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{{f5samples
{{f5samples
|id=FF:10663-109C6
|F5samples=
|name=neuroectodermal tumor cell line:FU-RPNT-2
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000468,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001062,UBERON:0002050,UBERON:0002346,UBERON:0002532,UBERON:0005423
|sample_id=10663
|rna_tube_id=109C6
|rna_box=109
|rna_position=C6
|sample_cell_lot=
|sample_cell_catalog=RCB2078
|sample_company=RIKEN Bioresource centre
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=kidney
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=10
|sample_ethnicity=J
|rna_rin=
|rna_od260/230=2.14
|rna_od260/280=2.08
|sample_cell_type=unclassifiable
|sample_cell_line=FU-RPNT-2
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_experimental_condition=
|sample_disease=neuroectodermal tumor
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=93.84913
|rna_concentration=1.99679
|sample_note=
|profile_hcage=CNhs11753,LSID820,release009,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000468,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0001062,UBERON:0002050,UBERON:0002346,UBERON:0002532,UBERON:0005423
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:171,DOID:2994,DOID:3095,DOID:4
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:171,DOID:2994,DOID:3095,DOID:4
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:10663-109C6
|fonse_cell_line=FF:10663-109C6
|fonse_cell_line_closure=FF:10663-109C6
|fonse_cell_line_closure=FF:10663-109C6
Line 66: Line 34:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=TOPORS:4.28708651435;PITX1..3:4.10554169973;FOXP1:3.91252758068;PAX4:3.23293686208;ALX1:3.1595784344;AIRE:2.62620344742;ZBTB16:2.19014776549;CDX1,2,4:2.16851063033;POU1F1:1.94991437435;FOXD3:1.89284913102;POU3F1..4:1.428417362;PRRX1,2:1.42047896505;ARID5B:1.33040395342;STAT5{A,B}:1.31122686624;PBX1:1.25236894232;HOXA9_MEIS1:1.23113285029;POU2F1..3:1.21162951698;GATA4:1.20587732193;LHX3,4:1.20283262918;DBP:1.16755421189;IKZF2:1.16704663582;OCT4_SOX2{dimer}:1.11224612899;E2F1..5:1.0650869204;FOXL1:1.01831699331;POU6F1:1.00962970603;FOXM1:0.971881575305;BREu{core}:0.960543990279;ZNF143:0.955909660247;NRF1:0.946100071114;GTF2A1,2:0.930954265512;YY1:0.904225701666;bHLH_family:0.897914121777;ATF4:0.890923878997;NKX6-1,2:0.890860062408;EGR1..3:0.872868333643;SOX{8,9,10}:0.853675659394;ATF5_CREB3:0.852442499938;T:0.851483528515;POU5F1:0.825488574021;PAX3,7:0.811157796855;PRDM1:0.795247588841;GFI1:0.785442502873;CUX2:0.77357141769;HOX{A5,B5}:0.760659508098;NKX3-1:0.735040933985;FOXQ1:0.717722318239;CRX:0.716776185181;ZIC1..3:0.698685143751;DMAP1_NCOR{1,2}_SMARC:0.693401947675;RFX1:0.670149405162;ZNF384:0.670001672158;HOX{A6,A7,B6,B7}:0.63667189593;NR6A1:0.629760274873;TFDP1:0.623509608485;UFEwm:0.615994744082;NFY{A,B,C}:0.597211138322;ELK1,4_GABP{A,B1}:0.587349329435;FOX{D1,D2}:0.572214406963;REST:0.542239948355;ZNF423:0.500574739434;ATF6:0.493738031145;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.472762251233;RFX2..5_RFXANK_RFXAP:0.429937272715;TEF:0.390683020294;GTF2I:0.357866835346;ZBTB6:0.331585075629;AHR_ARNT_ARNT2:0.312