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(Created page with "{{f5samples |id=FF:12988-138I9 |name=EBF KO HPCs induced to T cell, 00hr00min, biol_rep2 |sample_id=12988 |rna_tube_id= |rna_box=138 |rna_position=I9 |sample_cell_lot= ...")
 
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{{f5samples
{{f5samples
|id=FF:12988-138I9
|DRA_sample_Accession=CAGE@SAMD00005159
|name=EBF KO HPCs induced to T cell, 00hr00min, biol_rep2
|accession_numbers=CAGE;DRX008900;DRR009772;DRZ001197;DRZ002582;DRZ012547;DRZ013932
|sample_id=12988
|ancestors_in_anatomy_facet=
|rna_tube_id=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0002371,CL:0000542,CL:0000219,CL:0000738,CL:0002087,CL:0002242,CL:0000255,CL:0000084,CL:0000837
|rna_box=138
|rna_position=I9
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_dev_stage=
|sample_tissue=
|sample_donor(cell lot)=
|sample_sex=
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=1.75000
|rna_od260/280=2.07000
|sample_cell_type=unclassifiable
|sample_cell_line=
|sample_collaboration=Tomokatsu Ikawa (RCAI)
|sample_experimental_condition=T cell differentiation
|sample_disease=
|rna_sample_type=
|rna_extraction_protocol=
|rna_weight_ug=4.46040
|rna_concentration=0.15930
|sample_note=
|profile_hcage=,LSID993,,SEQUENCING QUEUE
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000048,CL:0000051,CL:0000063,CL:0000084,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000542,CL:0000548,CL:0000566,CL:0000723,CL:0000738,CL:0000827,CL:0000837,CL:0000838,CL:0000988,CL:0002031,CL:0002032,CL:0002087,CL:0002320,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|ancestors_in_ff_facet=FF:0000101,FF:0000103,FF:0000001,FF:0000350,FF:0000357,FF:0000342,FF:0000729
 
