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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008116
|DRA_sample_Accession=CAGE@SAMD00005386
|accession_numbers=CAGE;DRX008224;DRR009096;DRZ000521;DRZ001906
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00005386
|accession_numbers=CAGE;DRX008224;DRR009096;DRZ000521;DRZ001906;DRZ011871;DRZ013256
|accession_numbers_RNASeq=sRNA-Seq;DRX037043;DRR041409;DRZ007051
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000055,UBERON:0004111,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002049,UBERON:0007798,UBERON:0001473,UBERON:0002465,UBERON:0004535,UBERON:0004536,UBERON:0006558,UBERON:0002193,UBERON:0002405,UBERON:0001009
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000055,UBERON:0004111,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002049,UBERON:0007798,UBERON:0001473,UBERON:0002465,UBERON:0004535,UBERON:0004536,UBERON:0006558,UBERON:0002193,UBERON:0002405,UBERON:0001009
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002139,CL:0000213,CL:0002078,CL:0000215,CL:0000255,CL:0000115,CL:0002138
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002139,CL:0000213,CL:0002078,CL:0000215,CL:0000255,CL:0000115,CL:0002138
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|created_by=
|created_by=
|creation_date=
|creation_date=
|datafreeze_phase=1
|data_phase=2
|datafreeze_phase=2
|def=
|def=
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Line 40: Line 44:
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|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Endothelial%2520Cells%2520-%2520Lymphatic%252c%2520donor2.CNhs11901.11317-117D3.hg38.nobarcode.bam
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|id=FF:11317-117D3
|id=FF:11317-117D3
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|is_obsolete=
|is_obsolete=
|library_id=CNhs11901
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|library_ids=CNhs11901
|library_id_phase_based=2:CNhs11901
|microRNAs=
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|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11317
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10004.AGTCAA.11317
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11317
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10004.AGTCAA.11317
|name=Endothelial Cells - Lymphatic, donor2
|name=Endothelial Cells - Lymphatic, donor2
|namespace=FANTOM5
|namespace=FANTOM5
Line 50: Line 65:
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|sample_category=primary cells
Line 89: Line 106:
|top_motifs=FOX{I1,J2}:1.93744873705;PAX6:1.66442804053;SREBF1,2:1.57459360664;NFATC1..3:1.54313411048;SOX5:1.43174097548;SOX{8,9,10}:1.41230232396;RXR{A,B,G}:1.38946555438;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.34184006581;TEF:1.25379597279;SOX2:1.24828556886;IKZF2:1.19195023897;PAX1,9:1.08405217384;SPZ1:1.06750160641;TLX1..3_NFIC{dimer}:1.06664180906;HBP1_HMGB_SSRP1_UBTF:1.00814118395;POU3F1..4:0.991538347194;ARID5B:0.956571114249;bHLH_family:0.909329225415;ADNP_IRX_SIX_ZHX:0.872897511774;ZFP161:0.822762687176;FOXQ1:0.800504763483;ELF1,2,4:0.798280895116;STAT1,3:0.787763597281;LEF1_TCF7_TCF7L1,2:0.714811397888;ETS1,2:0.696055363655;AR:0.649366678018;TFAP4:0.636718621275;NR3C1:0.619331855853;STAT2,4,6:0.602025277537;HOXA9_MEIS1:0.601674445755;LHX3,4:0.562989191997;TFAP2{A,C}:0.551315988615;TEAD1:0.540365659452;GATA6:0.528109398241;SPIB:0.523075804857;XCPE1{core}:0.522081315234;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.522018104446;RBPJ:0.520429602596;ALX1:0.520407661679;FOX{D1,D2}:0.506976081673;SOX17:0.505340519934;TAL1_TCF{3,4,12}:0.494842012876;FOXD3:0.491150281024;NRF1:0.491081294285;PAX5:0.460346506516;TP53:0.454735228677;EVI1:0.453435301591;GZF1:0.442172894143;SP1:0.432752267388;PDX1:0.414703991348;EN1,2:0.363012579678;EGR1..3:0.334262835468;GFI1B:0.323601283115;TGIF1:0.301314750964;PRDM1:0.30077437801;FOX{F1,F2,J1}:0.296111