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{{f5samples
{{f5samples
|id=FF:713-19D3
|DRA_sample_Accession=CAGE@SAMD00005656
|name=thymus, neonate N07, biol_rep1
|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=713-19D3
|rna_box=713-19D3
|rna_position=713-19D3
|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,,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=
|has_quality=
|id=FF:713-19D3
|is_a=EFO:0002091;;FF:0011407
|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
|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
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11211,LSID747,release008,COMPLETED
|profile_rnaseq=
|profile_srnaseq=,,,
|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
|rna_box=19
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=D3
|rna_rin=
|rna_sample_type=
|rna_tube_id=19D3
|rna_weight_ug=
|sample_age=
|sample_category=developmental
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=
|sample_description=
|sample_dev_stage=7 days neonate
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|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
|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=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:713-19D3;search_select_hide=table117:713-19D3
}}
}}

Latest revision as of 19:19, 4 June 2020


Name:thymus, neonate N07
Species:Mouse (Mus musculus)
Library ID:CNhs11211
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :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

CAGE 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. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs11211

00
10
100
1000
1000-0.00631
10010.0876
1002-0.0186
1003-0.107
10040
10050
1006-0.143
10070.135
10080
1009-0.101
1010.127
10100
10110.056
10120.463
1013-0.135
1014-0.0874
10150.0415
1016-0.33
10170
10180.0319
10190
1020.0319
10200
10210.0319
1022-0.226
10230
1024-0.0861
1025-0.0611
10260
1027-0.0278
10280
10290.389
103-0.0605
10300.0616
1031-0.629
1032-0.463
10330
10340
10350
10360.219
10370
1038-0.305
1039-0.131
1040
1040-0.0865
10410.0319



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



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: CNhs11211

Jaspar motifP-value
MA0002.20.00371
MA0003.10.244
MA0004.10.255
MA0006.10.932
MA0007.10.375
MA0009.10.519
MA0014.10.2
MA0017.10.676
MA0018.20.0595
MA0019.10.156
MA0024.14.4207e-6
MA0025.10.00791
MA0027.10.53
MA0028.13.84657e-7
MA0029.10.0787
MA0030.10.936
MA0031.10.176
MA0035.20.402
MA0038.10.998
MA0039.20.263
MA0040.10.986
MA0041.10.303
MA0042.10.987
MA0043.10.204
MA0046.12.74959e-15
MA0047.20.505
MA0048.10.603
MA0050.13.59826e-6
MA0051.13.16333e-5
MA0052.11.36674e-4
MA0055.10.948
MA0057.10.727
MA0058.10.406
MA0059.10.0127
MA0060.10.00587
MA0061.12.9366e-4
MA0062.23.25436e-18
MA0065.20.541
MA0066.10.0155
MA0067.10.475
MA0068.10.848
MA0069.10.844
MA0070.10.526
MA0071.10.359
MA0072.11.57721e-6
MA0073.10.751
MA0074.10.886
MA0076.12.96056e-9
MA0077.10.178
MA0078.10.619
MA0079.20.0254
MA0080.28.23782e-13
MA0081.10.0367
MA0083.10.0124
MA0084.10.37
MA0087.10.349
MA0088.10.279
MA0090.10.0491
MA0091.10.0712
MA0092.10.994
MA0093.10.308
MA0099.20.062
MA0100.10.00462
MA0101.15.92615e-4
MA0102.20.4
MA0103.11.9694e-4
MA0104.20.089
MA0105.17.31932e-7
MA0106.10.858
MA0107.10.001
MA0108.22.74993e-4
MA0111.10.33
MA0112.20.0457
MA0113.10.77
MA0114.10.265
MA0115.10.738
MA0116.10.00577
MA0117.10.749
MA0119.10.846
MA0122.10.965
MA0124.10.329
MA0125.10.404
MA0131.10.054
MA0135.10.151
MA0136.14.04598e-21
MA0137.20.123
MA0138.21.18861e-5
MA0139.10.205
MA0140.10.656
MA0141.10.484
MA0142.10.746
MA0143.10.293
MA0144.10.534
MA0145.10.261
MA0146.10.345
MA0147.10.0373
MA0148.10.512
MA0149.10.0345
MA0150.10.415
MA0152.10.645
MA0153.17.26973e-8
MA0154.10.36
MA0155.10.941
MA0156.11.40276e-25
MA0157.10.325
MA0159.10.14
MA0160.10.275
MA0162.10.557
MA0163.19.30226e-4
MA0164.10.688
MA0258.10.0994
MA0259.10.394



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: CNhs11211

Novel motifP-value
10.245
100.0144
1000.641
1010.886
1020.44
1030.181
1040.942
1050.749
1060.94
1070.724
1080.217
1090.361
110.166
1100.0922
1110.807
1120.256
1130.404
1140.852
1150.438
1160.809
1174.99026e-4
1180.128
1190.344
120.6
1200.277
1210.335
1220.725
1230.635
1240.975
1250.0708
1260.35
1270.784
1280.655
1290.162
130.0126
1300.33
1310.469
1320.662
1330.846
1340.581
1350.433
1360.396
1370.341
1380.694
1390.549
140.692
1400.728
1410.95
1420.691
1430.236
1440.177
1450.121
1460.842
1470.328
1480.288
1490.647
150.112
1500.363
1510.246
1520.0337
1530.199
1540.0639
1550.0961
1560.0448
1570.663
1580.0702
1590.022
1600.889
1610.442
1620.635
1630.965
1640.126
1650.335
1660.226
1670.18
1680.206
1690.589
170.681
180.774
190.512
20.0493
200.228
210.435
220.749
230.525
240.16
250.192
260.0231
270.487
280.235
290.0632
30.164
300.152
310.432
320.095
330.377
340.918
350.0958
360.144
370.285
380.439
390.974
40.901
400.499
410.928
420.0256
430.629
440.956
450.628
460.11
470.444
480.199
490.207
50.273
500.771
510.897
520.147
530.907
540.254
550.469
560.904
570.24
580.26
590.6
60.27
600.803
610.0649
620.132
630.677
640.766
650.863
660.653
670.745
680.342
690.551
70.129
700.412
710.0419
720.576
730.644
740.74
750.0238
760.0248
770.133
780.141
790.72
80.458
800.105
810.931
820.92
830.944
840.176
850.534
860.357
870.118
880.312
890.297
90.331
900.0306
910.594
920.618
930.829
940.326
950.373
960.0293
970.502
980.503
990.307



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: CNhs11211


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

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)<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
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)

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