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|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|top_motifs=REST:3.4612153696;SOX2:3.26847257765;MYFfamily:3.25720988543;NHLH1,2:3.1926523195;MTF1:3.17597833668;SOX5:3.11723342931;RREB1:3.07495197278;ZFP161:2.97161365241;HIC1:2.82044729224;DBP:2.73683031051;MED-1{core}:2.63268911072;NFIX:2.61926454577;PRDM1:2.61461677855;PRRX1,2:2.55195947251;MTE{core}:2.54256120786;ATF2:2.49698064446;RFX1:2.48625688943;SOX{8,9,10}:2.47400080459;RFX2..5_RFXANK_RFXAP:2.41887829559;ZBTB6:2.409318411;TFAP2B:2.37338760627;CUX2:2.37268629176;NANOG:2.29772577751;LMO2:2.24834892161;GFI1B:2.22705347954;OCT4_SOX2{dimer}:2.22424281469;EGR1..3:2.202735277;GATA4:2.19212214499;NKX3-2:2.18006628059;GTF2I:2.17794203561;KLF4:2.16808997816;PAX6:2.15119172651;SMAD1..7,9:2.14486352473;HOXA9_MEIS1:2.13430002242;FOXP3:2.11279044092;TGIF1:2.05958290483;HOX{A6,A7,B6,B7}:2.05454003262;PATZ1:2.05242099696;SOX17:1.99883892868;JUN:1.99090069329;HBP1_HMGB_SSRP1_UBTF:1.92926540026;MZF1:1.91456556428;MAZ:1.76236469253;EP300:1.75830779643;BREu{core}:1.73542754936;FOXD3:1.69792833156;SP1:1.69294373999;ZNF384:1.63683783841;PAX5:1.63298467978;GCM1,2:1.61007581336;NKX6-1,2:1.60414865484;AHR_ARNT_ARNT2:1.5899397087;EBF1:1.56392946264;XBP1:1.54243101565;PDX1:1.51199414622;STAT2,4,6:1.50946317993;POU6F1:1.47505309352;FOXM1:1.47251600387;ZNF423:1.45915454318;TFDP1:1.41282739735;LEF1_TCF7_TCF7L1,2:1.3953982831;BPTF:1.35868645554;MYBL2:1.32370666205;FOXP1:1.28525526481;RBPJ:1.23371814522;POU5F1:1.23295099008;NR3C1:1.19865923251;STAT1,3:1.17381931286;NRF1:1.1734158979;RORA:1.16502925818;POU3F1..4:1.15345431815;IKZF2:1.1448834086;ZIC1..3:1.13654104034;TFAP2{A,C}:1.13142209846;CDC5L:1.10772719417;ARID5B:1.06533030224;TLX1..3_NFIC{dimer}:1.02253655765;VSX1,2:1.01491920051;FOXQ1:0.996437319196;NKX2-3_NKX2-5:0.970222462504;HOX{A4,D4}:0.909130809355;ONECUT1,2:0.847569930825;FOX{D1,D2}:0.83548915154;AR:0.764225752728;SREBF1,2:0.761159280039;CRX:0.73850932352;MAFB:0.707446416353;ZNF143:0.689192998852;LHX3,4:0.663356160293;ADNP_IRX_SIX_ZHX:0.64009222103;ZBTB16:0.628451345664;HMGA1,2:0.61175983417;PAX4:0.504485105883;CREB1:0.471432125052;GTF2A1,2:0.443717262151;FOXO1,3,4:0.440905925087;ESRRA:0.421624454881;T:0.420956320079;FOXN1:0.418598892451;NKX3-1:0.398190782075;ATF5_CREB3:0.317350056504;XCPE1{core}:0.310050967761;FOX{F1,F2,J1}:0.300845394414;IRF7:0.282013065057;FOX{I1,J2}:0.253852631567;ATF4:0.21054774742;GFI1:0.210192538507;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.155148317182;NFIL3:0.131394840093;EVI1:0.130683118449;PAX2:0.122302678184;HMX1:0.11609045008;GZF1:0.098230400282;MEF2{A,B,C,D}:0.0280197190496;PBX1:0.016836579756;NFY{A,B,C}:0.00548663563213;ALX1:-0.00715185644759;ZEB1:-0.0111020490585;HAND1,2:-0.0526798276773;NR5A1,2:-0.0748315978365;NFATC1..3:-0.0776234939237;IRF1,2:-0.0928309631718;SPZ1:-0.0944717758489;TFCP2:-0.0963175302361;NFE2L2:-0.098030067777;MYOD1:-0.119451471581;TOPORS:-0.120797505289;FOXL1:-0.178153747349;AIRE:-0.194314743359;ZNF238:-0.241518959283;NR1H4:-0.271014641218;NFE2L1:-0.275409052166;CEBPA,B_DDIT3:-0.277649403806;UFEwm:-0.282534065905;PAX3,7:-0.287809898827;CDX1,2,4:-0.307843555284;NFE2:-0.316750580281;ATF6:-0.329981772314;POU1F1:-0.339848685699;PITX1..3:-0.380874743071;NKX2-1,4:-0.390399578058;ALX4:-0.393494358076;GATA6:-0.469785895947;TBX4,5:-0.473235721751;YY1:-0.534181808042;FOXA2:-0.534259096111;SPI1:-0.577917426206;NANOG{mouse}:-0.581700490288;TP53:-0.591658027452;TBP:-0.596892931839;TLX2:-0.601202886153;TEF:-0.65698837616;ETS1,2:-0.659064052531;HNF4A_NR2F1,2:-0.666558495347;IKZF1:-0.68158762729;TFAP4:-0.702841512057;HNF1A:-0.73889951789;DMAP1_NCOR{1,2}_SMARC:-0.75438384131;NKX2-2,8:-0.77344025755;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.781022444692;SPIB:-0.806621209063;bHLH_family:-0.81142766039;HSF1,2:-0.88055871951;SNAI1..3:-0.905126291912;PAX8:-0.907077101738;HIF1A:-0.93185683147;TEAD1:-0.937193329778;ESR1:-0.940216968836;BACH2:-0.942597842913;FOS_FOS{B,L1}_JUN{B,D}:-0.948073139394;FOSL2:-0.990727282183;PAX1,9:-1.01080500855;SRF:-1.09195916311;E2F1..5:-1.2223350223;NFKB1_REL_RELA:-1.22604444369;HLF:-1.23533488092;ELK1,4_GABP{A,B1}:-1.24650392647;ELF1,2,4:-1.32985581098;RUNX1..3:-1.34702588647;RXR{A,B,G}:-1.3620364759;POU2F1..3:-1.36997617815;ZNF148:-1.43932916314;NR6A1:-1.52446640412;MYB:-1.53379996216;HES1:-1.59129664022;TAL1_TCF{3,4,12}:-1.71925284182;GLI1..3:-1.83532879427;PPARG:-1.96568154983;RXRA_VDR{dimer}:-2.33995500824;HOX{A5,B5}:-2.40760983777;STAT5{A,B}:-2.55389876892;EN1,2:-2.80531514899
|comment=
|comment=
|created_by=
|created_by=

Revision as of 17:59, 14 March 2012


Name:locus coeruleus - adult, donor10196
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelocus coeruleus
dev stageNA
sexfemale
age60
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationPeter Heutink
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]





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: CNhs13808



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: CNhs13808



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: CNhs13808


FANTOM5 (FF) ontology


Direct parent terms


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

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