893259;IKZF1:0.291905625449;TFDP1:0.287896238435;IRF1,2:0.285647999534;FOXN1:0.282070647324;NKX2-3_NKX2-5:0.279890097858;HAND1,2:0.27706262874;HMGA1,2:0.240537411042;GCM1,2:0.233595288768;PAX2:0.216206747211;CDC5L:0.215879849261;ZBTB16:0.215242421539;MED-1{core}:0.185485430175;NANOG:0.165905588841;NFE2:0.151736111945;ZNF143:0.131339575716;SPI1:0.11457475117;DMAP1_NCOR{1,2}_SMARC:0.107973039148;CRX:0.106471200915;HIC1:0.103599931761;FOXP1:0.0910975840871;ZBTB6:0.0768704000109;MAZ:0.0728173282116;MYOD1:0.0717624973138;MTE{core}:0.0637298363842;YY1:0.0595484149187;ONECUT1,2:0.0588687907268;TFAP2B:0.0500677696759;BPTF:0.0498531360962;BACH2:0.0370155061906;ATF2:0.0357394946626;NANOG{mouse}:0.0348978739488;PITX1..3:0.0331975376275;FOSL2:0.0307922306315;HNF4A_NR2F1,2:0.0161043239077;POU1F1:-0.0142560325969;NFIX:-0.0191974665413;NFY{A,B,C}:-0.0230438376767;NR5A1,2:-0.0260277795136;FOXA2:-0.0599544552969;CREB1:-0.0623061903468;SMAD1..7,9:-0.0688297403686;EP300:-0.0751581671031;AIRE:-0.0805890407964;NHLH1,2:-0.0831044718533;FOS_FOS{B,L1}_JUN{B,D}:-0.0837881315877;NFKB1_REL_RELA:-0.0941154706385;TLX2:-0.113405775251;GFI1:-0.123707044474;GTF2I:-0.133234037995;SRF:-0.137528489342;LMO2:-0.138685561187;POU6F1:-0.139085142183;REST:-0.142353486102;CUX2:-0.14483027097;NFE2L2:-0.148940117125;NKX2-2,8:-0.160520594491;HNF1A:-0.160906589075;MEF2{A,B,C,D}:-0.162439121166;PAX3,7:-0.16319269344;MZF1:-0.165711011045;FOXL1:-0.186970719276;IRF7:-0.204053065578;PBX1:-0.20596383934;GATA4:-0.226102862209;MYB:-0.227088311576;UFEwm:-0.230656731766;PATZ1:-0.242495961768;HSF1,2:-0.247168703429;ZIC1..3:-0.261938876275;PRRX1,2:-0.263772998726;FOXO1,3,4:-0.264519723203;GTF2A1,2:-0.27046623034;CDX1,2,4:-0.279944721894;MYFfamily:-0.293096870878;PAX8:-0.295659988457;RFX1:-0.307027416763;HIF1A:-0.309253702522;AHR_ARNT_ARNT2:-0.338826094409;NR1H4:-0.340481477707;NKX6-1,2:-0.36655697235;STAT5{A,B}:-0.399031075887;E2F1..5:-0.404412910854;ATF6:-0.426146832351;HLF:-0.426551763295;ELK1,4_GABP{A,B1}:-0.427499323902;RORA:-0.444079779814;PPARG:-0.467025465459;NFE2L1:-0.471997825618;ZNF238:-0.475493973801;ZNF148:-0.515689044768;MTF1:-0.539348532403;ESRRA:-0.547175026887;OCT4_SOX2{dimer}:-0.565536910191;XBP1:-0.579104370626;CEBPA,B_DDIT3:-0.580716065423;HMX1:-0.582532213774;ATF4:-0.591051575591;MYBL2:-0.592586548021;RREB1:-0.597207769397;JUN:-0.600090183009;TOPORS:-0.601941183499;HOX{A5,B5}:-0.614971419112;NKX2-1,4:-0.618636289804;HES1:-0.621540339953;TBP:-0.631403502823;GLI1..3:-0.643247025878;RUNX1..3:-0.64698808969;TFCP2:-0.654262127332;SNAI1..3:-0.67419792344;ALX4:-0.69599452105;EBF1:-0.720804723022;PAX4:-0.729343108071;FOXP3:-0.72981091294;ATF5_CREB3:-0.739288011905;NKX3-2:-0.793040307533;ZNF423:-0.804213337931;VSX1,2:-0.807277835438;ESR1:-0.81414705334;NKX3-1:-0.824071276708;POU5F1:-0.833528366695;MAFB:-0.836362170084;BREu{core}:-0.852302682113;T:-0.85376832776;HOX{A4,D4}:-0.865965621893;KLF4:-0.888845697393;ZEB1:-0.889280198739;FOXM1:-0.9259636315;ZNF384:-0.931418863196;TBX4,5:-0.937105537063;NR6A1:-0.954052551081;NFIL3:-1.00306747642;RFX2..5_RFXANK_RFXAP:-1.05999752659;DBP:-1.12183365326;HOX{A6,A7,B6,B7}:-1.17732599926;RXRA_VDR{dimer}:-1.18226987381;POU2F1..3:-1.46704328031
|top_motifs=FOX{I1,J2}:1.93744873705;PAX6:1.66442804053;SREBF1,2:1.57459360664;NFATC1..3:1.54313411048;SOX5:1.43174097548;SOX{8,9,10}:1.41230232396;RXR{A,B,G}:1.38946555438;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.34184006581;TEF:1.25379597279;SOX2:1.24828556886;IKZF2:1.19195023897;PAX1,9:1.08405217384;SPZ1:1.06750160641;TLX1..3_NFIC{dimer}:1.06664180906;HBP1_HMGB_SSRP1_UBTF:1.00814118395;POU3F1..4:0.991538347194;ARID5B:0.956571114249;bHLH_family:0.909329225415;ADNP_IRX_SIX_ZHX:0.872897511774;ZFP161:0.822762687176;FOXQ1:0.800504763483;ELF1,2,4:0.798280895116;STAT1,3:0.787763597281;LEF1_TCF7_TCF7L1,2:0.714811397888;ETS1,2:0.696055363655;AR:0.649366678018;TFAP4:0.636718621275;NR3C1:0.619331855853;STAT2,4,6:0.602025277537;HOXA9_