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{{f5samples
 
{{f5samples
|id=FF:713-19D3
+
|DRA_sample_Accession=CAGE@SAMD00005656
|name=thymus, neonate N07
+
|accession_numbers=CAGE;DRX009121;DRR009995;DRZ001420;DRZ002803;DRZ012770;DRZ014153
|sample_id=713
+
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002370,UBERON:0000479,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0004177,UBERON:0005057,UBERON:0002530,UBERON:0005058,UBERON:0010317,UBERON:0000153,UBERON:0002390,UBERON:0000949,UBERON:0002193,UBERON:0002405,UBERON:0009113
|rna_tube_id=19D3
 
|rna_box=19
 
|rna_position=D3
 
|sample_cell_lot=
 
|sample_cell_catalog=
 
|sample_company=
 
|rna_lot_number=
 
|rna_catalog_number=
 
|sample_species=Mouse (Mus musculus)
 
|sample_strain=C57BL/6J
 
|sample_dev_stage=7 days neonate
 
|sample_tissue=thymus
 
|sample_donor(cell lot)=
 
|sample_sex=mixture
 
|sample_age=
 
|sample_ethnicity=
 
|rna_rin=
 
|rna_od260/230=
 
|rna_od260/280=
 
|sample_cell_type=CELL MIXTURE - tissue sample
 
|sample_cell_line=
 
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
 
|sample_experimental_condition=
 
|sample_disease=
 
|rna_sample_type=
 
|rna_extraction_protocol=
 
|rna_weight_ug=
 
|rna_concentration=
 
|sample_note=
 
|profile_hcage=CNhs11211,LSID747,release008,COMPLETED
 
|profile_cagescan=,,,
 
|profile_srnaseq=,,,
 
|profile_rnaseq=,,,
 
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000065,UBERON:0000072,UBERON:0000077,UBERON:0000078,UBERON:0000119,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000490,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0000974,UBERON:0001004,UBERON:0001007,UBERON:0001041,UBERON:0001042,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0001557,UBERON:0002050,UBERON:0002193,UBERON:0002342,UBERON:0002346,UBERON:0002368,UBERON:0002370,UBERON:0002390,UBERON:0002405,UBERON:0002530,UBERON:0002532,UBERON:0003075,UBERON:0003104,UBERON:0003295,UBERON:0003351,UBERON:0003408,UBERON:0003929,UBERON:0004119,UBERON:0004120,UBERON:0004121,UBERON:0004177,UBERON:0004185,UBERON:0004807,UBERON:0004921,UBERON:0005057,UBERON:0005058,UBERON:0005291,UBERON:0005423,UBERON:0005428,UBERON:0005434,UBERON:0005562,UBERON:0005911,UBERON:0006562,UBERON:0006598,UBERON:0007026,UBERON:0007284,UBERON:0007690,UBERON:0009113,UBERON:0009142,UBERON:0009145
 
