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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005598
|DRA_sample_Accession=CAGE@SAMD00005598
|accession_numbers=CAGE;DRX007828;DRR008700;DRZ000125;DRZ001510
|DRA_sample_Accession_RNASeq=RNA-Seq@SAMD00005598
|accession_numbers=CAGE;DRX007828;DRR008700;DRZ000125;DRZ001510;DRZ011475;DRZ012860
|accession_numbers_RNASeq=RNA-Seq;DRX057143;DRR062902;DRZ007978
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000076,CL:0000255
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000076,CL:0000255
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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.cell_line.hCAGE/anaplastic%2520squamous%2520cell%2520carcinoma%2520cell%2520line%253aRPMI%25202650.CNhs11889.10805-111A4.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/anaplastic%2520squamous%2520cell%2520carcinoma%2520cell%2520line%253aRPMI%25202650.CNhs11889.10805-111A4.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/anaplastic%2520squamous%2520cell%2520carcinoma%2520cell%2520line%253aRPMI%25202650.CNhs11889.10805-111A4.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/anaplastic%2520squamous%2520cell%2520carcinoma%2520cell%2520line%253aRPMI%25202650.CNhs11889.10805-111A4.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/anaplastic%2520squamous%2520cell%2520carcinoma%2520cell%2520line%253aRPMI%25202650.CNhs11889.10805-111A4.hg38.nobarcode.ctss.bed.gz
|id=FF:10805-111A4
|id=FF:10805-111A4
|is_a=EFO:0002091;;FF:0000210;;FF:0104205
|is_a=EFO:0002091;;FF:0000210;;FF:0104205
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|library_id=CNhs11889
|library_id=CNhs11889
|library_id_phase_based=2:CNhs11889
|library_id_phase_based=2:CNhs11889
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10805
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10805
|name=anaplastic squamous cell carcinoma cell line:RPMI 2650
|name=anaplastic squamous cell carcinoma cell line:RPMI 2650
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_rnaseq=
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|refex=http://refex.dbcls.jp/genelist.php?lang
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Line 66: Line 78:
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|sample_category=cell lines
Line 89: Line 102:
|top_motifs=FOXP1:4.11842010193;TOPORS:3.40375240093;PITX1..3:3.25800569276;TEF:2.8818015384;LHX3,4:2.87309973186;ALX1:2.634358848;VSX1,2:2.58407779138;FOXD3:2.40548637408;RBPJ:2.31761564175;PAX4:2.30697073792;NANOG:2.25646352597;POU1F1:2.05184804805;ZBTB16:2.03243559428;PAX8:1.99972673991;HOX{A4,D4}:1.79451458658;CRX:1.73350365241;AIRE:1.7281959369;CDC5L:1.6471261871;T:1.64254143166;TFDP1:1.54301254132;NRF1:1.53669443744;POU6F1:1.52553442166;NKX2-3_NKX2-5:1.50175530244;NFY{A,B,C}:1.48675232484;ZNF143:1.48329182483;E2F1..5:1.47586456232;RFX1:1.4680803843;CDX1,2,4:1.44659212366;HOX{A6,A7,B6,B7}:1.44095516048;NKX6-1,2:1.41216472374;LEF1_TCF7_TCF7L1,2:1.38249551507;YY1:1.29987527358;ADNP_IRX_SIX_ZHX:1.21905968944;SOX5:1.20816327034;HMGA1,2:1.18102489076;GFI1:1.16250655399;SOX17:1.11707997202;ONECUT1,2:1.10805403653;FOXL1:1.09568435767;BREu{core}:1.01490739487;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.963263097663;ATF4:0.956459752781;SP1:0.907704830184;IKZF2:0.846773059041;POU2F1..3:0.843430503408;RXR{A,B,G}:0.813699236197;PDX1:0.804282601041;FOXQ1:0.799229911909;ZNF384:0.773012967668;RFX2..5_RFXANK_RFXAP:0.769289825757;CREB1:0.767343545278;EVI1:0.719941355963;STAT5{A,B}:0.69935102256;SOX{8,9,10}:0.677144620853;PATZ1:0.662410924725;RORA:0.644667179178;FOXA2:0.637883419917;BPTF:0.62353717341;NKX3-1:0.598549869703;RREB1:0.598068927426;PRRX1,2:0.591093989782;PBX1:0.585736717927;HOX{A5,B5}:0.568452385151;SOX2:0.565872397434;MED-1{core}:0.541307670544;