MEIS1:0.601674445755;LHX3,4:0.562989191997;TFAP2{A,C}:0.551315988615;TEAD1:0.540365659452;GATA6:0.528109398241;SPIB:0.523075804857;XCPE1{core}:0.522081315234;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.522018104446;RBPJ:0.520429602596;ALX1:0.520407661679;FOX{D1,D2}:0.506976081673;SOX17:0.505340519934;TAL1_TCF{3,4,12}:0.494842012876;FOXD3:0.491150281024;NRF1:0.491081294285;PAX5:0.460346506516;TP53:0.454735228677;EVI1:0.453435301591;GZF1:0.442172894143;SP1:0.432752267388;PDX1:0.414703991348;EN1,2:0.363012579678;EGR1..3:0.334262835468;GFI1B:0.323601283115;TGIF1:0.301314750964;PRDM1:0.30077437801;FOX{F1,F2,J1}:0.296111893259;IKZF1:0.291905625449;TFDP1:0.287896238435;IRF1,2:0.285647999534;FOXN1:0.282070647324;NKX2-3_NKX2-5:0.279890097858;HAND1,2:0.27706262874;HMGA1,2:0.240537411042;GCM1,2:0.233595288768;PAX2:0.216206747211;CDC5L:0.215879849261;ZBTB16:0.215242421539;MED-1{core}:0.185485430175;NANOG:0.165905588841;NFE2:0.151736111945;ZNF143:0.131339575716;SPI1:0.11457475117;DMAP1_NCOR{1,2}_SMARC:0.107973039148;CRX:0.106471200915;HIC1:0.103599931761;FOXP1:0.0910975840871;ZBTB6:0.0768704000109;MAZ:0.0728173282116;MYOD1:0.0717624973138;MTE{core}:0.0637298363842;YY1:0.0595484149187;ONECUT1,2:0.0588687907268;TFAP2B:0.0500677696759;BPTF:0.0498531360962;BACH2:0.0370155061906;ATF2:0.0357394946626;NANOG{mouse}:0.0348978739488;PITX1..3:0.0331975376275;FOSL2:0.0307922306315;HNF4A_NR2F1,2:0.0161043239077;POU1F1:-0.0142560325969;NFIX:-0.0191974665413;NFY{A,B,C}:-0.0230438376767;NR5A1,2:-0.0260277795136;FOXA2:-0.0599544552969;CREB1:-0.0623061903468;SMAD1..7,9:-0.0688297403686;EP300:-0.0751581671031;AIRE:-0.0805890407964;NHLH1,2:-0.0831044718533;FOS_FOS{B,L1}_JUN{B,D}:-0.0837881315877;NFKB1_REL_RELA:-0.0941154706385;TLX2:-0.113405775251;GFI1:-0.123707044474;GTF2I:-0.133234037995;SRF:-0.137528489342;LMO2:-0.138685561187;POU6F1:-0.139085142183;REST:-0.142353486102;CUX2:-0.14483027097;NFE2L2:-0.148940117125;NKX2-2,8:-0.160520594491;HNF1A:-0.160906589075;MEF2{A,B,C,D}:-0.162439121166;PAX3,7:-0.16319269344;MZF1:-0.165711011045;FOXL1:-0.186970719276;IRF7:-0.204053065578;PBX1:-0.20596383934;GATA4:-0.226102862209;MYB:-0.227088311576;UFEwm:-0.230656731766;PATZ1:-0.242495961768;HSF1,2:-0.247168703429;ZIC1..3:-0.261938876275;PRRX1,2:-0.263772998726;FOXO1,3,4:-0.264519723203;GTF2A1,2:-0.27046623034;CDX1,2,4:-0.279944721894;MYFfamily:-0.293096870878;PAX8:-0.295659988457;RFX1:-0.307027416763;HIF1A:-0.309253702522;AHR_ARNT_ARNT2:-0.338826094409;NR1H4:-0.340481477707;NKX6-1,2:-0.36655697235;STAT5{A,B}:-0.399031075887;E2F1..5:-0.404412910854;ATF6:-0.426146832351;HLF:-0.426551763295;ELK1,4_GABP{A,B1}:-0.427499323902;RORA:-0.444079779814;PPARG:-0.467025465459;NFE2L1:-0.471997825618;ZNF238:-0.475493973801;ZNF148:-0.515689044768;MTF1:-0.539348532403;ESRRA:-0.547175026887;OCT4_SOX2{dimer}:-0.565536910191;XBP1:-0.579104370626;CEBPA,B_DDIT3:-0.580716065423;HMX1:-0.582532213774;ATF4:-0.591051575591;MYBL2:-0.592586548021;RREB1:-0.597207769397;JUN:-0.600090183009;TOPORS:-0.601941183499;HOX{A5,B5}:-0.614971419112;NKX2-1,4:-0.618636289804;HES1:-0.621540339953;TBP:-0.631403502823;GLI1..3:-0.643247025878;RUNX1..3:-0.64698808969;TFCP2:-0.654262127332;SNAI1..3:-0.67419792344;ALX4:-0.69599452105;EBF1:-0.720804723022;PAX4:-0.729343108071;FOXP3:-0.72981091294;ATF5_CREB3:-0.739288011905;NKX3-2:-0.793040307533;ZNF423:-0.804213337931;VSX1,2:-0.807277835438;ESR1:-0.81414705334;NKX3-1:-0.824071276708;POU5F1:-0.833528366695;MAFB:-0.836362170084;BREu{core}:-0.852302682113;T:-0.85376832776;HOX{A4,D4}:-0.865965621893;KLF4:-0.888845697393;ZEB1:-0.889280198739;FOXM1:-0.9259636315;ZNF384:-0.931418863196;TBX4,5:-0.937105537063;NR6A1:-0.954052551081;NFIL3:-1.00306747642;RFX2..5_RFXANK_RFXAP:-1.05999752659;DBP:-1.12183365326;HOX{A6,A7,B6,B7}:-1.17732599926;RXRA_VDR{dimer}:-1.18226987381;POU2F1..3:-1.46704328031
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11317-117D3;search_select_hide=table117:FF:11317-117D3
}}
}}

