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{{f5samples
{{f5samples
|id=FF:10684-109E9
|F5samples=
|name=myxofibrosarcoma cell line:NMFH-1
|ancestors_in_anatomy_facet=UBERON:0000014,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0001062,UBERON:0002097,UBERON:0002199,UBERON:0002384,UBERON:0002416,UBERON:0003102
|sample_id=10684
|rna_tube_id=109E9
|rna_box=109
|rna_position=E9
|sample_cell_lot=
|sample_cell_catalog=RCB2346
|sample_company=RIKEN Bioresource centre
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=unclassifiable
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=89
|sample_ethnicity=J
|rna_rin=
|rna_od260/230=2.18
|rna_od260/280=2.14
|sample_cell_type=fibroblast
|sample_cell_line=NMFH-1
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_experimental_condition=
|sample_disease=myxofibrosarcoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=45.12893
|rna_concentration=0.96019
|sample_note=
|profile_hcage=CNhs11821,LSID829,release010,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000057,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000014,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0001062,UBERON:0002097,UBERON:0002199,UBERON:0002384,UBERON:0002416,UBERON:0003102
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:0060100,DOID:1115,DOID:14566,DOID:162,DOID:1907,DOID:201,DOID:4,DOID:4231
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:0060100,DOID:1115,DOID:14566,DOID:162,DOID:1907,DOID:201,DOID:4,DOID:4231
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:0100400,FF:0100453
|fonse_cell_line=FF:0100400,FF:0100453
|fonse_cell_line_closure=FF:0100400,FF:0100453
|fonse_cell_line_closure=FF:0100400,FF:0100453
Line 66: Line 34:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.75059758101;HOX{A4,D4}:1.49675078236;ZNF238:1.44841204252;HBP1_HMGB_SSRP1_UBTF:1.28764013759;HES1:1.21814747026;TFDP1:1.19681297782;E2F1..5:1.1258781841;GFI1B:1.11747203136;EN1,2:1.10948536258;GFI1:1.089953369;FOXQ1:1.02180001229;PBX1:1.01131694716;NFY{A,B,C}:1.00829191455;ELK1,4_GABP{A,B1}:1.00498818573;CDC5L:0.992148608576;bHLH_family:0.889825831203;ZBTB16:0.877821277231;SREBF1,2:0.850602035696;MYB:0.829976411407;NKX6-1,2:0.81791235962;PAX3,7:0.782322646107;ZNF384:0.781391388434;FOXD3:0.755760027908;GZF1:0.654173907259;NFIX:0.602195319335;ZNF143:0.561645138375;PAX1,9:0.546764278107;XBP1:0.545330537492;VSX1,2:0.509225086339;TEF:0.495907765142;TLX1..3_NFIC{dimer}:0.494739881681;PAX4:0.489327034152;FOS_FOS{B,L1}_JUN{B,D}:0.479326987925;SOX{8,9,10}:0.459108523897;YY1:0.451946159106;POU6F1:0.444017791322;EVI1:0.433646473597;PAX8:0.408585758802;NFE2:0.397772571451;POU1F1:0.394452101365;NR1H4:0.393813387984;NKX2-2,8:0.386315981033;ALX1:0.381267406034;PDX1:0.378515897244;NFE2L2:0.375631627483;PAX2:0.37385342879;POU3F1..4:0.368721950865;FOX{I1,J2}:0.367136449212;NR6A1:0.356657167511;NKX3-1:0.354561706833;CREB1:0.346185415502;GTF2I:0.343726094658;TAL1_TCF{3,4,12}:0.33729582095;AHR_ARNT_ARNT2:0.331875039828;TFAP2B:0.316081859552;TOPORS:0.313685111471;CUX2:0.307331939377;BACH2:0.303429213128;FOXP1:0.302747683856;PPARG:0.301319241577;NHLH1,2:0.290743468792;BREu{core}:0.279935546726;FOSL2:0.278440528089;MTE{core}:0.271751427961;ATF5_CREB3:0.259598589234;ADNP_IRX_SIX_ZHX:0.254259525185;HOX{A5,B5}:0.247352522344;DMAP1_NCOR{1,2}_SMARC:0.246213878653;NFATC1..3:0.24261170986;PAX6:0.232874930134;ARID5B:0.228726074133;GTF2A1,2:0.226644117615;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.225686899158;PAX5:0.212526900172;PRRX1,2:0.212084261022;TEAD1:0.20423830674;ZBTB6:0.194280895269;RFX1:0.190563738127;CRX:0.18802696491;MAFB:0.186509790665;MED-1{core}:0.186057701978;AIRE:0.181939930342;STAT2,4,6:0.170911310951;NRF1:0.160372975089;UFEwm:0.159150082492;ATF6:0.15474095554;TLX2:0.147435175584;PRDM1:0.146816466977;MYFfamily:0.146606109128;FOXL1:0.131082888583;MYBL2:0.130839232431;ZFP161:0.122963648957;ALX4:0.1208252592;HLF:0.105317927758;ATF4:0.10318236966;NKX2-1,4:0.101879909992;LHX3,4:0.100194594629;FOXO1,3,4:0.0739043731141;POU2F1..3:0.0547851421078;HOXA9_MEIS1:0.0432162440891;XCPE1{core}:0.0285493983128;STAT5{A,B}:0.0162129676491;JUN:0.00106276629898;NFIL3:-0.00120247257353;LEF1_TCF7_TCF7L1,2:-0.0176539552469;MZF1:-0.0246854835807;ESR1:-0.0366521381909;BPTF:-0.0405889992885;ELF1,2,4:-0.0447220546402;POU5F1:-0.0484324617947;TBX4,5:-0.0562321384176;FOXA2:-0.0725769425373;RUNX1..3:-0.0883054299214;TFCP2:-0.0883760407874;ATF2:-0.0932975357154;PITX1..3:-0.0937365937205;RXR{A,B,G}:-0.102614373411;HIC1:-0.125956941139;ESRRA:-0.127826848931;SOX17:-0.136710435229;STAT1,3:-0.139534024266;IKZF1:-0.140316341032;TP53:-0.142797567987;PATZ1:-0.15928935863;EGR1..3:-0.169952024826;TFAP2{A,C}:-0.173831363013;HNF1A:-0.177823271506;CDX1,2,4:-0.17857992381;MTF1:-0.18331298021;IKZF2:-0.186361590771;RFX2..5_RFXANK_RFXAP:-0.207016970672;FOXN1:-0.214372753021;NKX3-2:-0.219028092969;HNF4A_NR2F1,2:-0.222856911838;NFKB1_REL_RELA:-0.229035986055;TFAP4:-0.229609192312;MEF2{A,B,C,D}:-0.231453632577;SRF:-0.240088708377;RORA:-0.240511122772;SP1:-0.242998820682;NFE2L1:-0.245972160958;TBP:-0.253540889341;HSF1,2:-0.282227224805;RXRA_VDR{dimer}:-0.293781805886;FOX{D1,D2}:-0.304574130921;SPI1:-0.319043113238;ONECUT1,2:-0.323322845967;DBP:-0.32840643335;HIF1A:-0.329934137713;NANOG{mouse}:-0.3308724827;AR:-0.331208767494;KLF4:-0.354183832904;IRF1,2:-0.371486732758;GATA6:-0.376101453334;SOX5:-0.386401034515;FOXP3:-0.386762486588;OCT4_SOX2{dimer}:-0.393636384082;HAND1,2:-0.420269892239;CEBPA,B_DDIT3:-0.424055501923;REST:-0.440746264623;MAZ:-0.442929957113;GATA4:-0.452542413445;SPIB:-0.464940190593;IRF7:-0.465327985295;ETS1,2:-0.46734382462;RBPJ:-0.488671849883;ZIC1..3:-0.505291060956;HOX{A6,A7,B6,B7}:-0.531804626751;SPZ1:-0.532238301293;LMO2:-0.547973430946;NKX2-3_NKX2-5:-0.584423471698;TGIF1:-0.586536581543;RREB1:-0.629686540162;FOX{F1,F2,J1}:-0.645599379247;GLI1..3:-0.726334249244;GCM1,2:-0.731835112275;HMX1:-0.7431125887;SMAD1..7,9:-0.743937117855;FOXM1:-0.754321368839;NR3C1:-0.762229722575;NR5A1,2:-0.780337432028;ZNF423:-0.821592483554;ZNF148:-0.870350697812;SOX2:-0.919380122594;NANOG:-0.971631252924;EBF1:-0.98019957915;HMGA1,2:-1.03138906305;MYOD1:-1.08503148607;ZEB1:-1.16290937701;SNAI1..3:-1.16884148619;T:-1.18428191842;EP300:-1.30139249992
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10684-109E9
|is_a=CL:0002620;;DOID:1907;;EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100460
|is_a=CL:0002620;;DOID:1907;;EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100460
|name=myxofibrosarcoma cell line:NMFH-1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11821,LSID829,release010,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=109