FOXM1:0.519277729699;CUX2:0.514361263311;SNAI1..3:0.511672835303;ZFP161:0.504854640027;ZIC1..3:0.487488979912;ELK1,4_GABP{A,B1}:0.467047884652;FOX{I1,J2}:0.401947404702;MTE{core}:0.354057051861;ZEB1:0.337632014318;OCT4_SOX2{dimer}:0.296687818016;FOX{F1,F2,J1}:0.277366077433;STAT1,3:0.260655240115;NKX2-2,8:0.244244578389;TFAP2B:0.237505388912;FOXN1:0.231754029764;ARID5B:0.22343503755;HBP1_HMGB_SSRP1_UBTF:0.215692492816;POU3F1..4:0.200331194545;TP53:0.193178116232;GZF1:0.189355617167;NR5A1,2:0.170683996675;MYB:0.151246896974;FOX{D1,D2}:0.114871981227;XCPE1{core}:0.111742246791;PAX3,7:0.110002877583;MEF2{A,B,C,D}:0.102037111057;HIC1:0.0954917778822;HIF1A:0.0446179514399;NKX2-1,4:0.0348263596563;POU5F1:0.0200717792611;PAX5:0.00212449018296;GATA6:0.00133844488732;HNF1A:-0.0203098910053;HOXA9_MEIS1:-0.03585076549;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.06758325868;ZBTB6:-0.105836198915;KLF4:-0.113241077996;MYBL2:-0.119953380849;bHLH_family:-0.153927205951;FOXO1,3,4:-0.159736094587;PRDM1:-0.184498344431;REST:-0.21690515052;ATF2:-0.218833430877;NFIL3:-0.22904512232;AHR_ARNT_ARNT2:-0.230675413624;TEAD1:-0.239095376064;FOXP3:-0.246250091972;ATF5_CREB3:-0.257367311116;ESR1:-0.285453223468;GTF2A1,2:-0.333464485527;EN1,2:-0.372785306103;GTF2I:-0.378323078457;MZF1:-0.405291070899;DBP:-0.427843313539;EGR1..3:-0.434204191658;HNF4A_NR2F1,2:-0.434610388012;LMO2:-0.435014049392;NR3C1:-0.450351731149;MAZ:-0.467328610742;MTF1:-0.4794014387;AR:-0.500738057543;TFAP2{A,C}:-0.522626216133;TAL1_TCF{3,4,12}:-0.5976349174;MYFfamily:-0.642594156656;NKX3-2:-0.65317343944;PAX6:-0.65532919323;TLX2:-0.660515224305;DMAP1_NCOR{1,2}_SMARC:-0.662816284834;SPIB:-0.665324801838;IRF7:-0.667070165763;NR1H4:-0.678525898011;BACH2:-0.697731673771;FOS_FOS{B,L1}_JUN{B,D}:-0.698468676298;TBP:-0.702943935786;RUNX1..3:-0.708265447347;RXRA_VDR{dimer}:-0.731727578445;TLX1..3_NFIC{dimer}:-0.76457355985;ESRRA:-0.805020906702;UFEwm:-0.815980888595;GATA4:-0.819003633549;NFKB1_REL_RELA:-0.824099995369;CEBPA,B_DDIT3:-0.871059463656;SREBF1,2:-0.87371979939;NFE2:-0.875869958492;MYOD1:-0.888081359638;FOSL2:-0.944333870443;TGIF1:-0.981787009252;GFI1B:-0.983321516734;NANOG{mouse}:-1.01075796841;PAX1,9:-1.01098848222;HLF:-1.0124159014;HAND1,2:-1.02289704931;ALX4:-1.03960948923;JUN:-1.07787735339;ETS1,2:-1.09628732038;SPI1:-1.1193917635;ELF1,2,4:-1.12575238241;IRF1,2:-1.1538009889;NHLH1,2:-1.19247593782;IKZF1:-1.22335337818;PPARG:-1.23050827597;STAT2,4,6:-1.24477357736;SRF:-1.26354565983;GCM1,2:-1.26869065958;ZNF148:-1.30116944144;TBX4,5:-1.31959467837;EBF1:-1.32916001726;PAX2:-1.39119514008;ZNF238:-1.39386407284;XBP1:-1.41727849119;ZNF423:-1.43252165189;TFAP4:-1.5541636813;TFCP2:-1.67248968081;NFE2L2:-1.6751707128;GLI1..3:-1.68912047709;HSF1,2:-1.7388100045;NFIX:-1.98002982368;NR6A1:-1.98738183396;HES1:-1.99653453537;ATF6:-2.02324130864;NFATC1..3:-2.12163030436;SMAD1..7,9:-2.25465394368;SPZ1:-2.30214121573;MAFB:-2.32330023077;HMX1:-2.37097379298;EP300:-2.43021600498;NFE2L1:-2.71913215955
|top_motifs=FOXP1:4.11842010193;TOPORS:3.40375240093;PITX1..3:3.25800569276;TEF:2.8818015384;LHX3,4:2.87309973186;ALX1:2.634358848;VSX1,2:2.58407779138;FOXD3:2.40548637408;RBPJ:2.31761564175;PAX4:2.30697073792;NANOG:2.25646352597;POU1F1:2.05184804805;ZBTB16:2.03243559428;PAX8:1.99972673991;HOX{A4,D4}:1.79451458658;CRX:1.73350365241;AIRE:1.7281959369;CDC5L:1.6471261871;T:1.64254143166;TFDP1:1.54301254132;NRF1:1.53669443744;POU6F1:1.52553442166;NKX2-3_NKX2-5:1.50175530244;NFY{A,B,C}:1.48675232484;ZNF143:1.48329182483;E2F1..5:1.47586456232;RFX1:1.4680803843;CDX1,2,4:1.44659212366;HOX{A6,A7,B6,B7}:1.44095516048;NKX6-1,2:1.41216472374;LEF1_TCF7_TCF7L1,2:1.38249551507;YY1:1.29987527358;ADNP_IRX_SIX_ZHX:1.21905968944;SOX5:1.20816327034;HMGA1,2:1.18102489076;GFI1:1.16250655399;SOX17:1.11707997202