Latest revision as of 16:33, 3 June 2020

Name:Endothelial Cells - Lymphatic, donor2
Species:Human (Homo sapiens)
Library ID:CNhs11901
Sample type:primary cells
Genomic View: UCSC
RefEX:Specific genes
FANTOM CAT:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuelymph node
dev stagefetus
sexunknown
agefetal
cell typeendothelial cell, lymphatic
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number2714
catalog numberSC2015
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005386
CollapseLibrary accession numbers

Library idMethodExp. accession idRun accession id
CNhs11901 CAGE DRX008224 DRR009096
CollapseAccession ID Hg19

Library idBAMCTSS
CNhs11901 DRZ000521 DRZ001906
CollapseAccession ID Hg38

Library idBAMCTSS
CNhs11901 DRZ011871 DRZ013256
Download raw sequence, BAM & CTSS
CollapseHg19
FastaBAMCTSS
downloaddownloaddonwload
CollapseHg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00005386
CollapseLibrary accession numbers

Library idMethodExp. accession idRun accession id
SRhi10004.AGTCAA sRNA-Seq DRX037043 DRR041409
CollapseAccession ID Hg19

Library idBAMCTSS
SRhi10004.AGTCAA DRZ007051


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



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: CNhs11901



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: CNhs11901



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: CNhs11901


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)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002139 (endothelial cell of vascular tree)
0000213 (lining cell)
0002078 (meso-epithelial cell)
0000215 (barrier cell)
0000255 (eukaryotic cell)
0000115 (endothelial cell)
0002138 (endothelial cell of lymphatic vessel)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000055 (vessel)
0004111 (anatomical conduit)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002049 (vasculature)
0007798 (vascular system)
0001473 (lymphatic vessel)
0002465 (lymphoid system)
0004535 (cardiovascular system)
0004536 (lymph vasculature)
0006558 (lymphatic part of lymphoid system)
0002193 (hemolymphoid system)
0002405 (immune system)
0001009 (circulatory system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000046 (human endothelial cell sample)
0000001 (sample)
0000049 (human lymphatic endothelial cell 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:0000222 (mesodermal cell)
CL:0005022 (vascular lymphangioblast)