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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004847
|DRA_sample_Accession=CAGE@SAMD00004847
|accession_numbers=CAGE;DRX008414;DRR009286;DRZ000711;DRZ002096
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00004847
|accession_numbers=CAGE;DRX008414;DRR009286;DRZ000711;DRZ002096;DRZ012061;DRZ013446
|accession_numbers_RNASeq=sRNA-Seq;DRX037145;DRR041511;DRZ007153
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002199,UBERON:0002384,UBERON:0000479,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003102,UBERON:0010317,UBERON:0002072,UBERON:0002416
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002199,UBERON:0002384,UBERON:0000479,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003102,UBERON:0010317,UBERON:0002072,UBERON:0002416
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0000057,CL:0002334,CL:0002583
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0000057,CL:0002334,CL:0002583
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|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Preadipocyte%2520-%2520subcutaneous%252c%2520donor2.CNhs11981.11356-117H6.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Preadipocyte%2520-%2520subcutaneous%252c%2520donor2.CNhs11981.11356-117H6.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Preadipocyte%2520-%2520subcutaneous%252c%2520donor2.CNhs11981.11356-117H6.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Preadipocyte%2520-%2520subcutaneous%252c%2520donor2.CNhs11981.11356-117H6.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Preadipocyte%2520-%2520subcutaneous%252c%2520donor2.CNhs11981.11356-117H6.hg38.nobarcode.ctss.bed.gz
|id=FF:11356-117H6
|id=FF:11356-117H6
|is_a=EFO:0002091;;FF:0000142
|is_a=EFO:0002091;;FF:0000142
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|library_id=CNhs11981
|library_id=CNhs11981
|library_id_phase_based=2:CNhs11981
|library_id_phase_based=2:CNhs11981
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11356
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10009.CGTACG.11356
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11356
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10009.CGTACG.11356
|name=Preadipocyte - subcutaneous, donor2
|name=Preadipocyte - subcutaneous, donor2
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq=SRhi10009,,,
|profile_srnaseq=SRhi10009,,,
|refex=http://refex.dbcls.jp/genelist.php?lang
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|sample_category=primary cells
Line 91: Line 106:
|top_motifs=UFEwm:1.81529635012;ALX4:1.77921625269;EN1,2:1.69501260246;NKX2-2,8:1.65601877751;KLF4:1.41957534417;HES1:1.32669609952;PAX1,9:1.24219609724;GATA4:1.22579190992;GZF1:1.21037619093;ZNF238:1.20951029739;PAX8:1.15871656151;HOX{A5,B5}:1.09982446122;TAL1_TCF{3,4,12}:1.03884348724;ZNF384:1.02138985132;TFDP1:1.02077369158;HSF1,2:0.99281671246;HOX{A6,A7,B6,B7}:0.96907719945;NR3C1:0.841127177995;CDC5L:0.838720959811;FOXL1:0.798167094326;RXR{A,B,G}:0.780946985585;NANOG{mouse}:0.772350853434;ESR1:0.763303343629;E2F1..5:0.76100457118;HOX{A4,D4}:0.740893822007;TEF:0.732289251306;NFIX:0.714330437215;NKX3-1:0.665527959885;YY1:0.653379427191;TOPORS:0.648384252198;GLI1..3:0.64660541429;PRDM1:0.620849474475;MYB:0.62033888563;GFI1B:0.618736350519;HAND1,2:0.6110727291;MYBL2:0.60096031433;SRF:0.585531397708;ZIC1..3:0.581320726856;IKZF1:0.560473323729;EVI1:0.538506985774;ARID5B:0.508524619385;ATF6:0.498994499644;RXRA_VDR{dimer}:0.495698711061;TLX1..3_NFIC{dimer}:0.494086903317;ZBTB6:0.493249238206;MZF1:0.457665510768;TEAD1:0.454289958143;NFE2L1:0.454175281927;TFCP2:0.441006903459;NKX3-2:0.435807668583;NKX6-1,2:0.431177700111;GFI1:0.428815068936;TP53:0.423668660942;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.420878956562;GCM1,2:0.408718422431;NFATC1..3:0.406039617355;NFE2L2:0.394527963352;SPZ1:0.354588017163;NR1H4:0.315717038633;FOXD3:0.272002326034