;ONECUT1,2:1.10805403653;FOXL1:1.09568435767;BREu{core}:1.01490739487;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.963263097663;ATF4:0.956459752781;SP1:0.907704830184;IKZF2:0.846773059041;POU2F1..3:0.843430503408;RXR{A,B,G}:0.813699236197;PDX1:0.804282601041;FOXQ1:0.799229911909;ZNF384:0.773012967668;RFX2..5_RFXANK_RFXAP:0.769289825757;CREB1:0.767343545278;EVI1:0.719941355963;STAT5{A,B}:0.69935102256;SOX{8,9,10}:0.677144620853;PATZ1:0.662410924725;RORA:0.644667179178;FOXA2:0.637883419917;BPTF:0.62353717341;NKX3-1:0.598549869703;RREB1:0.598068927426;PRRX1,2:0.591093989782;PBX1:0.585736717927;HOX{A5,B5}:0.568452385151;SOX2:0.565872397434;MED-1{core}:0.541307670544;FOXM1:0.519277729699;CUX2:0.514361263311;SNAI1..3:0.511672835303;ZFP161:0.504854640027;ZIC1..3:0.487488979912;ELK1,4_GABP{A,B1}:0.467047884652;FOX{I1,J2}:0.401947404702;MTE{core}:0.354057051861;ZEB1:0.337632014318;OCT4_SOX2{dimer}:0.296687818016;FOX{F1,F2,J1}:0.277366077433;STAT1,3:0.260655240115;NKX2-2,8:0.244244578389;TFAP2B:0.237505388912;FOXN1:0.231754029764;ARID5B:0.22343503755;HBP1_HMGB_SSRP1_UBTF:0.215692492816;POU3F1..4:0.200331194545;TP53:0.193178116232;GZF1:0.189355617167;NR5A1,2:0.170683996675;MYB:0.151246896974;FOX{D1,D2}:0.114871981227;XCPE1{core}:0.111742246791;PAX3,7:0.110002877583;MEF2{A,B,C,D}:0.102037111057;HIC1:0.0954917778822;HIF1A:0.0446179514399;NKX2-1,4:0.0348263596563;POU5F1:0.0200717792611;PAX5:0.00212449018296;GATA6:0.00133844488732;HNF1A:-0.0203098910053;HOXA9_MEIS1:-0.03585076549;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.06758325868;ZBTB6:-0.105836198915;KLF4:-0.113241077996;MYBL2:-0.119953380849;bHLH_family:-0.153927205951;FOXO1,3,4:-0.159736094587;PRDM1:-0.184498344431;REST:-0.21690515052;ATF2:-0.218833430877;NFIL3:-0.22904512232;AHR_ARNT_ARNT2:-0.230675413624;TEAD1:-0.239095376064;FOXP3:-0.246250091972;ATF5_CREB3:-0.257367311116;ESR1:-0.285453223468;GTF2A1,2:-0.333464485527;EN1,2:-0.372785306103;GTF2I:-0.378323078457;MZF1:-0.405291070899;DBP:-0.427843313539;EGR1..3:-0.434204191658;HNF4A_NR2F1,2:-0.434610388012;LMO2:-0.435014049392;NR3C1:-0.450351731149;MAZ:-0.467328610742;MTF1:-0.4794014387;AR:-0.500738057543;TFAP2{A,C}:-0.522626216133;TAL1_TCF{3,4,12}:-0.5976349174;MYFfamily:-0.642594156656;NKX3-2:-0.65317343944;PAX6:-0.65532919323;TLX2:-0.660515224305;DMAP1_NCOR{1,2}_SMARC:-0.662816284834;SPIB:-0.665324801838;IRF7:-0.667070165763;NR1H4:-0.678525898011;BACH2:-0.697731673771;FOS_FOS{B,L1}_JUN{B,D}:-0.698468676298;TBP:-0.702943935786;RUNX1..3:-0.708265447347;RXRA_VDR{dimer}:-0.731727578445;TLX1..3_NFIC{dimer}:-0.76457355985;ESRRA:-0.805020906702;UFEwm:-0.815980888595;GATA4:-0.819003633549;NFKB1_REL_RELA:-0.824099995369;CEBPA,B_DDIT3:-0.871059463656;SREBF1,2:-0.87371979939;NFE2:-0.875869958492;MYOD1:-0.888081359638;FOSL2:-0.944333870443;TGIF1:-0.981787009252;GFI1B:-0.983321516734;NANOG{mouse}:-1.01075796841;PAX1,9:-1.01098848222;HLF:-1.0124159014;HAND1,2:-1.02289704931;ALX4:-1.03960948923;JUN:-1.07787735339;ETS1,2:-1.09628732038;SPI1:-1.1193917635;ELF1,2,4:-1.12575238241;IRF1,2:-1.1538009889;NHLH1,2:-1.19247593782;IKZF1:-1.22335337818;PPARG:-1.23050827597;STAT2,4,6:-1.24477357736;SRF:-1.26354565983;GCM1,2:-1.26869065958;ZNF148:-1.30116944144;TBX4,5:-1.31959467837;EBF1:-1.32916001726;PAX2:-1.39119514008;ZNF238:-1.39386407284;XBP1:-1.41727849119;ZNF423:-1.43252165189;TFAP4:-1.5541636813;TFCP2:-1.67248968081;NFE2L2:-1.6751707128;GLI1..3:-1.68912047709;HSF1,2:-1.7388100045;NFIX:-1.98002982368;NR6A1:-1.98738183396;HES1:-1.99653453537;ATF6:-2.02324130864;NFATC1..3:-2.12163030436;SMAD1..7,9:-2.25465394368;SPZ1:-2.30214121573;MAFB:-2.32330023077;HMX1:-2.37097379298;EP300:-2.43021600498;NFE2L1:-2.71913215955
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10805-111A4;search_select_hide=table117:FF:10805-111A4
}}
}}