 
|ancestors_in_disease_facet=
 
|ancestors_in_disease_facet=
|sample_description=
+
|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000103,FF:0000001,FF:0000004,FF:0000303,FF:0000313,FF:0011407
 +
|comment=
 +
|created_by=
 +
|creation_date=
 +
|data_phase=2
 +
|datafreeze_phase=2
 +
|def=
 +
|expression_enrichment_score=chr11:52096066..52096081,-!p2@Tcf7!2.65!533.98!Tcf7;;chr17:51971960..51971979,-!p1@Satb1!2.41!334.47!Satb1;;chr17:51971932..51971958,-!p2@Satb1!2.16!194.63!Satb1;;chr1:38721792..38721845,-!p1@Aff3!2.03!130.85!Aff3;;chr3:94181376..94181403,+!p2@Rorc!1.94!85.89!Rorc;;chr12:109242266..109242295,-!p1@Bcl11b!1.90!617.50!Bcl11b;;chr11:52096804..52096896,-!p1@Tcf7!1.89!585.19!Tcf7;;chr11:52095821..52095836,-!p3@Tcf7!1.85!70.42!Tcf7;;chr3:130815703..130815721,+!p2@Lef1!1.70!58.68!Lef1;;chr16:92826249..92826325,-!p1@Runx1!1.69!113.47!Runx1;;chr3:94181427..94181449,+!p3@Rorc!1.64!42.45!Rorc;;chr2:147190749..147190769,+!p1@Pax1!1.59!37.95!Pax1;;chr11:11590117..11590138,+!p4@Ikzf1!1.58!36.81!Ikzf1;;chr11:52095797..52095809,-!p5@Tcf7!1.54!33.53!Tcf7;;chr11:98407264..98407295,-!p1@Ikzf3!1.53!33.15!Ikzf3;;chr2:9800207..9800234,-!p1@Gata3!1.51!92.74!Gata3;;chr17:51971991..51972003,-!p4@Satb1!1.51!31.40!Satb1;;chr10:20880731..20880775,-!p2@Myb!1.50!62.34!Myb;;chr4:102787521..102787588,+!p4@Mier1!1.49!53.12!Mier1;;chr11:11584970..11585030,+!p2@Ikzf1!1.48!41.30!Ikzf1;;chr11:11590140..11590187,+!p3@Ikzf1!1.48!34.98!Ikzf1;;chr10:20880629..20880683,-!p1@Myb!1.47!79.86!Myb;;chr17:51965903..51965926,-!p5@Satb1!1.47!28.20!Satb1;;chr4:135728311..135728342,+!p3@E2f2!1.43!26.14!E2f2;;chr11:11585912..11585950,+!p6@Ikzf1!1.42!32.08!Ikzf1;;chr17:51972530..51972571,-!p7@Satb1!1.41!24.77!Satb1;;chr3:130813200..130813252,+!p1@Lef1!1.39!101.74!Lef1;;chr12:109241728..109241781,-!p2@Bcl11b!1.37!24.01!Bcl11b;;chr3:94181331..94181345,+!p4@Rorc!1.37!22.63!Rorc;;chr10:20880698..20880717,-!p3@Myb!1.35!33.23!Myb;;chr11:11585678..11585745,+!p5@Ikzf1!1.32!28.73!Ikzf1;;chr11:98407234..98407259,-!p2@Ikzf3!1.31!19.43!Ikzf3;;chr17:51972603..51972624,-!p9@Satb1!1.30!19.13!Satb1;;chr14:79915425..79915501,+!p1@Elf1!1.29!160.11!Elf1;;chr17:48025139..48025166,-!p8@Foxp4!1.27!20.50!Foxp4;;chr17:51972438..51972463,-!p8@Satb1!1.27!17.45!Satb1;;chr11:11586218..11586285,+!p1@Ikzf1!1.22!49.53!Ikzf1;;chr3:94181461..94181472,+!p6@Rorc!1.22!15.47!Rorc;;chr1:52065454..52065495,+!p1@Stat4!1.21!25.00!Stat4;;chr8:108583550..108583595,+!p2@Nfatc3!1.20!66.68!Nfatc3;;chr4:6917606..6917681,-!p1@Tox!1.20!60.89!Tox;;chr4:135728282..135728310,+!p4@E2f2!1.20!16.61!E2f2;;chr3:94181355..94181373,+!p5@Rorc!1.20!14.94!Rorc;;chr17:51952856..51952876,-!p12@Satb1!1.19!14.48!Satb1;;chr17:51972400..51972428,-!p11@Satb1!1.19!14.33!Satb1;;chr