|rna_catalog_number=
|rna_concentration=0.96019
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.18
|rna_od260/280=2.14
|rna_position=E9
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=109E9
|rna_weight_ug=45.12893
|sample_age=89
|sample_cell_catalog=RCB2346
|sample_cell_line=NMFH-1
|sample_cell_lot=
|sample_cell_type=fibroblast
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_company=RIKEN Bioresource centre
|sample_description=
|sample_dev_stage=
|sample_disease=myxofibrosarcoma
|sample_donor(cell lot)=
|sample_ethnicity=J
|sample_experimental_condition=
|sample_id=10684
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=unclassifiable
|top_motifs=ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.75059758101;HOX{A4,D4}:1.49675078236;ZNF238:1.44841204252;HBP1_HMGB_SSRP1_UBTF:1.28764013759;HES1:1.21814747026;TFDP1:1.19681297782;E2F1..5:1.1258781841;GFI1B:1.11747203136;EN1,2:1.10948536258;GFI1:1.089953369;FOXQ1:1.02180001229;PBX1:1.01131694716;NFY{A,B,C}:1.00829191455;ELK1,4_GABP{A,B1}:1.00498818573;CDC5L:0.992148608576;bHLH_family:0.889825831203;ZBTB16:0.877821277231;SREBF1,2:0.850602035696;MYB:0.829976411407;NKX6-1,2:0.81791235962;PAX3,7:0.782322646107;ZNF384:0.781391388434;FOXD3:0.755760027908;GZF1:0.654173907259;NFIX:0.602195319335;ZNF143:0.561645138375;PAX1,9:0.546764278107;XBP1:0.545330537492;VSX1,2:0.509225086339;TEF:0.495907765142;TLX1..3_NFIC{dimer}:0.494739881681;PAX4:0.489327034152;FOS_FOS{B,L1}_JUN{B,D}:0.479326987925;SOX{8,9,10}:0.459108523897;YY1:0.451946159106;POU6F1:0.444017791322;EVI1:0.433646473597;PAX8:0.408585758802;NFE2:0.397772571451;POU1F1:0.394452101365;NR1H4:0.393813387984;NKX2-2,8:0.386315981033;ALX1:0.381267406034;PDX1:0.378515897244;NFE2L2:0.375631627483;PAX2:0.37385342879;POU3F1..4:0.368721950865;FOX{I1,J2}:0.367136449212;NR6A1:0.356657167511;NKX3-1:0.354561706833;CREB1:0.346185415502;GTF2I:0.343726094658;TAL1_TCF{3,4,12}:0.33729582095;AHR_ARNT_ARNT2:0.331875039828;TFAP2B:0.316081859552;TOPORS:0.313685111471;CUX2:0.307331939377;BACH2:0.303429213128;FOXP1:0.302747683856;PPARG:0.301319241577;NHLH1,2:0.290743468792;BREu{core}:0.279935546726;FOSL2:0.278440528089;MTE{core}:0.271751427961;ATF5_CREB3:0.259598589234;ADNP_IRX_SIX_ZHX:0.254259525185;HOX{A5,B5}:0.247352522344;DMAP1_NCOR{1,2}_SMARC:0.246213878653;NFATC1..3:0.24261170986;PAX6:0.232874930134;ARID5B:0.228726074133;GTF2A1,2:0.226644117615;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.225686899158;PAX5:0.212526900172;PRRX1,2:0.212084261022;TEAD1:0.20423830674;ZBTB6:0.194280895269;RFX1:0.190563738127;CRX:0.18802696491;MAFB:0.186509790665;MED-1{core}:0.186057701978;AIRE:0.181939930342;STAT2,4,6:0.170911310951;NRF1:0.160372975089;UFEwm:0.159150082492;ATF6:0.15474095554;TLX2:0.147435175584;PRDM1:0.146816466977;MYFfamily:0.146606109128;FOXL1:0.131082888583;MYBL2:0.130839232431;ZFP161:0.122963648957;ALX4:0.1208252592;HLF:0.105317927758;ATF4:0.10318236966;NKX2-1,4:0.101879909992;LHX3,4:0.100194594629;FOXO1,3,4:0.0739043731141;POU2F1..3:0.0547851421078;HOXA9_MEIS1:0.0432162440891;XCPE1{core}:0.0285493983128;STAT5{A,B}:0.0162129676491;JUN:0.00106276629898;NFIL3:-0.00120247257353;LEF1_TCF7_TCF7L1,2:-0.0176539552469;MZF1:-0.0246854835807;ESR1:-0.0366521381909;BPTF:-0.0405889992885;ELF1,2,4:-0.0447220546402;POU5F1:-0.0484324