:0.787417572377;PAX3,7:0.770354024509;RBPJ:0.761885608996;CRX:0.738003963873;TOPORS:0.737057253089;BPTF:0.704690268718;ESRRA:0.682335901555;FOXD3:0.653975266174;GATA4:0.593582162263;ZNF143:0.571851620382;FOXP3:0.544793444097;TBP:0.496469613449;XCPE1{core}:0.479371341479;PAX1,9:0.44099586997;MEF2{A,B,C,D}:0.425994338625;SP1:0.386411498309;PBX1:0.295724632107;NR3C1:0.295491244531;ZNF238:0.24473368837;ATF4:0.230122776129;POU2F1..3:0.224680860151;GATA6:0.219666530527;FOX{D1,D2}:0.210259938408;EP300:0.197015157643;EVI1:0.172834966856;PITX1..3:0.15998414231;EBF1:0.117777697793;AIRE:0.0457282198876;PDX1:0.038277534813;YY1:0.037378242311;FOXQ1:-0.0133448454378;NKX3-2:-0.0292729431849;ZEB1:-0.0386868398021;XBP1:-0.0464487728116;HNF1A:-0.0691298470405;TEF:-0.106745604153;FOXA2:-0.118710199608;ATF5_CREB3:-0.121206665394;STAT1,3:-0.152675483786;FOX{F1,F2,J1}:-0.197840320115;NFY{A,B,C}:-0.259340448228;UFEwm:-0.283772139997;AR:-0.329459435427;PAX2:-0.329476979066;NFIL3:-0.340582938093;NFIX:-0.343731013709;PAX4:-0.346802576034;STAT5{A,B}:-0.356598095368;bHLH_family:-0.378455976563;SNAI1..3:-0.402939188022;CEBPA,B_DDIT3:-0.410802907921;NFATC1..3:-0.438813546512;NR1H4:-0.447698453534;HNF4A_NR2F1,2:-0.456560338668;TLX2:-0.462231911503;ALX1:-0.466102364317;HMX1:-0.485194246407;ZBTB16:-0.510848887296;TFAP2{A,C}:-0.518083624134;MYBL2:-0.534447342978;NFE2L2:-0.538832314156;HOX{A6,A7,B6,B7}:-0.550200627517;STAT2,4,6:-0.562824151399;ZNF148:-0.572598378231;SPIB:-0.593746176418;RUNX1..3:-0.614783847482;SREBF1,2:-0.628546915445;CREB1:-0.640207815181;DMAP1_NCOR{1,2}_SMARC:-0.651648185518;TLX1..3_NFIC{dimer}:-0.664763417396;HOX{A5,B5}:-0.679358656021;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.691585439533;FOSL2:-0.710289625599;HBP1_HMGB_SSRP1_UBTF:-0.720882876828;CDX1,2,4:-0.730763901346;FOS_FOS{B,L1}_JUN{B,D}:-0.759254220749;TEAD1:-0.785185143745;TP53:-0.786230069919;FOX{I1,J2}:-0.802230806331;NKX3-1:-0.805997921343;NANOG{mouse}:-0.816826086218;HES1:-0.817927593293;EN1,2:-0.821002237718;BACH2:-0.822710864246;TFCP2:-0.825369383453;TBX4,5:-0.828822320929;NFKB1_REL_RELA:-0.833250611051;MYB:-0.851878106625;ETS1,2:-0.86609674203;ATF6:-0.878140036422;E2F1..5:-0.926825440992;SPI1:-0.935761442497;IKZF1:-0.944202504883;GLI1..3:-0.983412140346;FOXO1,3,4:-0.988582410801;NFE2:-1.00990027363;TFAP4:-1.02588416172;HLF:-1.08595737291;NR5A1,2:-1.13377269446;PPARG:-1.14213900692;RXR{A,B,G}:-1.16195881523;IRF7:-1.1627455097;SPZ1:-1.16798192162;NKX2-1,4:-1.17130431354;ESR1:-1.17440715593;IRF1,2:-1.22085900684;FOXN1:-1.32045520082;SRF:-1.39206037447;HIF1A:-1.40024752585;ALX4:-1.44522267752;RXRA_VDR{dimer}:-1.44801590919;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.46599041477;NFE2L1:-1.49877186524;TAL1_TCF{3,4,12}:-1.50345720284;ELK1,4_GABP{A,B1}:-1.59487109503;NR6A1:-1.61105175912;HSF1,2:-1.70610297225;NKX2-2,8:-2.20577222179;ELF1,2,4:-2.48153109579 | ||
|comment= | |comment= | ||
|created_by= | |created_by= |
Revision as of 17:54, 14 March 2012
Name: | brain, fetal, pool1 |
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Species: | Human (Homo sapiens) |
Library ID: | {{{library_id}}} |
Sample type: | {{{sample_category}}} |
Genomic View: | UCSC |
CAGEd-oPOSSUM: | link |
ExpandAdditional information |
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ExpandDownload 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: CNhs11797
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: CNhs11797
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: CNhs11797
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000004 tissue sample
FF:0000210 human sample
FF:0010085 human brain - fetal 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
UBERON: Anatomy
0000033 (head)
0000061 (anatomical structure)
0000073 (regional part of nervous 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)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004121 (ectoderm-derived structure)
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