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{{f5samples
{{f5samples
|id=FF:10648-109A9
|F5samples=
|name=mucinous adenocarcinoma cell line:JHOM-1
|ancestors_in_anatomy_facet=
|sample_id=10648
|rna_tube_id=109A9
|rna_box=109
|rna_position=A9
|sample_cell_lot=
|sample_cell_catalog=RCB1676
|sample_company=RIKEN Bioresource centre
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=ovary
|sample_donor(cell lot)=
|sample_sex=female
|sample_age=88
|sample_ethnicity=J
|rna_rin=
|rna_od260/230=1.76
|rna_od260/280=2.02
|sample_cell_type=unclassifiable
|sample_cell_line=JHOM-1
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_experimental_condition=
|sample_disease=mucinous adenocarcinoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=17.94131
|rna_concentration=0.38173
|sample_note=
|profile_hcage=CNhs11752,LSID820,release009,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000144,CL:0000151,CL:0000159,CL:0000255,CL:0000319,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000144,CL:0000151,CL:0000159,CL:0000255,CL:0000319,CL:0000548
|ancestors_in_anatomy_facet=
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:299,DOID:3030,DOID:305,DOID:4
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:299,DOID:3030,DOID:305,DOID:4
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:0101120
|fonse_cell_line=FF:0101120
|fonse_cell_line_closure=FF:0101120
|fonse_cell_line_closure=FF:0101120
Line 66: Line 34:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=FOXQ1:2.08578242762;NKX3-1:1.88857773257;NFE2L2:1.84050893209;PAX1,9:1.49793897385;HOXA9_MEIS1:1.48158519923;NKX2-1,4:1.47610627186;NFE2:1.40023178169;NFIX:1.36394936335;ZBTB16:1.34395486698;ARID5B:1.32320820461;FOXL1:1.28886526608;EVI1:1.23419346683;PITX1..3:1.23280538721;ALX1:1.20574111652;HSF1,2:1.19955090652;RXRA_VDR{dimer}:1.18297230303;ESRRA:1.10887369645;PPARG:1.05450794791;POU1F1:0.990495944138;PAX6:0.931614430372;PAX4:0.893261832615;CDX1,2,4:0.878000035172;FOXP1:0.85191641241;ONECUT1,2:0.779236589415;POU6F1:0.752500090096;IKZF1:0.721496871932;FOXP3:0.715394080586;HIF1A:0.705775294872;FOXD3:0.677830074047;UFEwm:0.677800316803;EBF1:0.663183059506;E2F1..5:0.662934357216;BACH2:0.624388850765;NFE2L1:0.604642873929;STAT5{A,B}:0.5964745553;ALX4:0.594007489168;PBX1:0.570239392835;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.569518889113;HOX{A5,B5}:0.561236568352;NFY{A,B,C}:0.561016407539;YY1:0.558262884114;GFI1:0.545176823553;NKX6-1,2:0.542380277122;IKZF2:0.531665119774;T:0.520800160561;RXR{A,B,G}:0.514111354527;ELK1,4_GABP{A,B1}:0.501231752749;NR6A1:0.48926041418;TEF:0.477518990329;DBP:0.474532259956;FOXM1:0.471189604232;POU3F1..4:0.462498562115;TLX1..3_NFIC{dimer}:0.445100533686;STAT2,4,6:0.440389356763;CDC5L:0.428574888915;MYBL2:0.411563801486;HMGA1,2:0.392847043299;ZIC1..3:0.351670855686;FOS_FOS{B,L1}_JUN{B,D}:0.338229781568;XBP1:0.321934132115;TBX4,5:0.31255616532;TEAD1:0.309711049179;FOX{I1,J2}:0.309396733968;FOSL2:0.294283045642;TFDP1:0.284796745831;TFCP2:0.271229452715;NANOG:0.248490888796;AIRE:0.245138871447;GFI1B:0.241802686754;SRF:0.220422848268