Latest revision as of 15:05, 3 June 2020

Name:anaplastic squamous cell carcinoma cell line:RPMI 2650
Species:Human (Homo sapiens)
Library ID:CNhs11889
Sample type:cell lines
Genomic View: UCSC
RefEX:Specific genes
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuenasal septum
dev stageNA
sexmale
ageunknown
cell typeunclassifiable
cell lineRPMI 2650
companyJAPAN HEALTH SCIENCES FOUNDATION - Health Science Research Resources Bank
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005598
CollapseLibrary accession numbers

Library idMethodExp. accession idRun accession id
CNhs11889 CAGE DRX007828 DRR008700
CollapseAccession ID Hg19

Library idBAMCTSS
CNhs11889 DRZ000125 DRZ001510
CollapseAccession ID Hg38

Library idBAMCTSS
CNhs11889 DRZ011475 DRZ012860
Download raw sequence, BAM & CTSS
CollapseHg19
FastaBAMCTSS
downloaddownloaddonwload
CollapseHg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
RNA-Seq  SAMD00005598
CollapseLibrary accession numbers

Library idMethodExp. accession idRun accession id
RDhi10086 RNA-Seq DRX057143 DRR062902
CollapseAccession ID Hg19

Library idBAMCTSS
RDhi10086 DRZ007978


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: CNhs11889



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: CNhs11889



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: CNhs11889


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)
0000076 (squamous epithelial cell)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
305 (carcinoma)
1749 (squamous cell carcinoma)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100297 (carcinoma cell line sample)
0102024 (squamous cell carcinoma cell line sample)
0101120 (epithelial cell line sample)
0104204 (nasal squamous cell carcinoma cell line sample)
0104205 (RPMI-2650 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
NA

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