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|donor= biol_rep2
|expression_enrichment_score=chr1:38721792..38721845,-!p1@Aff3!1.80!76.01!Aff3;;chr16:55966492..55966517,+!p2@Rpl24,p2@Zbtb11!1.78!74.44!Zbtb11;;chr11:11584970..11585030,+!p2@Ikzf1!1.72!72.87!Ikzf1;;chr3:135257325..135257364,-!p11@Nfkb1!1.65!43.62!Nfkb1;;chr3:135257370..135257389,-!p9@Nfkb1!1.62!40.75!Nfkb1;;chr6:52176164..52176195,-!p1@Hoxa9!1.50!37.87!Hoxa9;;chr10:20880629..20880683,-!p1@Myb!1.47!79.40!Myb;;chr11:11586218..11586285,+!p1@Ikzf1!1.45!84.11!Ikzf1;;chr4:134676555..134676575,+!p2@Runx3!1.44!26.38!Runx3;;chr12:12948633..12948651,-!p1@Mycn!1.43!239.78!Mycn;;chr2:28477452..28477483,-!p1@Gfi1b!1.39!29.25!Gfi1b;;chr14:79915425..79915501,+!p1@Elf1!1.37!190.68!Elf1;;chr17:51971932..51971958,-!p2@Satb1!1.29!25.34!Satb1;;chr6:52167459..52167492,-!p1@Hoxa7!1.29!21.94!Hoxa7;;chr17:51971960..51971979,-!p1@Satb1!1.28!24.29!Satb1;;chr10:20880731..20880775,-!p2@Myb!1.21!31.34!Myb;;chr12:12947182..12947194,-!p3@Mycn!1.19!14.63!Mycn;;chr8:87225329..87225396,+!p1@Lyl1!1.16!50.93!Lyl1;;chr11:11590140..11590187,+!p3@Ikzf1!1.15!15.67!Ikzf1;;chr11:16908650..16908690,-!p1@Plek!1.14!78.36!Plek;;chr7:51787434..51787448,-!p1@Spib!1.12!17.50!Spib;;chr19:25685023..25685043,+!p1@Dmrt3!1.11!11.75!Dmrt3;;chr2:90936901..90936945,+!p1@Sfpi1!1.08!58.77!Sfpi1;;chr2:153475178..153475196,+!p1@Dnmt3b!1.08!23.77!Dnmt3b;;chr6:99216488..99216534,-!p2@Foxp1!1.06!29.78!Foxp1;;chr11:11585912..11585950,+!p6@Ikzf1!1.05!13.06!Ikzf1;;chr8:125921689..125921725,+!p3@Tcf25!1.05!10.19!Tcf25;;chr11:3191741..3191769,+!p5@Patz1!1.04!12.80!Patz1;;chr7:20162663..20162678,+!p1@Zfp296!1.02!12.54!Zfp296;;chr15:103085802..103085817,-!p4@Nfe2!1.01!11.75!Nfe2;;chr12:12947199..12947213,-!p2@Mycn!1.01!9.14!Mycn;;chr13:83663902..83663927,+!p1@Mef2c!0.99!216.80!Mef2c;;chr1:87497610..87497645,+!p1@Gm2427,p1@Sp140!0.99!8.88!Sp140;;chr15:103085660..103085681,-!p1@Nfe2!0.97!12.80!Nfe2;;chr3:135271185..135271254,-!p4@Nfkb1!0.96!15.15!Nfkb1;;chr17:44872561..44872615,-!p1@Runx2!0.94!18.02!Runx2;;chr10:20880698..20880717,-!p3@Myb!0.94!12.28!Myb;;chr15:61816932..61816952,+!p2@Myc!0.93!65.04!Myc;;chr4:63064364..63064384,-!p1@Akna!0.93!22.72!Akna;;chr2:90936947..90936977,+!p2@Sfpi1!0.93!15.41!Sfpi1;;chr17:21626055..21626081,+!p2@Zfp53!0.93!12.80!Zfp53;;chr1:87497443..87497454,+!p3@Gm2427,p3@Sp140!0.93!7.57!Sp140;;chr4:134708451..134708469,+!p1@Runx3!0.92!13.32!Runx3;;chr6:52176144..52176161,-!p2@Hoxa9!0.92!7.31!Hoxa9;;chr6:52163319..52163342,-!p1@Hoxa3!0.91!10.45!Hoxa3;;chr14:79915521..79915539,+!p5@Elf1!0.91!8.62!Elf1;;chr12:12947406..12947418,-!p5@Mycn!0.91!7.05!Mycn;;chr7:123174606..123174636,-!p5@Sox6!0.90!8.88!Sox6;;chr12:87027598..87027652,+!p1@Batf!0.89!16.19!Batf;;chr1:36364590..36364608,+!p1@Arid5a!0.86!67.65!Arid5a;;chr16:92826249..92826325,-!p1@Runx1!0.86!15.93!Runx1;;chr11:11585678..11585745,+!p5@Ikzf1!0.86!9.40!Ikzf1;;chr9:32348943..32349001,-!p1@Fli1!0.85!52.24!Fli1;;chr19:37509324..37509337,+!p1@Hhex!0.85!45.71!Hhex;;chr8:87225702..87225726,+!p3@Lyl1!0.84!12.54!Lyl1;;chr12:3891810..3891829,+!p2@Dnmt3a!0.84!9.40!