;EBF1:0.25220566774;SOX17:0.243526430315;BACH2:0.231408421786;FOX{I1,J2}:0.227942668018;GTF2I:0.214606595446;ELK1,4_GABP{A,B1}:0.214155373777;ZNF143:0.213972240957;IRF1,2:0.204800925973;TFAP4:0.172789121632;POU3F1..4:0.170677191138;FOS_FOS{B,L1}_JUN{B,D}:0.154065572416;POU2F1..3:0.14883628714;XBP1:0.128731531194;XCPE1{core}:0.113259747506;TBP:0.0811643628696;FOXQ1:0.0803024411703;GTF2A1,2:0.0569663036219;ZNF423:0.0555692741045;MAFB:0.0347747666151;PAX3,7:0.0152190697441;LHX3,4:0.013214708323;AIRE:-0.000317228314667;TBX4,5:-0.00224980752055;ALX1:-0.0193232777277;PAX4:-0.0304321427708;bHLH_family:-0.0316966741146;NRF1:-0.0439297885371;HNF1A:-0.0439960059622;FOXM1:-0.0457527441305;HLF:-0.0558863987672;ESRRA:-0.0669289200105;TFAP2{A,C}:-0.0716380332562;HBP1_HMGB_SSRP1_UBTF:-0.0757062707286;PPARG:-0.0853032626161;PBX1:-0.101573180382;HIC1:-0.130594317625;AR:-0.136808678385;NR6A1:-0.155087994468;HIF1A:-0.163591326965;HMGA1,2:-0.165164553817;PATZ1:-0.166817392804;TFAP2B:-0.170242901025;RUNX1..3:-0.177134391583;MTE{core}:-0.190462042067;NFKB1_REL_RELA:-0.214663808066;DBP:-0.216946223117;T:-0.218249865395;EGR1..3:-0.230279302252;ONECUT1,2:-0.233447109224;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.234996960178;NR5A1,2:-0.237279305877;NFY{A,B,C}:-0.251734742838;ZNF148:-0.254436597827;POU6F1:-0.254829033938;FOSL2:-0.257755109092;STAT5{A,B}:-0.261162107771;STAT2,4,6:-0.269446223439;DMAP1_NCOR{1,2}_SMARC:-0.273940154029;OCT4_SOX2{dimer}:-0.279987497229;MYFfamily:-0.300807139419;ELF1,2,4:-0.302784808852;CREB1:-0.30708605698;AHR_ARNT_ARNT2:-0.307146671921;MTF1:-0.307774711499;SOX{8,9,10}:-0.30802580079;NFIL3:-0.308985556717;SPI1:-0.315040882577;SMAD1..7,9:-0.316201542729;REST:-0.323811571632;RREB1:-0.327362750347;IRF7:-0.329364526749;HNF4A_NR2F1,2:-0.332719817633;NKX2-1,4:-0.339935937605;HMX1:-0.355687144582;ZBTB16:-0.36735097261;PRRX1,2:-0.370408767952;LEF1_TCF7_TCF7L1,2:-0.378827890533;TLX2:-0.379309296761;STAT1,3:-0.383310835605;CDX1,2,4:-0.415557726618;RFX1:-0.422509648283;NHLH1,2:-0.422798283277;POU5F1:-0.431664436184;ZFP161:-0.451742455595;NFE2:-0.468604156798;CRX:-0.471457630403;SPIB:-0.48543970748;MEF2{A,B,C,D}:-0.487824739214;PITX1..3:-0.489669040142;FOXO1,3,4:-0.49012840296;JUN:-0.49412631074;IKZF2:-0.524146724849;MAZ:-0.534210265393;MED-1{core}:-0.564244454665;FOXP1:-0.565804240952;CUX2:-0.57307301124;NKX2-3_NKX2-5:-0.615772371903;ETS1,2:-0.619499574428;HOXA9_MEIS1:-0.646199152824;BREu{core}:-0.65825546693;SOX5:-0.683065246687;LMO2:-0.686129048513;PAX5:-0.697016749805;PAX2:-0.705658622829;TGIF1:-0.741688945259;SNAI1..3:-0.779468591603;ATF5_CREB3:-0.783279356143;BPTF:-0.785807843443;GATA6:-0.78586406542;VSX1,2:-0.806688673488;EP300:-0.817679760283;RFX2..5_RFXANK_RFXAP:-0.856863241239;CEBPA,B_DDIT3:-0.856918733947;FOXP3:-0.885091404651;ZEB1:-0.899326208058;POU1F1:-0.900423054454;FOXA2:-0.912804744018;SP1:-0.913175287683;SOX2:-1.01016285896;PDX1:-1.03286782238;ATF2:-1.03623699307;FOXN1:-1.07991639193;RBPJ:-1.14746831163;NANOG:-1.22118886245;PAX6:-1.2269587236;ADNP_IRX_SIX_ZHX:-1.23021406629;FOX{D1,D2}:-1.24646754734;MYOD1:-1.24848076274;ATF4:-1.33116511265;SREBF1,2:-1.44470130358;RORA:-1.56889609805;FOX{F1,F2,J1}:-1.85905600875
|top_motifs=UFEwm:1.81529635012;ALX4:1.77921625269;EN1,2:1.69501260246;NKX2-2,8:1.65601877751;KLF4:1.41957534417;HES1:1.32669609952;PAX1,9:1.24219609724;GATA4:1.22579190992;GZF1:1.21037619093;ZNF238:1.20951029739;PAX8:1.15871656151;HOX{A5,B5}:1.09982446122;TAL1_TCF{3,4,12}:1.03884348724;ZNF384:1.02138985132;TFDP1:1.02077369158;HSF1,2:0.99281671246;HOX{A6,A7,B6,B7}:0.96907719945;NR3C1:0.841127177995;CDC5L:0.838720959811;FOXL1:0.798167094326;RXR{A,B,G}:0.780946985585;NANOG{mouse}:0.772350853434;ESR1:0.763303343629;E2F1..5:0.76100457118;HOX{A4,D4}:0.740893822007;TEF:0.732289251306;NFIX:0.714330437215;NKX3-1:0.665527959885;YY1:0.653379427191;TOPORS:0.648384252198;GLI1..3:0.64660541429;PRDM1:0.620849474475;MYB:0.62033888563;GFI1B:0.618736