5:104182963..104182982,+!p5@Aff1!1.18!29.49!Aff1;;chr4:63064364..63064384,-!p1@Akna!1.13!36.12!Akna;;chr2:147190725..147190747,+!p2@Pax1!1.13!12.57!Pax1;;chr9:32503590..32503680,+!p1@Ets1!1.11!426.61!Ets1;;chr12:109241852..109241873,-!p4@Bcl11b!1.11!14.17!Bcl11b;;chr11:98407370..98407395,-!p3@Ikzf3!1.11!11.81!Ikzf3;;chr8:124984566..124984595,-!p1@Snai3!1.09!17.53!Snai3;;chr11:52096750..52096772,-!p4@Tcf7!1.09!17.45!Tcf7;;chr17:51965928..51965960,-!p10@Satb1!1.09!11.43!Satb1;;chr11:98407142..98407159,-!p5@Ikzf3!1.09!11.20!Ikzf3;;chr11:98826178..98826197,+!p7@Rara!1.08!11.13!Rara;;chr5:108494765..108494786,+!p2@Mtf2!1.07!14.48!Mtf2;;chr10:20881160..20881175,-!p4@Myb!1.07!10.82!Myb;;chr5:108155007..108155034,-!p1@Gfi1!1.07!10.67!Gfi1;;chr16:25801993..25802014,+!p1@Trp63!1.06!10.36!Trp63;;chr17:51972575..51972595,-!p13@Satb1!1.06!10.36!Satb1;;chr11:100800901..100800921,-!p4@Stat3!1.03!11.66!Stat3;;chr2:173044380..173044432,-!p1@Zbp1!1.02!22.71!Zbp1;;chr11:98407340..98407359,-!p4@Ikzf3!1.01!9.30!Ikzf3;;chr17:51965860..51965876,-!p14@Satb1!1.01!9.22!Satb1;;chr11:52096732..52096741,-!p6@Tcf7!1.01!9.14!Tcf7;;chr3:94181408..94181419,+!p7@Rorc!0.99!8.69!Rorc;;chr9:71959562..71959624,-!p3@Tcf12!0.97!29.42!Tcf12;;chr11:98338697..98338709,-!p9@Ikzf3!0.97!8.31!Ikzf3;;chr17:45692642..45692663,+!p1@Nfkbie!0.96!26.52!Nfkbie;;chr4:135728181..135728203,+!p2@E2f2!0.96!10.75!E2f2;;chr9:71958979..71959032,-!p4@Tcf12!0.96!10.36!Tcf12;;chr5:138186979..138187025,+!p4@Tsc22d4!0.95!29.87!Tsc22d4;;chr19:25746898..25746910,+!p1@Dmrt2!0.95!11.96!Dmrt2;;chr6:99216488..99216534,-!p2@Foxp1!0.94!22.71!Foxp1;;chr7:148514080..148514108,-!p4@Deaf1!0.93!16.38!Deaf1;;chr12:57796615..57796687,+!p1@Pax9!0.93!7.47!Pax9;;chr16:23988711..23988727,-!p1@Bcl6!0.92!89.54!Bcl6;;chr4:102787381..102787397,+!p9@Mier1!0.92!8.69!Mier1;;chr10:20881176..20881191,-!p6@Myb!0.91!7.16!Myb;;chr11:98407305..98407321,-!p6@Ikzf3!0.91!7.09!Ikzf3;;chr5:108155037..108155060,-!p2@Gfi1!0.90!7.01!Gfi1;;chr11:98407121..98407133,-!p10@Ikzf3!0.89!6.71!Ikzf3;;chr7:51787434..51787448,-!p1@Spib!0.88!9.75!Spib;;chr3:130813254..130813263,+!p4@Lef1!0.88!6.55!Lef1;;chr1:133904862..133904893,+!p6@Elk4!0.86!13.34!Elk4;;chr17:51951634..51951651,-!p6@Satb1!0.86!12.35!Satb1;;chr1:69732354..69732402,-!p1@Ikzf2!0.86!7.09!Ikzf2;;chr11:52074095..52074127,-!p8@Tcf7!0.86!6.17!Tcf7;;chr4:102792039..102792052,+!p7@Mier1!0.85!8.76!Mier1;;chr11:98407087..98407102,-!p11@Ikzf3!0.85!6.10!Ikzf3;;chr11:106134241..106134320,-!p2@Smarcd2!0.84!72.85!Smarcd2;;chr5:104183477..104183548,+!p6@Aff1!0.83!11.89!Aff1;;chr12:77470718..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 +
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006595,UBERON:0006603,UBERON:0010316,FF:0000294
 