Dnmt3a;;chr7:123174485..123174514,-!p6@Sox6!0.80!6.79!Sox6;;chr8:123260252..123260264,+!p1@Irf8!0.79!39.70!Irf8;;chr6:116578973..116579022,-!p1@Zfp422!0.78!94.03!Zfp422;;chr6:29476690..29476724,+!p1@Irf5!0.78!25.34!Irf5;;chr11:11590117..11590138,+!p4@Ikzf1!0.78!4.96!Ikzf1;;chr5:92391466..92391471,+!p2@Thap6!0.77!7.31!Thap6;;chr6:99471223..99471254,-!p7@Foxp1!0.76!7.57!Foxp1;;chr15:103085690..103085710,-!p3@Nfe2!0.76!5.22!Nfe2;;chr14:79915502..79915514,+!p4@Elf1!0.75!7.31!Elf1;;chr8:87225670..87225697,+!p2@Lyl1!0.74!14.37!Lyl1;;chr6:99216375..99216395,-!p5@Foxp1!0.74!4.44!Foxp1;;chr6:29479277..29479296,+!p2@Irf5!0.74!4.44!Irf5;;chr1:38721767..38721778,-!p5@Aff3!0.74!4.44!Aff3;;chr2:90936978..90937023,+!p3@Sfpi1!0.73!8.88!Sfpi1;;chr7:19895354..19895369,-!p1@Fosb!0.73!6.27!Fosb;;chr11:18918434..18918489,-!p3@Meis1!0.72!7.05!Meis1;;chr13:83663868..83663894,+!p2@Mef2c!0.71!67.65!Mef2c;;chr17:44873258..44873281,-!p5@Runx2!0.71!5.75!Runx2;;chr6:29479308..29479325,+!p3@Irf5!0.71!4.18!Irf5;;chr1:38721779..38721790,-!p6@Aff3!0.71!4.18!Aff3;;chr4:6917606..6917681,-!p1@Tox!0.69!18.28!Tox;;chr17:51971991..51972003,-!p4@Satb1!0.69!3.92!Satb1;;chr17:51972603..51972624,-!p9@Satb1!0.69!3.92!Satb1;;chr6:99216360..99216372,-!p8@Foxp1!0.69!3.92!Foxp1;;chr2:153475210..153475252,+!p2@Dnmt3b!0.68!11.49!Dnmt3b;;chr11:60036258..60036276,-!p3@Srebf1!0.68!7.05!Srebf1;;chr1:133904901..133904934,+!p3@Elk4!0.67!12.02!Elk4;;chr11:100683839..100683890,-!p2@Stat5b!0.67!9.40!Stat5b;;chr1:133904862..133904893,+!p6@Elk4!0.67!8.36!Elk4;;chr17:51965903..51965926,-!p5@Satb1!0.67!3.66!Satb1;;chr4:124805061..124805087,-!p1@Zc3h12a!0.64!11.75!Zc3h12a;;chr6:116578939..116578952,-!p2@Zfp422!0.64!8.88!Zfp422;;chr6:99471044..99471066,-!p4@Foxp1!0.64!7.84!Foxp1;;chr13:59923965..59924003,-!p2@Zcchc6!0.64!4.18!Zcchc6;;chr3:135271325..135271343,-!p15@Nfkb1!0.64!3.40!Nfkb1;;chr6:52167434..52167450,-!p3@Hoxa7!0.62!3.13!Hoxa7;;chr10:20881239..20881254,-!p5@Myb!0.62!3.13!Myb;;chr11:95609863..95609870,+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|ffid_belonging_in_development=CL:0000134,CL:0000051
|fonse_cell_line=
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|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 67: Line 41:
|fonse_treatment=EFO:0000369,FF:0000342,FF:0000729,FF:12988-138I9
|fonse_treatment=EFO:0000369,FF:0000342,FF:0000729,FF:12988-138I9
|fonse_treatment_closure=EFO:0000369,FF:0000342,FF:0000729,FF:12988-138I9
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|has_quality=
|id=FF:12988-138I9
|is_a=EFO:0002091;;FF:0000729
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|library_id=CNhs12980
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|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12988
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12988