350519;HAND1,2:0.6110727291;MYBL2:0.60096031433;SRF:0.585531397708;ZIC1..3:0.581320726856;IKZF1:0.560473323729;EVI1:0.538506985774;ARID5B:0.508524619385;ATF6:0.498994499644;RXRA_VDR{dimer}:0.495698711061;TLX1..3_NFIC{dimer}:0.494086903317;ZBTB6:0.493249238206;MZF1:0.457665510768;TEAD1:0.454289958143;NFE2L1:0.454175281927;TFCP2:0.441006903459;NKX3-2:0.435807668583;NKX6-1,2:0.431177700111;GFI1:0.428815068936;TP53:0.423668660942;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.420878956562;GCM1,2:0.408718422431;NFATC1..3:0.406039617355;NFE2L2:0.394527963352;SPZ1:0.354588017163;NR1H4:0.315717038633;FOXD3:0.272002326034;EBF1:0.25220566774;SOX17:0.243526430315;BACH2:0.231408421786;FOX{I1,J2}:0.227942668018;GTF2I:0.214606595446;ELK1,4_GABP{A,B1}:0.214155373777;ZNF143:0.213972240957;IRF1,2:0.204800925973;TFAP4:0.172789121632;POU3F1..4:0.170677191138;FOS_FOS{B,L1}_JUN{B,D}:0.154065572416;POU2F1..3:0.14883628714;XBP1:0.128731531194;XCPE1{core}:0.113259747506;TBP:0.0811643628696;FOXQ1:0.0803024411703;GTF2A1,2:0.0569663036219;ZNF423:0.0555692741045;MAFB:0.0347747666151;PAX3,7:0.0152190697441;LHX3,4:0.013214708323;AIRE:-0.000317228314667;TBX4,5:-0.00224980752055;ALX1:-0.0193232777277;PAX4:-0.0304321427708;bHLH_family:-0.0316966741146;NRF1:-0.0439297885371;HNF1A:-0.0439960059622;FOXM1:-0.0457527441305;HLF:-0.0558863987672;ESRRA:-0.0669289200105;TFAP2{A,C}:-0.0716380332562;HBP1_HMGB_SSRP1_UBTF:-0.0757062707286;PPARG:-0.0853032626161;PBX1:-0.101573180382;HIC1:-0.130594317625;AR:-0.136808678385;NR6A1:-0.155087994468;HIF1A:-0.163591326965;HMGA1,2:-0.165164553817;PATZ1:-0.166817392804;TFAP2B:-0.170242901025;RUNX1..3:-0.177134391583;MTE{core}:-0.190462042067;NFKB1_REL_RELA:-0.214663808066;DBP:-0.216946223117;T:-0.218249865395;EGR1..3:-0.230279302252;ONECUT1,2:-0.233447109224;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.234996960178;NR5A1,2:-0.237279305877;NFY{A,B,C}:-0.251734742838;ZNF148:-0.254436597827;POU6F1:-0.254829033938;FOSL2:-0.257755109092;STAT5{A,B}:-0.261162107771;STAT2,4,6:-0.269446223439;DMAP1_NCOR{1,2}_SMARC:-0.273940154029;OCT4_SOX2{dimer}:-0.279987497229;MYFfamily:-0.300807139419;ELF1,2,4:-0.302784808852;CREB1:-0.30708605698;AHR_ARNT_ARNT2:-0.307146671921;MTF1:-0.307774711499;SOX{8,9,10}:-0.30802580079;NFIL3:-0.308985556717;SPI1:-0.315040882577;SMAD1..7,9:-0.316201542729;REST:-0.323811571632;RREB1:-0.327362750347;IRF7:-0.329364526749;HNF4A_NR2F1,2:-0.332719817633;NKX2-1,4:-0.339935937605;HMX1:-0.355687144582;ZBTB16:-0.36735097261;PRRX1,2:-0.370408767952;LEF1_TCF7_TCF7L1,2:-0.378827890533;TLX2:-0.379309296761;STAT1,3:-0.383310835605;CDX1,2,4:-0.415557726618;RFX1:-0.422509648283;NHLH1,2:-0.422798283277;POU5F1:-0.431664436184;ZFP161:-0.451742455595;NFE2:-0.468604156798;CRX:-0.471457630403;SPIB:-0.48543970748;MEF2{A,B,C,D}:-0.487824739214;PITX1..3:-0.489669040142;FOXO1,3,4:-0.49012840296;JUN:-0.49412631074;IKZF2:-0.524146724849;MAZ:-0.534210265393;MED-1{core}:-0.564244454665;FOXP1:-0.565804240952;CUX2:-0.57307301124;NKX2-3_NKX2-5:-0.615772371903;ETS1,2:-0.619499574428;HOXA9_MEIS1:-0.646199152824;BREu{core}:-0.65825546693;SOX5:-0.683065246687;LMO2:-0.686129048513;PAX5:-0.697016749805;PAX2:-0.705658622829;TGIF1:-0.741688945259;SNAI1..3:-0.779468591603;ATF5_CREB3:-0.783279356143;BPTF:-0.785807843443;GATA6:-0.78586406542;VSX1,2:-0.806688673488;EP300:-0.817679760283;RFX2..5_RFXANK_RFXAP:-0.856863241239;CEBPA,B_DDIT3:-0.856918733947;FOXP3:-0.885091404651;ZEB1:-0.899326208058;POU1F1:-0.900423054454;FOXA2:-0.912804744018;SP1:-0.913175287683;SOX2:-1.01016285896;PDX1:-1.03286782238;ATF2:-1.03623699307;FOXN1:-1.07991639193;RBPJ:-1.14746831163;NANOG:-1.22118886245;PAX6:-1.2269587236;ADNP_IRX_SIX_ZHX:-1.23021406629;FOX{D1,D2}:-1.24646754734;MYOD1:-1.24848076274;ATF4:-1.33116511265;SREBF1,2:-1.44470130358;RORA:-1.56889609805;FOX{F1,F2,J1}:-1.85905600875
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11356-117H6;search_select_hide=table117:FF:11356-117H6
}}
}}