;TBP:0.220013205625;PRRX1,2:0.217637725798;LHX3,4:0.200246034653;EP300:0.171585727863;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.162561579685;POU2F1..3:0.156268224378;PAX5:0.149818797298;ATF4:0.130236583508;IRF1,2:0.127276904968;IRF7:0.126582732279;MYB:0.123852827133;GTF2A1,2:0.112378574451;CEBPA,B_DDIT3:0.110067688111;SOX{8,9,10}:0.0986427328581;PDX1:0.0964496377063;NKX3-2:0.0623787452429;ZNF143:0.0569764958136;SOX5:0.051713709276;HNF4A_NR2F1,2:0.0396388333747;MTE{core}:0.0294146604932;NFKB1_REL_RELA:0.0261614265706;HOX{A4,D4}:0.0192761353711;TOPORS:0.0140497391279;PAX3,7:0.00919493946067;bHLH_family:-0.00269138968836;EN1,2:-0.00284346549797;NR3C1:-0.0176705492502;GLI1..3:-0.0334764816131;NR1H4:-0.0406069051376;ATF6:-0.0423214199009;ZFP161:-0.0424269818399;FOXN1:-0.0481037899911;NRF1:-0.0566102485664;ZBTB6:-0.0842394621481;HIC1:-0.0964115846529;CRX:-0.100576052155;OCT4_SOX2{dimer}:-0.116665084935;MEF2{A,B,C,D}:-0.123722431648;HLF:-0.142063180065;MYOD1:-0.14214227916;ZNF384:-0.1421894596;ESR1:-0.142683572359;HNF1A:-0.143385590742;MED-1{core}:-0.159051241047;POU5F1:-0.159876392475;AHR_ARNT_ARNT2:-0.167485207968;RFX1:-0.171469091546;FOXA2:-0.217750114942;ATF2:-0.220953318578;MAFB:-0.223569716421;TFAP2B:-0.22616971369;NR5A1,2:-0.229634924932;SOX17:-0.236800543213;ATF5_CREB3:-0.244910437251;JUN:-0.254382234175;GZF1:-0.25949478212;GATA4:-0.272072264877;RFX2..5_RFXANK_RFXAP:-0.273309130056;KLF4:-0.307486240222;HOX{A6,A7,B6,B7}:-0.307494728668;TP53:-0.311684128583;ZNF423:-0.324704867935;LEF1_TCF7_TCF7L1,2:-0.327231912007;HBP1_HMGB_SSRP1_UBTF:-0.332575242327;VSX1,2:-0.33603234759;SNAI1..3:-0.337960196624;SOX2:-0.340200430784;PAX2:-0.343687293999;MYFfamily:-0.348175518041;SP1:-0.395141865337;HES1:-0.417464481941;REST:-0.421866997743;XCPE1{core}:-0.452520116721;BREu{core}:-0.452588236247;NFATC1..3:-0.456955641331;DMAP1_NCOR{1,2}_SMARC:-0.464005759026;ELF1,2,4:-0.469516042764;NANOG{mouse}:-0.477578640908;SREBF1,2:-0.50172240091;SMAD1..7,9:-0.517410906679;GTF2I:-0.542264706527;RBPJ:-0.549349349806;HMX1:-0.550894820256;ZEB1:-0.572132574051;GATA6:-0.580077154712;TFAP2{A,C}:-0.59685917733;ZNF148:-0.604539172709;PAX8:-0.606837471521;RUNX1..3:-0.616126715091;TAL1_TCF{3,4,12}:-0.625598868263;TFAP4:-0.663831226535;FOX{F1,F2,J1}:-0.664467429524;CREB1:-0.670213924512;NHLH1,2:-0.681080901668;SPIB:-0.681558851332;MZF1:-0.686795327867;RORA:-0.688586169281;PRDM1:-0.700050284368;NKX2-3_NKX2-5:-0.718592426191;HAND1,2:-0.727720049972;NFIL3:-0.737176583719;ZNF238:-0.764586739446;CUX2:-0.766438778552;NKX2-2,8:-0.768017781341;EGR1..3:-0.813944888751;MAZ:-0.815521371431;AR:-0.820563207544;FOX{D1,D2}:-0.831117956032;LMO2:-0.911449689814;PATZ1:-0.929518677549;RREB1:-0.937716969333;FOXO1,3,4:-0.94349475704;ADNP_IRX_SIX_ZHX:-0.946171575707;SPI1:-0.974973569782;ETS1,2:-0.994373278092;GCM1,2:-1.01364962093;BPTF:-1.08728136024;MTF1:-1.1893382594;SPZ1:-1.19350399644;TGIF1:-1.40531608791;TLX2:-1.54295481118;STAT1,3:-1.71252593894
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10648-109A9
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102788