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/EBF%2520KO%2520HPCs%2520induced%2520to%2520T%2520cell%252c%252000hr00min%252c%2520biol_rep2.CNhs12980.12988-138I9.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/EBF%2520KO%2520HPCs%2520induced%2520to%2520T%2520cell%252c%252000hr00min%252c%2520biol_rep2.CNhs12980.12988-138I9.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/EBF%2520KO%2520HPCs%2520induced%2520to%2520T%2520cell%252c%252000hr00min%252c%2520biol_rep2.CNhs12980.12988-138I9.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/EBF%2520KO%2520HPCs%2520induced%2520to%2520T%2520cell%252c%252000hr00min%252c%2520biol_rep2.CNhs12980.12988-138I9.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/EBF%2520KO%2520HPCs%2520induced%2520to%2520T%2520cell%252c%252000hr00min%252c%2520biol_rep2.CNhs12980.12988-138I9.mm9.nobarcode.rdna.fa.gz
|name=EBF KO HPCs induced to T cell
|namespace=FANTOM5
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12980,LSID993,release014,COMPLETED
|profile_rnaseq=
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|rna_box=138
|rna_catalog_number=
|rna_concentration=0.16
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=1.75
|rna_od260/280=2.07
|rna_position=I9
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|rna_sample_type=
|rna_tube_id=138I9
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|sample_age=
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|sample_cell_type=unclassifiable
|sample_collaboration=Tomokatsu Ikawa (RCAI)
|sample_company=
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|sample_disease=
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|sample_ethnicity=
|sample_experimental_condition=T cell differentiation
|sample_id=12988
|sample_note=
|sample_sex=
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_tissue=
|time= 00hr00min
|timecourse=T-cell_differentiation
|top_motifs=STAT5{A,B}:3.61153905782;YY1:2.94167986965;RUNX1..3:2.66846727237;ELK1,4_GABP{A,B1}:1.77880762612;ELF1,2,4:1.77346060489;DMAP1_NCOR{1,2}_SMARC:1.69442794021;E2F1..5:1.62782763507;SPI1:1.56405394313;SPIB:1.55607798046;PAX8:1.44950552541;AIRE:1.43744406403;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.37917467959;EN1,2:1.26123667971;TLX2:1.25017029196;MYB:1.20981420276;ETS1,2:1.19789869028;ZBTB16:1.14479833155;HES1:1.11552697646;FOXQ1:1.09874735278;IRF1,2:1.04674020612;BPTF:1.03361170815;ALX4:1.02705937197;NFE2L1:0.94188251456;PPARG:0.918246613612;NFY{A,B,C}:0.874736328049;bHLH_family:0.868177833461;STAT2,4,6:0.852658894194;POU1F1:0.852450353121;TP53:0.809702089184;NKX2-2,8:0.74580326335;CEBPA,B_DDIT3:0.744870635491;NRF1:0.674802746408;NFKB1_REL_RELA:0.661374565662;SREBF1,2:0.638328956774;NFIX:0.590749888114;ZNF143:0.454545499961;ATF4:0.451830542396;HOX{A4,D4}:0.438555540906;PITX1..3:0.400811206368;RFX2..5_RFXANK_RFXAP:0.371167185095;POU2F1..3:0.315916773284;NKX3-1:0.268932389392;ATF5_CREB3:0.21014922978;HLF:0.201450253223;TEF:0.19432987332;RXRA_VDR{dimer}:0.150348319363;POU3F1..4:0.101687308923;NFATC1..3:0.0747488215036;NR5A1,2:0.0487446830905;NANOG:0.0398770080736;FOXP3:0.0207963997094;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.00493291891301;SOX17:-0.00260876641841;NANOG{mouse}:-0.0521577471455;VSX1,2:-0.0558469796089;HIF1A:-0.0620821823505;HMX1:-0.0763892330313;ZNF384:-0.108078155555;RXR{A,B,G}:-0.115342588405;FOX{I1,J2}:-0.124644276