|fonse_cell_line=
 
|fonse_cell_line=
 
|fonse_cell_line_closure=
 
|fonse_cell_line_closure=
Line 66: Line 40:
 
|fonse_treatment=
 
|fonse_treatment=
 
|fonse_treatment_closure=
 
|fonse_treatment_closure=
|top_motifs=PITX1..3:2.57705380034;RORA:2.49777718769;ALX4:2.10013315465;E2F1..5:2.07637575422;PPARG:1.94722856165;TEF:1.90252881662;ELF1,2,4:1.87983936825;ETS1,2:1.8076035549;ZBTB16:1.77012960776;RUNX1..3:1.7504625833;AIRE:1.74608963496;DMAP1_NCOR{1,2}_SMARC:1.71410917049;NFY{A,B,C}:1.42879944628;IRF1,2:1.32125916514;SPI1:1.31490407835;POU1F1:1.30250429975;CDX1,2,4:1.26389234398;SPZ1:1.25332835201;MYB:1.19473072084;SPIB:1.17067554832;TLX2:1.14216710048;ELK1,4_GABP{A,B1}:1.12252659998;FOXD3:1.10138439266;IRF7:1.08520689467;FOXP1:1.05522374808;BPTF:0.974718371095;NFATC1..3:0.936856520234;LMO2:0.836480814792;NFKB1_REL_RELA:0.835611036269;RXRA_VDR{dimer}:0.73303965486;EN1,2:0.674627542402;NFIX:0.634664621204;POU5F1:0.632613225542;YY1:0.614885357372;PAX4:0.594445735851;NRF1:0.474245043218;NR6A1:0.436341914518;ZEB1:0.415060239219;SNAI1..3:0.388377220678;GFI1:0.371874476992;ZNF143:0.369615274711;FOX{I1,J2}:0.341214220627;TAL1_TCF{3,4,12}:0.322177287723;HBP1_HMGB_SSRP1_UBTF:0.281028249316;STAT1,3:0.258018440731;RBPJ:0.252861747232;SOX{8,9,10}:0.198084930362;ZNF238:0.175635529429;POU2F1..3:0.162006224314;ZNF384:0.153865774422;SREBF1,2:0.145206263234;TFDP1:0.140528997208;LEF1_TCF7_TCF7L1,2:0.134916368203;FOXO1,3,4:0.131411209333;TOPORS:0.119835174307;PDX1:0.113805523736;FOXP3:0.111745146194;SOX2:0.0679139383537;PBX1:0.0565923311054;OCT4_SOX2{dimer}:0.0544784653845;FOX{D1,D2}:0.0386641520931;FOXQ1:-0.00924143805726;IKZF2:-0.0509922664799;STAT5{A,B}:-0.0531312827625;HES1:-0.0637612440263;HLF:-0.106607750521;ATF5_CREB3:-0.11607576217;BREu{core}:-0.127657617511;RFX2..5_RFXANK_RFXAP:-0.139201357229;PRDM1:-0.166706254992;SOX17:-0.18050803581;ALX1:-0.18140532116;CRX:-0.23218475336;NR1H4:-0.240048888986;NHLH1,2:-0.250686595387;CEBPA,B_DDIT3:-0.255549998926;NANOG:-0.258001249279;TBP:-0.264770060588;HOX{A4,D4}:-0.270360501819;NKX2-1,4:-0.281082316996;KLF4:-0.297779886668;NANOG{mouse}:-0.31848379982;CUX2:-0.326840467295;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.329972739929;TGIF1:-0.374379898827;ZFP161:-0.375505836603;GATA6:-0.382463364311;PAX8:-0.382603583604;RREB1:-0.388829367773;FOS_FOS{B,L1}_JUN{B,D}:-0.40110487881;NKX6-1,2:-0.418226772547;HOX{A5,B5}:-0.440003061484;FOX{F1,F2,J1}:-0.456122665059;PRRX1,2:-0.48514744244;T:-0.487032589498;MYOD1:-0.487428230787;NKX2-2,8:-0.487897253262;NR5A1,2:-0.528778705104;RXR{A,B,G}:-0.530959557242;MZF1:-0.532499457511;NFE2L1:-0.547753580977;FOXL1:-0.553783384155;HNF4A_NR2F1,2:-0.558086505252;MTE{core}:-0.579410079256;POU3F1..4:-0.580156444207;POU6F1:-0.58101422973;JUN:-0.58315387747;EVI1:-0.593647819779;PAX6:-0.606027598612;HMX1:-0.614246009385;AHR_ARNT_ARNT2:-0.627155491286;ARID5B:-0.635356366851;EBF1:-0.645519209776;RFX1:-0.662403200365;MTF1:-0.671947975699;AR:-0.674489065497;MYFfamily:-0.687839755443;CREB1:-0.690684615147;SRF:-0.722747165392;HNF1A:-0.740217292415;NKX3-1:-0.752349005463;EP300:-0.756884532186;NKX2-3_NKX2-5:-0.77628812696;BACH2:-0.77965277811;bHLH_family:-0.783340140449;MED-1{core}:-0.788523965277;TBX4,5:-0.796486183106;ZNF423:-0.832555297457;LHX3,4:-0.850933874319;SMAD1..7,9:-0.855056100354;PATZ1:-0.861177061692;NR3C1:-0.87509905234;ATF4:-0.879835317292;MEF2{A,B,C,D}:-0.882684429761;FOXA2:-0.888882279447;ESR1:-0.894326716965;PAX2:-0.902711231756;ZNF148:-0.910144242046;DBP:-0.929651912485;STAT2,4,6:-0.968815481511;EGR1..3:-0.988922427147;CDC5L:-0.993491431319;UFEwm:-1.01524459758;NFE2:-1.02669007869;HIC1:-1.03949695606;REST:-1.04139291536;HMGA1,2:-1.05362124904;SOX5:-1.05747045271;FOXM1:-1.0746421816;XCPE1{core}:-1.07740438906;PAX1,9:-1.08905888093;TP53:-1.09413608328;MAFB:-1.10416694249;TEAD1:-1.10520374139;ONECUT1,2:-1.10841902839;TFAP2B:-1.11211667454;GATA4:-1.11552627644;FOXN1:-1.12285672058;NFIL3:-1.12322849221;VSX1,2:-1.1312213388;ZBTB6:-1.14541719607;MYBL2:-1.16888832917;TFAP4:-1.16936154214;GTF2I:-1.17378192838;HAND1,2:-1.17509847039;GZF1:-1.19079079305;ATF2:-1.20633582918;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.26991344811;MAZ:-1.27031131058;NKX3-2:-1.28151129253;HSF1,2:-1.30897276955;FOSL2:-1.31198033682;TFAP2{A,C}:-1.33972693676;ESRRA:-1.3421020414;TLX1..3_NFIC{dimer}:-1.34627023895;ZIC1..3:-1.35422460993;NFE2L2:-1.41971512789;TFCP2:-1.43499660715;HOXA9_MEIS1:-1.48698462329;GCM1,2:-1.58787283397;SP1:-1.59424155505;ATF6:-1.61170514516;ADNP_IRX_SIX_ZHX:-1.61858476552;IKZF1:-1.70743129302;GLI1..3:-1.90382766189;GFI1B:-1.98459697165;GTF2A1,2:-2.07487460591;PAX5:-2.2632458963;HIF1A:-2.63737755393
 