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102788
|name=mucinous adenocarcinoma cell line:JHOM-1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11752,LSID820,release009,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=109
|rna_catalog_number=
|rna_concentration=0.38173
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=1.76
|rna_od260/280=2.02
|rna_position=A9
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=109A9
|rna_weight_ug=17.94131
|sample_age=88
|sample_cell_catalog=RCB1676
|sample_cell_line=JHOM-1
|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=mucinous adenocarcinoma
|sample_donor(cell lot)=
|sample_ethnicity=J
|sample_experimental_condition=
|sample_id=10648
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=ovary
|top_motifs=FOXQ1:2.08578242762;NKX3-1:1.88857773257;NFE2L2:1.84050893209;PAX1,9:1.49793897385;HOXA9_MEIS1:1.48158519923;NKX2-1,4:1.47610627186;NFE2:1.40023178169;NFIX:1.36394936335;ZBTB16:1.34395486698;ARID5B:1.32320820461;FOXL1:1.28886526608;EVI1:1.23419346683;PITX1..3:1.23280538721;ALX1:1.20574111652;HSF1,2:1.19955090652;RXRA_VDR{dimer}:1.18297230303;ESRRA:1.10887369645;PPARG:1.05450794791;POU1F1:0.990495944138;PAX6:0.931614430372;PAX4:0.893261832615;CDX1,2,4:0.878000035172;FOXP1:0.85191641241;ONECUT1,2:0.779236589415;POU6F1:0.752500090096;IKZF1:0.721496871932;FOXP3:0.715394080586;HIF1A:0.705775294872;FOXD3:0.677830074047;UFEwm:0.677800316803;EBF1:0.663183059506;E2F1..5:0.662934357216;BACH2:0.624388850765;NFE2L1:0.604642873929;STAT5{A,B}:0.5964745553;ALX4:0.594007489168;PBX1:0.570239392835;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.569518889113;HOX{A5,B5}:0.561236568352;NFY{A,B,C}:0.561016407539;YY1:0.558262884114;GFI1:0.545176823553;NKX6-1,2:0.542380277122;IKZF2:0.531665119774;T:0.520800160561;RXR{A,B,G}:0.514111354527;ELK1,4_GABP{A,B1}:0.501231752749;NR6A1:0.48926041418;TEF:0.477518990329;DBP:0.474532259956;FOXM1:0.471189604232;POU3F1..4:0.462498562115;TLX1..3_NFIC{dimer}:0.445100533686;STAT2,4,6:0.440389356763;CDC5L:0.428574888915;MYBL2:0.411563801486;HMGA1,2:0.392847043299;ZIC1..3:0.351670855686;FOS_FOS{B,L1}_JUN{B,D}:0.338229781568;XBP1:0.321934132115;TBX4,5:0.31255616532;TEAD1:0.309711049179;FOX{I1,J2}:0.309396733968;FOSL2:0.294283045642;TFDP1:0.284796745831;TFCP2:0.271229452715;NANOG:0.248490888796;AIRE:0.245138871447;GFI1B:0.241802686754;SRF:0.220422848268;TBP:0.220013205625;PRRX1,2:0.217637725798;LHX3,4:0.200246034653;EP300:0.171585727863;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.162561579685;POU2F1..3:0.156268224378;PAX5:0.149818797298;ATF4:0.130236583508;IRF1,2:0.127276904968;IRF7:0.126582732279;MYB:0.123852827133;GTF2A1,2:0.112378574451;CEBPA,B_DDIT3:0.110067688111;SOX{8,9,10}:0.0986427328581;PDX1:0.0964496377063;NKX3-2:0.0623787452429;ZNF143:0.0569764958136;SOX5:0.051713709276;HNF4A_NR2F1,2:0.0396388333747;MTE{core}:0.0294146604932;NFKB1_REL_RELA:0.0261614265706;HOX{A4,D4}:0.0192761353711;TOPORS:0.0140497391279;PAX3,7:0.00919493946067;bHLH_family:-0.00269138968836;EN1,2:-0.00284346549797;NR3C1:-0.0176705492502;GLI1..3:-0.0334764816131;NR1H4:-0.0406