Latest revision as of 17:54, 4 June 2020

Name:Preadipocyte - subcutaneous, donor2
Species:Human (Homo sapiens)
Library ID:CNhs11981
Sample type:primary cells
Genomic View: UCSC
RefEX:Specific genes
FANTOM CAT:1, 2, 3, 4, 5
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueadipose tissue
dev stage53 years old adult
sexfemale
age53
cell typepreadipocyte
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1377
catalog numberCA802s-R10a
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004847
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11981 CAGE DRX008414 DRR009286
Accession ID Hg19

Library idBAMCTSS
CNhs11981 DRZ000711 DRZ002096
Accession ID Hg38

Library idBAMCTSS
CNhs11981 DRZ012061 DRZ013446
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00004847
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10009.CGTACG sRNA-Seq DRX037145 DRR041511
Accession ID Hg19

Library idBAMCTSS
SRhi10009.CGTACG DRZ007153


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: CNhs11981



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: CNhs11981



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: CNhs11981


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)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000057 (fibroblast)
0002334 (preadipocyte)
0002583 (subcutaneous preadipocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002199 (integument)
0002384 (connective tissue)
0000479 (tissue)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003102 (surface structure)
0010317 (germ layer / neural crest derived structure)
0002072 (hypodermis)
0002416 (integumental system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000137 (human preadipocyte sample)
0000142 (human subcutaneous preadipocyte 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)