|comment=
 
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|def=
 
 
|has_quality=
 
|has_quality=
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+
|id=FF:713-19D3
 +
|is_a=EFO:0002091;;FF:0011407
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|is_obsolete=
 +
|library_id=CNhs11211
 +
|library_id_phase_based=2:CNhs11211
 +
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;713
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;713
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|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N07.CNhs11211.713-19D3.mm10.nobarcode.bam
 +
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N07.CNhs11211.713-19D3.mm10.nobarcode.ctss.bed.gz
 +
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N07.CNhs11211.713-19D3.mm9.nobarcode.bam
 +
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N07.CNhs11211.713-19D3.mm9.ctss.bed.gz
 +
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N07.CNhs11211.713-19D3.mm9.nobarcode.rdna.fa.gz
 +
|name=thymus, neonate N07
 
|namespace=FANTOM5
 
|namespace=FANTOM5
 
|part_of=
 
|part_of=
 +
|profile_cagescan=,,,
 +
|profile_hcage=CNhs11211,LSID747,release008,COMPLETED
 +
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|repeat_enrich_byfamily=0.111939930704693,0.0158889756001152,0,0.031895734489288,0.751941990806014,0,0.132666381893857,0,0.0308041899510522,0,0,0.00507848872506521,0,0,0,0,0,0,0.271278224794984,0,0.0447088645608033,0,0,0,0,0,0,0,0,0,0.0447088645608033,0,0.268656240097819,0,0,0,0,0,0.160062829409683,-0.0289887960841883,0.00105826376082696,-0.719800915471967,-0.180450908888745,0,0,0,0,0,0,0,0,0,0,0,0.031895734489288,-0.00439716766133594,0,0,0,0,0.0187614248192296,0,0.111992617453481,0.0894177291216067,0.346217756059235,0,0.104659508828286,0.174727708469149,0.106319408234777,0.117007851131524,0,0.0285249404470723,-0.0576539277958799,0,0.0616083799021044,0,-0.00531120513120255,-0.0725408676462296,-0.313863665906317,0.106837358489769,0,0,0,0,0,0,-0.164592999154703,-0.221682036935015,-0.183752944400766,0,0,0,0,0
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|rna_box=19
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|sample_cell_type=CELL MIXTURE - tissue sample
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|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
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 +
|sample_description=
 +
|sample_dev_stage=7 days neonate
 +
|sample_disease=
 +
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 +
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 +
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 +
|sample_id=713
 +
|sample_note=
 +
|sample_sex=mixture
 +
|sample_species=Mouse (Mus musculus)
 +
|sample_strain=C57BL/6J
 +
|sample_tissue=thymus
 +
|top_motifs=PITX1..3:2.57705380034;RORA:2.49777718769;ALX4:2.10013315465;E2F1..5:2.07637575422;PPARG:1.94722856165;TEF:1.90252881662;ELF1,2,4:1.87983936825;ETS1,2:1.8076035549;ZBTB16:1.77012960776;RUNX1..3:1.7504625833;AIRE:1.74608963496;DMAP1_NCOR{1,2}_SMARC:1.71410917049;NFY{A,B,C}:1.42879944628;IRF1,2:1.32125916514;SPI1:1.31490407835;POU1F1:1.30250429975;CDX1,2,4:1.26389234398;SPZ1:1.25332835201;MYB:1.19473072084;SPIB:1.17067554832;TLX2:1.14216710048;ELK1,4_GABP{A,B1}:1.12252659998;FOXD3:1.10138439266;IRF7:1.08520689467;FOXP1:1.05522374808;BPTF:0.974718371095;NFATC1..3:0.936856520234;LMO2:0.836480814792;NFKB1_REL_RELA:0.835611036269;RXRA_VDR{dimer}:0.73303965486;EN1,2:0.674627542402;NFIX:0.634664621204;POU5F1:0.632613225542;YY1:0.614885357372;PAX4:0.594445735851;NRF1:0.474245043218;NR6A1:0.436341914518;ZEB1:0.415060239219