069051376;ATF6:-0.0423214199009;ZFP161:-0.0424269818399;FOXN1:-0.0481037899911;NRF1:-0.0566102485664;ZBTB6:-0.0842394621481;HIC1:-0.0964115846529;CRX:-0.100576052155;OCT4_SOX2{dimer}:-0.116665084935;MEF2{A,B,C,D}:-0.123722431648;HLF:-0.142063180065;MYOD1:-0.14214227916;ZNF384:-0.1421894596;ESR1:-0.142683572359;HNF1A:-0.143385590742;MED-1{core}:-0.159051241047;POU5F1:-0.159876392475;AHR_ARNT_ARNT2:-0.167485207968;RFX1:-0.171469091546;FOXA2:-0.217750114942;ATF2:-0.220953318578;MAFB:-0.223569716421;TFAP2B:-0.22616971369;NR5A1,2:-0.229634924932;SOX17:-0.236800543213;ATF5_CREB3:-0.244910437251;JUN:-0.254382234175;GZF1:-0.25949478212;GATA4:-0.272072264877;RFX2..5_RFXANK_RFXAP:-0.273309130056;KLF4:-0.307486240222;HOX{A6,A7,B6,B7}:-0.307494728668;TP53:-0.311684128583;ZNF423:-0.324704867935;LEF1_TCF7_TCF7L1,2:-0.327231912007;HBP1_HMGB_SSRP1_UBTF:-0.332575242327;VSX1,2:-0.33603234759;SNAI1..3:-0.337960196624;SOX2:-0.340200430784;PAX2:-0.343687293999;MYFfamily:-0.348175518041;SP1:-0.395141865337;HES1:-0.417464481941;REST:-0.421866997743;XCPE1{core}:-0.452520116721;BREu{core}:-0.452588236247;NFATC1..3:-0.456955641331;DMAP1_NCOR{1,2}_SMARC:-0.464005759026;ELF1,2,4:-0.469516042764;NANOG{mouse}:-0.477578640908;SREBF1,2:-0.50172240091;SMAD1..7,9:-0.517410906679;GTF2I:-0.542264706527;RBPJ:-0.549349349806;HMX1:-0.550894820256;ZEB1:-0.572132574051;GATA6:-0.580077154712;TFAP2{A,C}:-0.59685917733;ZNF148:-0.604539172709;PAX8:-0.606837471521;RUNX1..3:-0.616126715091;TAL1_TCF{3,4,12}:-0.625598868263;TFAP4:-0.663831226535;FOX{F1,F2,J1}:-0.664467429524;CREB1:-0.670213924512;NHLH1,2:-0.681080901668;SPIB:-0.681558851332;MZF1:-0.686795327867;RORA:-0.688586169281;PRDM1:-0.700050284368;NKX2-3_NKX2-5:-0.718592426191;HAND1,2:-0.727720049972;NFIL3:-0.737176583719;ZNF238:-0.764586739446;CUX2:-0.766438778552;NKX2-2,8:-0.768017781341;EGR1..3:-0.813944888751;MAZ:-0.815521371431;AR:-0.820563207544;FOX{D1,D2}:-0.831117956032;LMO2:-0.911449689814;PATZ1:-0.929518677549;RREB1:-0.937716969333;FOXO1,3,4:-0.94349475704;ADNP_IRX_SIX_ZHX:-0.946171575707;SPI1:-0.974973569782;ETS1,2:-0.994373278092;GCM1,2:-1.01364962093;BPTF:-1.08728136024;MTF1:-1.1893382594;SPZ1:-1.19350399644;TGIF1:-1.40531608791;TLX2:-1.54295481118;STAT1,3:-1.71252593894
}}
}}

Revision as of 14:12, 21 March 2012


Name:mucinous adenocarcinoma cell line:JHOM-1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueovary
dev stageNA
sexfemale
age88
cell typeunclassifiable
cell lineJHOM-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
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: CNhs11752



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: CNhs11752



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: CNhs11752


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)
0000066 (epithelial cell)
0000151 (secretory cell)
0000159 (seromucus secreting cell)
0000255 (eukaryotic cell)
0000319 (mucus secreting cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
299 (adenocarcinoma)
3030 (mucinous adenocarcinoma)
305 (carcinoma)
4 (disease)

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