289;CREB1:-0.12613064379;NR6A1:-0.128430120573;LMO2:-0.174645657012;IRF7:-0.191945522522;RORA:-0.195697204732;HOX{A5,B5}:-0.199747020859;AR:-0.202644377292;ARID5B:-0.222097427999;MEF2{A,B,C,D}:-0.226371888647;HAND1,2:-0.228578337452;HOXA9_MEIS1:-0.238531649438;PDX1:-0.252233138588;FOXM1:-0.257779324889;SOX2:-0.287262891704;FOS_FOS{B,L1}_JUN{B,D}:-0.295840693494;OCT4_SOX2{dimer}:-0.297041319258;AHR_ARNT_ARNT2:-0.299629754021;FOXO1,3,4:-0.317214760779;POU5F1:-0.318154657055;NFE2:-0.322371110345;FOXN1:-0.325888228387;GATA6:-0.332126387699;BREu{core}:-0.338322272991;GFI1:-0.342309362078;SOX{8,9,10}:-0.347789321257;FOXP1:-0.350182031082;RFX1:-0.350185969156;PAX4:-0.362554757663;ALX1:-0.380563875798;PAX6:-0.397997352655;CDX1,2,4:-0.403315719724;CRX:-0.40465578945;BACH2:-0.405485373617;PRRX1,2:-0.418703108383;GATA4:-0.446643381659;NKX6-1,2:-0.448883170525;NR1H4:-0.473939268878;ATF2:-0.50805167352;UFEwm:-0.513262666869;HNF4A_NR2F1,2:-0.528850188954;MTF1:-0.556622532175;TAL1_TCF{3,4,12}:-0.571986145403;PAX2:-0.577427842692;EVI1:-0.588361823287;TFDP1:-0.606716769361;NKX2-3_NKX2-5:-0.61629365542;FOXA2:-0.623713138531;FOXL1:-0.626373693031;ESR1:-0.628640068704;EP300:-0.631256117709;TBX4,5:-0.641185155435;SPZ1:-0.655608278138;TBP:-0.65727722026;POU6F1:-0.660888878866;GZF1:-0.664334157258;NFIL3:-0.672628912786;NR3C1:-0.681418677392;CDC5L:-0.685254284407;MYBL2:-0.69479329338;HNF1A:-0.700936114792;ZNF148:-0.709908180292;FOX{F1,F2,J1}:-0.721927641482;ZBTB6:-0.750715254414;SRF:-0.759288129122;FOSL2:-0.762598594485;LEF1_TCF7_TCF7L1,2:-0.763430953145;LHX3,4:-0.773371448774;ZNF238:-0.797874552916;HSF1,2:-0.807365649805;SNAI1..3:-0.822683308897;ZEB1:-0.82959003046;CUX2:-0.867581062386;TGIF1:-0.889667920421;MYOD1:-0.896614142037;ONECUT1,2:-0.896899999853;JUN:-0.904251838316;ATF6:-0.907836874757;NKX3-2:-0.930100775549;PAX1,9:-0.940183153966;FOX{D1,D2}:-0.94214420196;NFE2L2:-0.999121122797;PBX1:-1.00999220813;REST:-1.01399715192;GLI1..3:-1.02513875241;NHLH1,2:-1.03165828894;DBP:-1.03626427762;STAT1,3:-1.03645274585;HMGA1,2:-1.06169598922;MYFfamily:-1.10605913968;ESRRA:-1.1085744249;FOXD3:-1.11115892656;MZF1:-1.11693229448;ZFP161:-1.18582564162;HBP1_HMGB_SSRP1_UBTF:-1.19088622435;GTF2A1,2:-1.19139609566;IKZF2:-1.1922322491;PRDM1:-1.20429565496;RREB1:-1.22317643222;T:-1.26743747972;SMAD1..7,9:-1.29885474861;GFI1B:-1.34610732877;KLF4:-1.36367066579;MED-1{core}:-1.36623323738;TFAP2{A,C}:-1.41376951608;GCM1,2:-1.42355013755;HIC1:-1.4516772964;TEAD1:-1.46818107473;SOX5:-1.48026933064;EGR1..3:-1.54620008886;ZIC1..3:-1.54714396743;TOPORS:-1.55526188754;MAZ:-1.63426206065;MTE{core}:-1.65707893511;TFAP4:-1.66271911568;TLX1..3_NFIC{dimer}:-1.67308151116;PAX5:-1.71682505549;ADNP_IRX_SIX_ZHX:-1.74960424263;NKX2-1,4:-1.7781599266;EBF1:-1.81818919874;RBPJ:-1.8323503836;GTF2I:-1.92625561613;IKZF1:-1.93030334937;TFAP2B:-1.98466609996;ZNF423:-1.99130416384;MAFB:-2.02786335981;PATZ1:-2.02982979688;XCPE1{core}:-2.05895306435;TFCP2:-2.05987826445;SP1:-2.39268375088
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:12988-138I9;search_select_hide=table117:12988-138I9
}}
}}