381854086;BPTF:0.301882050731;MZF1:0.290373376251;MTE{core}:0.277854104316;PATZ1:0.273671804639;SOX17:0.270798527285;FOXN1:0.265548819956;SOX5:0.26005895125;STAT1,3:0.246028537711;TLX1..3_NFIC{dimer}:0.240760450747;KLF4:0.221798165056;RORA:0.213068201388;HMGA1,2:0.205016104808;RBPJ:0.196383991467;HOX{A4,D4}:0.180366591597;EVI1:0.165008486029;RXR{A,B,G}:0.153083958166;ONECUT1,2:0.150618907396;MYB:0.106491564503;ZFP161:0.101115851218;FOXP3:0.080929302599;CDC5L:0.0682928076445;PAX1,9:0.0583801119655;PAX8:0.0321502442075;CREB1:0.0149642468047;NHLH1,2:0.0100354468635;PDX1:-0.00413069588585;SREBF1,2:-0.0188535150433;MED-1{core}:-0.023628653039;NFE2L1:-0.0658157046;TBP:-0.0912980753635;NKX2-1,4:-0.107530122676;PAX2:-0.115140036721;ATF2:-0.131572777871;MEF2{A,B,C,D}:-0.143284832999;RREB1:-0.169131804949;PAX5:-0.192809140033;EN1,2:-0.209430633413;GZF1:-0.224965481141;MAZ:-0.225984888685;FOX{I1,J2}:-0.226935990638;ADNP_IRX_SIX_ZHX:-0.233425172143;NKX2-2,8:-0.233911207316;NKX2-3_NKX2-5:-0.23403881967;SP1:-0.253363249001;TFAP2B:-0.280800340622;JUN:-0.284123812175;XBP1:-0.293920412606;NFIX:-0.319269583175;GFI1B:-0.348614215783;SPIB:-0.352536260487;CEBPA,B_DDIT3:-0.360153184307;ALX4:-0.361933693215;XCPE1{core}:-0.380446765549;HNF1A:-0.383787664034;NANOG:-0.385364542078;PAX6:-0.388994760632;GATA6:-0.416749624415;MYFfamily:-0.450917473887;FOXO1,3,4:-0.460556071515;NFIL3:-0.473031795392;NKX3-2:-0.474217119734;NFE2L2:-0.493799066673;RUNX1..3:-0.494301318914;TLX2:-0.500540499191;MTF1:-0.504903551592;NFKB1_REL_RELA:-0.50795941823;TAL1_TCF{3,4,12}:-0.521848785092;FOXA2:-0.534888329017;EBF1:-0.57131422961;TEAD1:-0.574172381404;HIC1:-0.59468816737;IRF1,2:-0.599600122574;HES1:-0.642005863741;ZNF238:-0.642722935946;HNF4A_NR2F1,2:-0.644864579266;SPI1:-0.673847509637;EP300:-0.676519292458;IRF7:-0.676531315097;SRF:-0.696501713941;MAFB:-0.713793839853;TFAP2{A,C}:-0.716136612568;SOX2:-0.717274366863;LMO2:-0.729108902667;NFE2:-0.73143370006;STAT2,4,6:-0.735011912376;TP53:-0.741984286029;AR:-0.75444688592;ELF1,2,4:-0.759466970008;FOS_FOS{B,L1}_JUN{B,D}:-0.766082922391;NANOG{mouse}:-0.773836554888;SNAI1..3:-0.778560796942;HLF:-0.785275154744;ZEB1:-0.81109435967;HBP1_HMGB_SSRP1_UBTF:-0.818093358351;HMX1:-0.85295447092;FOSL2:-0.880942142748;MYOD1:-0.897924152322;SPZ1:-0.902574261879;MYBL2:-0.91407707129;BACH2:-0.927860891287;ETS1,2:-0.931669344735;NR1H4:-0.977957660531;TBX4,5:-0.992779540648;LEF1_TCF7_TCF7L1,2:-1.06206063657;TGIF1:-1.10292293193;HSF1,2:-1.12863038597;GLI1..3:-1.15118102103;ESRRA:-1.19844932787;GCM1,2:-1.20292859407;HIF1A:-1.21133811494;SMAD1..7,9:-1.23029076256;NR3C1:-1.23417167821;HAND1,2:-1.28989515865;PPARG:-1.30946425009;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.36292223969;NR5A1,2:-1.39442946492;IKZF1:-1.45382574991;NFATC1..3:-1.48337395688;FOX{F1,F2,J1}:-1.49365836515;VSX1,2:-1.56133730371;RXRA_VDR{dimer}:-1.63774155407;TFAP4:-1.63869669236;ZNF148:-1.9270647122;TFCP2:-1.93321115773;ESR1:-2.07261836761
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10663-109C6
|is_a=DOID:171;;EFO:0002091;;FF:0000003;;FF:0000210;;UBERON:0002346
|is_a=DOID:171;;EFO:0002091;;FF:0000003;;FF:0000210;;UBERON:0002346