;SNAI1..3:0.388377220678;GFI1:0.371874476992;ZNF143:0.369615274711;FOX{I1,J2}:0.341214220627;TAL1_TCF{3,4,12}:0.322177287723;HBP1_HMGB_SSRP1_UBTF:0.281028249316;STAT1,3:0.258018440731;RBPJ:0.252861747232;SOX{8,9,10}:0.198084930362;ZNF238:0.175635529429;POU2F1..3:0.162006224314;ZNF384:0.153865774422;SREBF1,2:0.145206263234;TFDP1:0.140528997208;LEF1_TCF7_TCF7L1,2:0.134916368203;FOXO1,3,4:0.131411209333;TOPORS:0.119835174307;PDX1:0.113805523736;FOXP3:0.111745146194;SOX2:0.0679139383537;PBX1:0.0565923311054;OCT4_SOX2{dimer}:0.0544784653845;FOX{D1,D2}:0.0386641520931;FOXQ1:-0.00924143805726;IKZF2:-0.0509922664799;STAT5{A,B}:-0.0531312827625;HES1:-0.0637612440263;HLF:-0.106607750521;ATF5_CREB3:-0.11607576217;BREu{core}:-0.127657617511;RFX2..5_RFXANK_RFXAP:-0.139201357229;PRDM1:-0.166706254992;SOX17:-0.18050803581;ALX1:-0.18140532116;CRX:-0.23218475336;NR1H4:-0.240048888986;NHLH1,2:-0.250686595387;CEBPA,B_DDIT3:-0.255549998926;NANOG:-0.258001249279;TBP:-0.264770060588;HOX{A4,D4}:-0.270360501819;NKX2-1,4:-0.281082316996;KLF4:-0.297779886668;NANOG{mouse}:-0.31848379982;CUX2:-0.326840467295;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.329972739929;TGIF1:-0.374379898827;ZFP161:-0.375505836603;GATA6:-0.382463364311;PAX8:-0.382603583604;RREB1:-0.388829367773;FOS_FOS{B,L1}_JUN{B,D}:-0.40110487881;NKX6-1,2:-0.418226772547;HOX{A5,B5}:-0.440003061484;FOX{F1,F2,J1}:-0.456122665059;PRRX1,2:-0.48514744244;T:-0.487032589498;MYOD1:-0.487428230787;NKX2-2,8:-0.487897253262;NR5A1,2:-0.528778705104;RXR{A,B,G}:-0.530959557242;MZF1:-0.532499457511;NFE2L1:-0.547753580977;FOXL1:-0.553783384155;HNF4A_NR2F1,2:-0.558086505252;MTE{core}:-0.579410079256;POU3F1..4:-0.580156444207;POU6F1:-0.58101422973;JUN:-0.58315387747;EVI1:-0.593647819779;PAX6:-0.606027598612;HMX1:-0.614246009385;AHR_ARNT_ARNT2:-0.627155491286;ARID5B:-0.635356366851;EBF1:-0.645519209776;RFX1:-0.662403200365;MTF1:-0.671947975699;AR:-0.674489065497;MYFfamily:-0.687839755443;CREB1:-0.690684615147;SRF:-0.722747165392;HNF1A:-0.740217292415;NKX3-1:-0.752349005463;EP300:-0.756884532186;NKX2-3_NKX2-5:-0.77628812696;BACH2:-0.77965277811;bHLH_family:-0.783340140449;MED-1{core}:-0.788523965277;TBX4,5:-0.796486183106;ZNF423:-0.832555297457;LHX3,4:-0.850933874319;SMAD1..7,9:-0.855056100354;PATZ1:-0.861177061692;NR3C1:-0.87509905234;ATF4:-0.879835317292;MEF2{A,B,C,D}:-0.882684429761;FOXA2:-0.888882279447;ESR1:-0.894326716965;PAX2:-0.902711231756;ZNF148:-0.910144242046;DBP:-0.929651912485;STAT2,4,6:-0.968815481511;EGR1..3:-0.988922427147;CDC5L:-0.993491431319;UFEwm:-1.01524459758;NFE2:-1.02669007869;HIC1:-1.03949695606;REST:-1.04139291536;HMGA1,2:-1.05362124904;SOX5:-1.05747045271;FOXM1:-1.0746421816;XCPE1{core}:-1.07740438906;PAX1,9:-1.08905888093;TP53:-1.09413608328;MAFB:-1.10416694249;TEAD1:-1.10520374139;ONECUT1,2:-1.10841902839;TFAP2B:-1.11211667454;GATA4:-1.11552627644;FOXN1:-1.12285672058;NFIL3:-1.12322849221;VSX1,2:-1.1312213388;ZBTB6:-1.14541719607;MYBL2:-1.16888832917;TFAP4:-1.16936154214;GTF2I:-1.17378192838;HAND1,2:-1.17509847039;GZF1:-1.19079079305;ATF2:-1.20633582918;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.26991344811;MAZ:-1.27031131058;NKX3-2:-1.28151129253;HSF1,2:-1.30897276955;FOSL2:-1.31198033682;TFAP2{A,C}:-1.33972693676;ESRRA:-1.3421020414;TLX1..3_NFIC{dimer}:-1.34627023895;ZIC1..3:-1.35422460993;NFE2L2:-1.41971512789;TFCP2:-1.43499660715;HOXA9_MEIS1:-1.48698462329;GCM1,2:-1.58787283397;SP1:-1.59424155505;ATF6:-1.61170514516;ADNP_IRX_SIX_ZHX:-1.61858476552;IKZF1:-1.70743129302;GLI1..3:-1.90382766189;GFI1B:-1.98459697165;GTF2A1,2:-2.07487460591;PAX5:-2.2632458963;HIF1A:-2.63737755393
 +
|xref=
 