Latest revision as of 18:48, 4 June 2020


Name:EBF KO HPCs induced to T cell
Species:Mouse (Mus musculus)
Library ID:CNhs12980
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexNA
ageNA
cell typeunclassifiable
cell lineNA
companyNA
collaborationTomokatsu Ikawa (RCAI)
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  SAMD00005159
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12980 CAGE DRX008900 DRR009772
Accession ID Mm9

Library idBAMCTSS
CNhs12980 DRZ001197 DRZ002582
Accession ID Mm10

Library idBAMCTSS
CNhs12980 DRZ012547 DRZ013932
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

CNhs12980

00
10
100
1000
10000
1001-0.0749
1002-0.116
1003-0.175
10040
10050
1006-0.24
1007-0.15
10080
1009-0.191
1010.207
10100
10110
10120
10130.0596
1014-0.0874
1015-0.0949
1016-0.379
10170
10180
10190
1020
10200
10210.183
1022-0.289
10230.101
10240.112
10250
10260
1027-0.048
10280
1029-0.148
103-0.0887
10300
1031-1.049
1032-0.383
10330.107
10340
10350
10360.375
10370
1038-0.476
1039-0.28
1040
1040-0.264
10410



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: CNhs12980

Jaspar motifP-value
MA0002.23.73789e-8
MA0003.10.479
MA0004.10.0671
MA0006.10.975
MA0007.10.466
MA0009.10.665
MA0014.10.709
MA0017.10.383
MA0018.20.771
MA0019.10.872
MA0024.15.38863e-4
MA0025.10.166
MA0027.10.893
MA0028.14.08035e-7
MA0029.10.195
MA0030.10.0424
MA0031.10.502
MA0035.20.791
MA0038.10.104
MA0039.20.379
MA0040.10.201
MA0041.10.363
MA0042.10.462
MA0043.10.944
MA0046.11.02195e-12
MA0047.20.364
MA0048.10.15
MA0050.16.55323e-6
MA0051.10.00173
MA0052.10.173
MA0055.10.073
MA0057.10.928
MA0058.10.0233
MA0059.14.19146e-4
MA0060.10.726
MA0061.10.0396
MA0062.21.24921e-15
MA0065.20.097
MA0066.10.0986
MA0067.10.74
MA0068.10.704
MA0069.10.628
MA0070.10.765
MA0071.10.26
MA0072.10.862
MA0073.10.812
MA0074.10.213
MA0076.15.16746e-9
MA0077.10.278
MA0078.10.607
MA0079.20.0381
MA0080.29.12579e-12
MA0081.18.98542e-4
MA0083.10.00139
MA0084.10.547
MA0087.10.991
MA0088.10.0602
MA0090.10.0195
MA0091.10.0809
MA0092.10.385
MA0093.10.0593
MA0099.20.638
MA0100.10.00136
MA0101.10.0164
MA0102.20.547
MA0103.10.498
MA0104.20.00743
MA0105.16.40596e-5
MA0106.10.0594
MA0107.10.111
MA0108.21.26844e-4
MA0111.10.459
MA0112.20.00836
MA0113.10.199
MA0114.10.677
MA0115.10.651
MA0116.18.21001e-4
MA0117.10.931
MA0119.10.871
MA0122.10.477
MA0124.10.573
MA0125.10.048
MA0131.10.195
MA0135.10.0895
MA0136.12.3385e-25
MA0137.24.91805e-5
MA0138.20.0119
MA0139.10.195
MA0140.10.396
MA0141.10.198
MA0142.10.562
MA0143.10.299
MA0144.10.0797
MA0145.10.669
MA0146.10.208
MA0147.10.00305
MA0148.10.488
MA0149.10.0842
MA0150.10.368
MA0152.10.949
MA0153.11.00276e-5
MA0154.10.118
MA0155.10.927
MA0156.11.92336e-19
MA0157.10.846
MA0159.10.00958
MA0160.10.305
MA0162.10.202
MA0163.13.87556e-6
MA0164.10.927
MA0258.10.0222
MA0259.10.351



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: CNhs12980

Novel motifP-value
10.275
100.0223
1000.861
1010.971
1020.338
1030.0377
1040.715
1050.749
1060.779
1070.345
1080.397
1090.0843
110.0885
1100.0361
1110.00897
1120.0439
1130.667
1140.888
1150.985
1160.707
1174.06246e-4
1180.145
1190.583
120.491
1200.42
1210.165
1220.885
1230.816
1240.71
1250.344
1260.223
1270.304
1280.386
1290.551
130.016
1300.786
1310.746
1320.506
1330.766
1340.268
1350.638
1360.719
1370.152
1380.372
1390.137
140.621
1400.534
1410.826
1420.862
1430.135
1440.83
1450.0445
1460.736
1470.726
1480.283
1490.447
150.0105
1500.464
1510.387
1520.474
1530.885
1540.686
1550.192
1560.092
1570.855
1580.344
1590.49
1600.953
1610.056
1620.395
1630.23
1640.0171
1650.379
1660.552
1670.274
1680.596
1690.0292
170.827
180.184
190.82
20.118
200.0697
210.182
220.865
230.355
240.0603
250.11
260.0216
270.94
280.653
290.00543
30.0576
300.144
310.895
320.96
330.345
340.718
350.15
360.0234
370.0775
380.437
390.522
40.731
400.18
410.138
420.167
430.455
440.12
450.563
460.175
470.225
480.113
490.203
50.0619
500.59
510.741
520.33
530.511
540.898
550.159
560.717
570.148
580.168
590.718
60.499
600.719
610.113
620.0727
630.688
640.336
650.594
660.619
670.538
680.664
690.787
70.159
700.0178
710.00685
720.294
730.141
740.641
750.0076
760.136
770.423
780.148
790.898
80.0237
800.118
810.799
820.557
830.221
840.64
850.693
860.0778
870.196
880.459
890.358
90.927
900.0178
910.813
920.598
930.41
940.113
950.0841
960.231
970.578
980.627
990.373



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: CNhs12980


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0000084 (T cell)
0000837 (hematopoietic multipotent progenitor cell)

FF: FANTOM5
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000357 (0 hr sample)
0000342 (T-cell induction sample)
0000729 (mouse EBF KO HPCs induced to T cell 0h 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
CL:0000134 (mesenchymal cell)
CL:0000051 (common lymphoid progenitor)

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