|name=neuroectodermal tumor cell line:FU-RPNT-2
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11753,LSID820,release009,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=109
|rna_catalog_number=
|rna_concentration=1.99679
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.14
|rna_od260/280=2.08
|rna_position=C6
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=109C6
|rna_weight_ug=93.84913
|sample_age=10
|sample_cell_catalog=RCB2078
|sample_cell_line=FU-RPNT-2
|sample_cell_lot=
|sample_cell_type=unclassifiable
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_company=RIKEN Bioresource centre
|sample_description=
|sample_dev_stage=
|sample_disease=neuroectodermal tumor
|sample_donor(cell lot)=
|sample_ethnicity=J
|sample_experimental_condition=
|sample_id=10663
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=kidney
|top_motifs=TOPORS:4.28708651435;PITX1..3:4.10554169973;FOXP1:3.91252758068;PAX4:3.23293686208;ALX1:3.1595784344;AIRE:2.62620344742;ZBTB16:2.19014776549;CDX1,2,4:2.16851063033;POU1F1:1.94991437435;FOXD3:1.89284913102;POU3F1..4:1.428417362;PRRX1,2:1.42047896505;ARID5B:1.33040395342;STAT5{A,B}:1.31122686624;PBX1:1.25236894232;HOXA9_MEIS1:1.23113285029;POU2F1..3:1.21162951698;GATA4:1.20587732193;LHX3,4:1.20283262918;DBP:1.16755421189;IKZF2:1.16704663582;OCT4_SOX2{dimer}:1.11224612899;E2F1..5:1.0650869204;FOXL1:1.01831699331;POU6F1:1.00962970603;FOXM1:0.971881575305;BREu{core}:0.960543990279;ZNF143:0.955909660247;NRF1:0.946100071114;GTF2A1,2:0.930954265512;YY1:0.904225701666;bHLH_family:0.897914121777;ATF4:0.890923878997;NKX6-1,2:0.890860062408;EGR1..3:0.872868333643;SOX{8,9,10}:0.853675659394;ATF5_CREB3:0.852442499938;T:0.851483528515;POU5F1:0.825488574021;PAX3,7:0.811157796855;PRDM1:0.795247588841;GFI1:0.785442502873;CUX2:0.77357141769;HOX{A5,B5}:0.760659508098;NKX3-1:0.735040933985;FOXQ1:0.717722318239;CRX:0.716776185181;ZIC1..3:0.698685143751;DMAP1_NCOR{1,2}_SMARC:0.693401947675;RFX1:0.670149405162;ZNF384:0.670001672158;HOX{A6,A7,B6,B7}:0.63667189593;NR6A1:0.629760274873;TFDP1:0.623509608485;UFEwm:0.615994744082;NFY{A,B,C}:0.597211138322;ELK1,4_GABP{A,B1}:0.587349329435;FOX{D1,D2}:0.572214406963;REST:0.542239948355;ZNF423:0.500574739434;ATF6:0.493738031145;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.472762251233;RFX2..5_RFXANK_RFXAP:0.429937272715;TEF:0.390683020294;GTF2I:0.357866835346;ZBTB6:0.331585075629;AHR_ARNT_ARNT2:0.312381854086;BPTF:0.301882050731;MZF1:0.290373376251;MTE{core}:0.277854104316;PATZ1:0.273671804639;SOX17:0.270798527285;FOXN1:0.265548819956;SOX5:0.26005895125;STAT1,3:0.246028537711;TLX1..3_NFIC{dimer}:0.240760450747;KLF4:0.221798165056;RORA:0.213068201388;HMGA1,2:0.205016104808;RBPJ:0.196383991467;HOX{A4,D4}:0.180366591597;EVI1:0.165008486029;RXR{A,B,G}:0.153083958166;ONECUT1,2:0.150618907396;MYB:0.106491564503;ZFP161:0.101115851218;FOXP3:0.080929302599;CDC5L:0.0682928076445;PAX1,9:0.0583801119655;PAX8:0.0321502442075;CREB1:0.0149642468047;NHLH1,2:0.0100354468635;PDX1:-0.00413069588585;SREBF1,2:-0.0188535150433;MED-1{core}:-0.023628653039;NFE2L1:-0.0658157046;TBP:-0.0912980753635;NKX2-1,4:-0.107530122676;PAX2:-0.115140036721;ATF2:-0.131572777871;MEF2{A,B,C,D}:-0.143284832999;RREB1:-0.169131804949;PAX5:-0.192809140033;EN1,2:-0.209430633413;GZF1:-0.224965481141;MAZ:-0.225984888685;FOX{I1,J2}:-0.226935990638;ADNP_IRX_SIX_ZHX:-0.233425172143;NKX2-2,8:-0.233911207316;NKX2-3_NKX2-5:-0.23403881967;SP1:-0.253363249001;TFAP2B:-0.280800340622;JUN:-0.284123812175;XBP1:-0.293920412606;NFIX:-0.319269583175;GFI1B:-0.348614215783;SPIB:-0.352536260487;CEBPA,B_DDIT3:-0.360153184307;ALX4:-0.361933693215;XCPE1{core}:-0.380446765549;HNF1A:-0.383787664034;NANOG:-0.385364542078;PAX6:-0.388994760632;GATA6:-0.416749624415;MYFfamily:-0.450917473887;FOXO1,3,4:-0.460556071515;NFIL3:-0.473031795392;NKX3-2:-0.474217119734;NFE2L2:-0.493799066673;RUNX1..3:-0.494301318914;TLX2:-0.500540499191;MTF1:-0.504903551592;NFKB1_REL_RELA:-0.50795941823;TAL1_TCF{3,4,12}:-0.521848785092;FOXA2:-0.534888329017;EBF1:-0.57131422961;TEAD1:-0.574172381404;HIC1:-0.59468816737;IRF1,2:-0.599600122574;HES1:-0.642005863741;ZNF238:-0.642722935946;HNF4A_NR2F1,2:-0.644864579266;SPI1:-0.673847509637;EP300:-0.676519292458;IRF7:-0.676531315097;SRF:-0.696501713941;MAFB:-0.713793839853;TFAP2{A,C}:-0.716136612568;SOX2:-0.717274366863;LMO2:-0.729108902667;NFE2:-0.73143370006;STAT2,4,6:-0.735011912376;TP53:-0.741984286029;AR:-0.75444688592;ELF1,2,4:-0.759466970008;FOS_FOS{B,L1}_JUN{B,D}:-0.766082922391;NANOG{mouse}:-0.773836554888;SNAI1..3:-0.778560796942;HLF:-0.785275154744;ZEB1:-0.81109435967;HBP1_HMGB_SSRP1_UBTF:-0.818093358351;HMX1:-0.85295447092;FOSL2:-0.880942142748;MYOD1:-0.897924152322;SPZ1:-0.902574261879;MYBL2:-0.91407707129;BACH2:-0.927860891287;ETS1,2:-0.931669344735;NR1H4:-0.977957660531;TBX4,5:-0.992779540648;LEF1_TCF7_TCF7L1,2:-1.06206063657;TGIF1:-1.10292293193;HSF1,2:-1.12863038597;GLI1..3:-1.15118102103;ESRRA:-1.19844932787;GCM1,2:-1.20292859407;HIF1A:-1.21133811494;SMAD1..7,9:-1.23029076256;NR3C1:-1.23417167821;HAND1,2:-1.28989515865;PPARG:-1.30946425009;RXR{A,B,G}_{NR1H2,PPAR}dimers:-1.36292223969;NR5A1,2:-1.39442946492;IKZF1:-1.45382574991;NFATC1..3:-1.48337395688;FOX{F1,F2,J1}:-1.49365836515;VSX1,2:-1.56133730371;RXRA_VDR{dimer}:-1.63774155407;TFAP4:-1.63869669236;ZNF148:-1.9270647122;TFCP2:-1.93321115773;ESR1:-2.07261836761
}}
}}

Revision as of 14:12, 21 March 2012


Name:neuroectodermal tumor cell line:FU-RPNT-2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuekidney
dev stageNA
sexmale
age10
cell typeunclassifiable
cell lineFU-RPNT-2
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
CollapseHg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
CollapseHg38
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: CNhs11753



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: CNhs11753



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: CNhs11753


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

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
171 (neuroectodermal tumor)
2994 (germ cell cancer)
3095 (germ cell and embryonal cancer)
4 (disease)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0005423 (developing anatomical 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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