}}
 
}}

Latest revision as of 13:43, 10 August 2017


Name:thymus, neonate N07
Species:Mouse (Mus musculus)
Library ID:CNhs11211
Sample type:developmental
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuethymus
dev stage7 days neonate
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005656
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11211 CAGE DRX009121 DRR009995
Accession ID Mm9

Library idBAMCTSS
CNhs11211 DRZ001420 DRZ002803
Accession ID Mm10

Library idBAMCTSS
CNhs11211 DRZ012770 DRZ014153
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



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.
Analyst:NA

link to dataset.
data

CNhs11211

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.00631
1001 0.0876
1002 --0.0186
1003 --0.107
1004 0
1005 0
1006 --0.143
1007 0.135
1008 0
1009 --0.101
101 0.127
1010 0
1011 0.056
1012 0.463
1013 --0.135
1014 --0.0874
1015 0.0415
1016 --0.33
1017 0
1018 0.0319
1019 0
102 0.0319
1020 0
1021 0.0319
1022 --0.226
1023 0
1024 --0.0861
1025 --0.0611
1026 0
1027 --0.0278
1028 0
1029 0.389
103 --0.0605
1030 0.0616
1031 --0.629
1032 --0.463
1033 0
1034 0
1035 0
1036 0.219
1037 0
1038 --0.305
1039 --0.131
104 0
1040 --0.0865
1041 0.0319



Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs11211

Jaspar motif P-value
MA0002.2 0.00371
MA0003.1 0.244
MA0004.1 0.255
MA0006.1 0.932
MA0007.1 0.375
MA0009.1 0.519
MA0014.1 0.2
MA0017.1 0.676
MA0018.2 0.0595
MA0019.1 0.156
MA0024.1 4.4207e-6
MA0025.1 0.00791
MA0027.1 0.53
MA0028.1 3.84657e-7
MA0029.1 0.0787
MA0030.1 0.936
MA0031.1 0.176
MA0035.2 0.402
MA0038.1 0.998
MA0039.2 0.263
MA0040.1 0.986
MA0041.1 0.303
MA0042.1 0.987
MA0043.1 0.204
MA0046.1 2.74959e-15
MA0047.2 0.505
MA0048.1 0.603
MA0050.1 3.59826e-6
MA0051.1 3.16333e-5
MA0052.1 1.36674e-4
MA0055.1 0.948
MA0057.1 0.727
MA0058.1 0.406
MA0059.1 0.0127
MA0060.1 0.00587
MA0061.1 2.9366e-4
MA0062.2 3.25436e-18
MA0065.2 0.541
MA0066.1 0.0155
MA0067.1 0.475
MA0068.1 0.848
MA0069.1 0.844
MA0070.1 0.526
MA0071.1 0.359
MA0072.1 1.57721e-6
MA0073.1 0.751
MA0074.1 0.886
MA0076.1 2.96056e-9
MA0077.1 0.178
MA0078.1 0.619
MA0079.2 0.0254
MA0080.2 8.23782e-13
MA0081.1 0.0367
MA0083.1 0.0124
MA0084.1 0.37
MA0087.1 0.349
MA0088.1 0.279
MA0090.1 0.0491
MA0091.1 0.0712
MA0092.1 0.994
MA0093.1 0.308
MA0099.2 0.062
MA0100.1 0.00462
MA0101.1 5.92615e-4
MA0102.2 0.4
MA0103.1 1.9694e-4
MA0104.2 0.089
MA0105.1 7.31932e-7
MA0106.1 0.858
MA0107.1 0.001
MA0108.2 2.74993e-4
MA0111.1 0.33
MA0112.2 0.0457
MA0113.1 0.77
MA0114.1 0.265
MA0115.1 0.738
MA0116.1 0.00577
MA0117.1 0.749
MA0119.1 0.846
MA0122.1 0.965
MA0124.1 0.329
MA0125.1 0.404
MA0131.1 0.054
MA0135.1 0.151
MA0136.1 4.04598e-21
MA0137.2 0.123
MA0138.2 1.18861e-5
MA0139.1 0.205
MA0140.1 0.656
MA0141.1 0.484
MA0142.1 0.746
MA0143.1 0.293
MA0144.1 0.534
MA0145.1 0.261
MA0146.1 0.345
MA0147.1 0.0373
MA0148.1 0.512
MA0149.1 0.0345
MA0150.1 0.415
MA0152.1 0.645
MA0153.1 7.26973e-8
MA0154.1 0.36
MA0155.1 0.941
MA0156.1 1.40276e-25
MA0157.1 0.325
MA0159.1 0.14
MA0160.1 0.275
MA0162.1 0.557
MA0163.1 9.30226e-4
MA0164.1 0.688
MA0258.1 0.0994
MA0259.1 0.394



FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs11211

Novel motif P-value
1 0.245
10 0.0144
100 0.641
101 0.886
102 0.44
103 0.181
104 0.942
105 0.749
106 0.94
107 0.724
108 0.217
109 0.361
11 0.166
110 0.0922
111 0.807
112 0.256
113 0.404
114 0.852
115 0.438
116 0.809
117 4.99026e-4
118 0.128
119 0.344
12 0.6
120 0.277
121 0.335
122 0.725
123 0.635
124 0.975
125 0.0708
126 0.35
127 0.784
128 0.655
129 0.162
13 0.0126
130 0.33
131 0.469
132 0.662
133 0.846
134 0.581
135 0.433
136 0.396
137 0.341
138 0.694
139 0.549
14 0.692
140 0.728
141 0.95
142 0.691
143 0.236
144 0.177
145 0.121
146 0.842
147 0.328
148 0.288
149 0.647
15 0.112
150 0.363
151 0.246
152 0.0337
153 0.199
154 0.0639
155 0.0961
156 0.0448
157 0.663
158 0.0702
159 0.022
160 0.889
161 0.442
162 0.635
163 0.965
164 0.126
165 0.335
166 0.226
167 0.18
168 0.206
169 0.589
17 0.681
18 0.774
19 0.512
2 0.0493
20 0.228
21 0.435
22 0.749
23 0.525
24 0.16
25 0.192
26 0.0231
27 0.487
28 0.235
29 0.0632
3 0.164
30 0.152
31 0.432
32 0.095
33 0.377
34 0.918
35 0.0958
36 0.144
37 0.285
38 0.439
39 0.974
4 0.901
40 0.499
41 0.928
42 0.0256
43 0.629
44 0.956
45 0.628
46 0.11
47 0.444
48 0.199
49 0.207
5 0.273
50 0.771
51 0.897
52 0.147
53 0.907
54 0.254
55 0.469
56 0.904
57 0.24
58 0.26
59 0.6
6 0.27
60 0.803
61 0.0649
62 0.132
63 0.677
64 0.766
65 0.863
66 0.653
67 0.745
68 0.342
69 0.551
7 0.129
70 0.412
71 0.0419
72 0.576
73 0.644
74 0.74
75 0.0238
76 0.0248
77 0.133
78 0.141
79 0.72
8 0.458
80 0.105
81 0.931
82 0.92
83 0.944
84 0.176
85 0.534
86 0.357
87 0.118
88 0.312
89 0.297
9 0.331
90 0.0306
91 0.594
92 0.618
93 0.829
94 0.326
95 0.373
96 0.0293
97 0.502
98 0.503
99 0.307



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs11211


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON: Anatomy
0000468 (multi-cellular organism)
0002370 (thymus)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0004177 (hemopoietic organ)
0005057 (immune organ)
0002530 (gland)
0005058 (hemolymphoid system gland)
0010317 (germ layer / neural crest derived structure)
0000153 (anterior region of body)
0002390 (hematopoietic system)
0000949 (endocrine system)
0002193 (hemolymphoid system)
0002405 (immune system)
0009113 (thymic region)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000313 (mouse neonate N7 sample)
0011407 (mouse thymus- neonate N07 sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)