617947;TBX4,5:-0.0562321384176;FOXA2:-0.0725769425373;RUNX1..3:-0.0883054299214;TFCP2:-0.0883760407874;ATF2:-0.0932975357154;PITX1..3:-0.0937365937205;RXR{A,B,G}:-0.102614373411;HIC1:-0.125956941139;ESRRA:-0.127826848931;SOX17:-0.136710435229;STAT1,3:-0.139534024266;IKZF1:-0.140316341032;TP53:-0.142797567987;PATZ1:-0.15928935863;EGR1..3:-0.169952024826;TFAP2{A,C}:-0.173831363013;HNF1A:-0.177823271506;CDX1,2,4:-0.17857992381;MTF1:-0.18331298021;IKZF2:-0.186361590771;RFX2..5_RFXANK_RFXAP:-0.207016970672;FOXN1:-0.214372753021;NKX3-2:-0.219028092969;HNF4A_NR2F1,2:-0.222856911838;NFKB1_REL_RELA:-0.229035986055;TFAP4:-0.229609192312;MEF2{A,B,C,D}:-0.231453632577;SRF:-0.240088708377;RORA:-0.240511122772;SP1:-0.242998820682;NFE2L1:-0.245972160958;TBP:-0.253540889341;HSF1,2:-0.282227224805;RXRA_VDR{dimer}:-0.293781805886;FOX{D1,D2}:-0.304574130921;SPI1:-0.319043113238;ONECUT1,2:-0.323322845967;DBP:-0.32840643335;HIF1A:-0.329934137713;NANOG{mouse}:-0.3308724827;AR:-0.331208767494;KLF4:-0.354183832904;IRF1,2:-0.371486732758;GATA6:-0.376101453334;SOX5:-0.386401034515;FOXP3:-0.386762486588;OCT4_SOX2{dimer}:-0.393636384082;HAND1,2:-0.420269892239;CEBPA,B_DDIT3:-0.424055501923;REST:-0.440746264623;MAZ:-0.442929957113;GATA4:-0.452542413445;SPIB:-0.464940190593;IRF7:-0.465327985295;ETS1,2:-0.46734382462;RBPJ:-0.488671849883;ZIC1..3:-0.505291060956;HOX{A6,A7,B6,B7}:-0.531804626751;SPZ1:-0.532238301293;LMO2:-0.547973430946;NKX2-3_NKX2-5:-0.584423471698;TGIF1:-0.586536581543;RREB1:-0.629686540162;FOX{F1,F2,J1}:-0.645599379247;GLI1..3:-0.726334249244;GCM1,2:-0.731835112275;HMX1:-0.7431125887;SMAD1..7,9:-0.743937117855;FOXM1:-0.754321368839;NR3C1:-0.762229722575;NR5A1,2:-0.780337432028;ZNF423:-0.821592483554;ZNF148:-0.870350697812;SOX2:-0.919380122594;NANOG:-0.971631252924;EBF1:-0.98019957915;HMGA1,2:-1.03138906305;MYOD1:-1.08503148607;ZEB1:-1.16290937701;SNAI1..3:-1.16884148619;T:-1.18428191842;EP300:-1.30139249992
}}
}}

Revision as of 14:12, 21 March 2012


Name:myxofibrosarcoma cell line:NMFH-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueunclassifiable
dev stageNA
sexmale
age89
cell typefibroblast
cell lineNMFH-1
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]





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 no result for this sample


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: CNhs11821



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: CNhs11821



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: CNhs11821


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)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000057 (fibroblast)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

DOID: Disease
0050686 (organ system cancer)
0050687 (cell type cancer)
0060100 (musculoskeletal system cancer)
1115 (sarcoma)
14566 (disease of cellular proliferation)
162 (cancer)
1907 (malignant fibroxanthoma)
201 (connective tissue cancer)
4 (disease)
4231 (histiocytoma)

UBERON: Anatomy
0000014 (zone of skin)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0001062 (anatomical entity)
0002097 (skin of body)
0002199 (integument)
0002384 (connective tissue)
0002416 (integumental system)
0003102 (surface structure)

FF: FANTOM5
NA

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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