Personal tools

FF:10820-111C1: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:10820-111C1
|F5samples=
|name=hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep3
|ancestors_in_anatomy_facet=UBERON:0000015,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002100,UBERON:0002107,UBERON:0002330,UBERON:0002365,UBERON:0002368,UBERON:0002405,UBERON:0002417,UBERON:0002423,UBERON:0002530,UBERON:0002532,UBERON:0003104,UBERON:0003894,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004921,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0006235,UBERON:0006925,UBERON:0007026,UBERON:0008835,UBERON:0008836,UBERON:0009142
|sample_id=10820
|rna_tube_id=111C1
|rna_box=111
|rna_position=C1
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=
|sample_strain=
|sample_dev_stage=
|sample_tissue=liver
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=15
|sample_ethnicity=
|rna_rin=
|rna_od260/230=2.18
|rna_od260/280=2.05
|sample_cell_type=hepatocyte
|sample_cell_line=HepG2
|sample_collaboration=Carrie Davis (Cold spring Harbor Laboratories)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=57.042
|rna_concentration=1.14084
|sample_note=
|profile_hcage=CNhs12330,LSID913,release011,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:0000255,CL:0000548
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_anatomy_facet=UBERON:0000015,UBERON:0000061,UBERON:0000062,UBERON:0000077,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0000949,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002100,UBERON:0002107,UBERON:0002330,UBERON:0002365,UBERON:0002368,UBERON:0002405,UBERON:0002417,UBERON:0002423,UBERON:0002530,UBERON:0002532,UBERON:0003104,UBERON:0003894,UBERON:0004119,UBERON:0004120,UBERON:0004161,UBERON:0004185,UBERON:0004921,UBERON:0005057,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005256,UBERON:0005423,UBERON:0006235,UBERON:0006925,UBERON:0007026,UBERON:0008835,UBERON:0008836,UBERON:0009142
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:305,DOID:4,DOID:7
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:305,DOID:4,DOID:7
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:0100224,FF:0101120
|fonse_cell_line=FF:0100224,FF:0101120
|fonse_cell_line_closure=FF:0100224,FF:0101120
|fonse_cell_line_closure=FF:0100224,FF:0101120
Line 66: Line 34:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=HNF4A_NR2F1,2:4.79489922739;HNF1A:4.15674580962;RXR{A,B,G}_{NR1H2,PPAR}dimers:3.70886331688;FOXA2:3.28094513886;LEF1_TCF7_TCF7L1,2:2.19703770575;bHLH_family:2.14861616564;FOX{F1,F2,J1}:1.86324120674;NFY{A,B,C}:1.66870148087;NR6A1:1.53232542716;ONECUT1,2:1.47765464728;E2F1..5:1.47592317324;ELK1,4_GABP{A,B1}:1.23872793575;NR1H4:1.23461280756;ADNP_IRX_SIX_ZHX:1.22934199989;ZNF143:1.22412043089;YY1:1.20862518294;EN1,2:1.06665004701;SOX{8,9,10}:1.06174733679;PBX1:1.04782136736;AIRE:0.98829447571;GFI1:0.98484139588;NRF1:0.920649391277;NR5A1,2:0.874768753787;SNAI1..3:0.856303376606;PAX3,7:0.837744510058;RORA:0.79861321017;NKX3-2:0.771750133057;TOPORS:0.759765491852;MYB:0.697958246999;SOX2:0.683448595365;LHX3,4:0.662898727197;ZEB1:0.65942116707;CEBPA,B_DDIT3:0.613502778284;RXRA_VDR{dimer}:0.586732412275;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.575912015516;FOXM1:0.567846136374;ALX4:0.497064052524;ESRRA:0.47231716769;FOX{D1,D2}:0.450645710745;PITX1..3:0.425379426971;TP53:0.423384381828;TFDP1:0.410184480164;EBF1:0.344287564557;MYOD1:0.329055318413;HIC1:0.324836155651;AR:0.320502696575;XCPE1{core}:0.300921503577;FOXD3:0.299343646739;HLF:0.253034137309;NFIL3:0.247875662216;POU6F1:0.19377342825;PPARG:0.181084785694;ELF1,2,4:0.157234911242;CUX2:0.151659047194;FOXP1:0.150339252802;STAT5{A,B}:0.118364349087;DBP:0.111274202656;PAX4:0.102549210155;MTE{core}:0.0843819045578;GATA6:0.0704830260118;SP1:0.0676730424047;MAZ:0.0574476049822;ZFP161:0.0432753769729;BREu{core}:0.034747475777;NKX3-1:0.0288551279048;UFEwm:-0.00115933343807;SOX5:-0.00375613758848;RBPJ:-0.0136885623597;TFCP2:-0.028940951366;TFAP2{A,C}:-0.0526428295901;ARID5B:-0.059325773711;SREBF1,2:-0.0727296082073;PAX2:-0.0964500460761;FOXQ1:-0.0971982231484;SOX17:-0.0997918067386;EVI1:-0.135058742636;T:-0.136089760285;CDC5L:-0.141628942961;PAX1,9:-0.1440933795;VSX1,2:-0.14497351687;TBX4,5:-0.152203793972;RXR{A,B,G}:-0.156010726229;NFKB1_REL_RELA:-0.16415423961;KLF4:-0.165227177282;STAT2,4,6:-0.165517342186;HOXA9_MEIS1:-0.189971082165;MED-1{core}:-0.205918083093;AHR_ARNT_ARNT2:-0.214634109497;LMO2:-0.233844518225;GLI1..3:-0.235065286609;PATZ1:-0.237935863777;TEAD1:-0.259816226482;POU3F1..4:-0.261919752527;ATF5_CREB3:-0.292632998736;MTF1:-0.303324225714;HOX{A5,B5}:-0.343292041025;STAT1,3:-0.346937591822;TLX1..3_NFIC{dimer}:-0.361979596959;TAL1_TCF{3,4,12}:-0.378302518924;ATF6:-0.385324785709;FOXN1:-0.389810556209;FOSL2:-0.404244924148;BPTF:-0.41064733055;ZNF148:-0.418390428381;NFE2:-0.421036518576;ESR1:-0.444171029788;CREB1:-0.447163137058;ZNF423:-0.449556038679;IRF7:-0.455765145368;DMAP1_NCOR{1,2}_SMARC:-0.45683060099;HOX{A4,D4}:-0.459790075376;HOX{A6,A7,B6,B7}:-0.467895264854;FOXO1,3,4:-0.470025126306;IKZF2:-0.474506016029;HES1:-0.50934388326;OCT4_SOX2{dimer}:-0.509672867534;POU2F1..3:-0.51370714317;REST:-0.521637185438;NKX6-1,2:-0.539231323858;NKX2-3_NKX2-5:-0.54144901116;IRF1,2:-0.550938756496;GTF2A1,2:-0.554792862096;FOS_FOS{B,L1}_JUN{B,D}:-0.559606984292;GATA4:-0.571006511047;NFE2L2:-0.572143578382;NANOG{mouse}:-0.584195857887;BACH2:-0.596434522525;POU5F1:-0.598747557707;PAX5:-0.598789630056;NR3C1:-0.614164326561;RFX2..5_RFXANK_RFXAP:-0.625690901673;CDX1,2,4:-0.630608083756;ATF4:-0.637273290144;FOXP3:-0.638749043053;EGR1..3:-0.641133517395;ZBTB16:-0.644252011753;TBP:-0.6488505454;IKZF1:-0.654981581328;PDX1:-0.656384877817;SPI1:-0.659815756185;ATF2:-0.660971287191;SPIB:-0.66265416194;PAX8:-0.663390241483;XBP1:-0.663461946158;RREB1:-0.672884714426;ALX1:-0.676959472369;NFIX:-0.706670308976;TFAP2B:-0.738307727604;MYBL2:-0.740243696716;SRF:-0.787934317686;NHLH1,2:-0.78864316682;HSF1,2:-0.793263623152;MEF2{A,B,C,D}:-0.803685989872;RFX1:-0.842381476787;NKX2-2,8:-0.847533213266;GTF2I:-0.851049930485;JUN:-0.851634836205;HMGA1,2:-0.85549949622;HAND1,2:-0.857144696788;MYFfamily:-0.876758402729;RUNX1..3:-0.888916293547;GCM1,2:-0.891126046233;ZBTB6:-0.943957369801;CRX:-1.00956012356;ETS1,2:-1.04814527658;ZIC1..3:-1.0537545522;POU1F1:-1.0574304188;TFAP4:-1.05945828406;MAFB:-1.05979860937;NKX2-1,4:-1.06799278697;GFI1B:-1.07202974465;PRDM1:-1.0785146347;NFE2L1:-1.08347923675;ZNF384:-1.09271843507;FOX{I1,J2}:-1.1022475061;PAX6:-1.14364054218;SPZ1:-1.1457298066;EP300:-1.1475564127;MZF1:-1.21280396701;PRRX1,2:-1.26983335219;NFATC1..3:-1.28640399381;NANOG:-1.32158074644;TGIF1:-1.41415422759;ZNF238:-1.44425329126;TEF:-1.53566371064;HBP1_HMGB_SSRP1_UBTF:-1.60651166154;GZF1:-1.66471205192;TLX2:-1.74346414584;SMAD1..7,9:-1.77536123114;HIF1A:-1.79732203238;FOXL1:-1.93984636463;HMX1:-1.94158043128
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10820-111C1
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100599
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100599
|name=hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep3
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12330,LSID913,release011,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=111
|rna_catalog_number=
|rna_concentration=1.14084
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.18
|rna_od260/280=2.05
|rna_position=C1
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=111C1
|rna_weight_ug=57.042
|sample_age=15
|sample_cell_catalog=
|sample_cell_line=HepG2
|sample_cell_lot=
|sample_cell_type=hepatocyte
|sample_collaboration=Carrie Davis (Cold spring Harbor Laboratories)
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10820
|sample_note=
|sample_sex=male
|sample_species=
|sample_strain=
|sample_tissue=liver
|top_motifs=HNF4A_NR2F1,2:4.79489922739;HNF1A:4.15674580962;RXR{A,B,G}_{NR1H2,PPAR}dimers:3.70886331688;FOXA2:3.28094513886;LEF1_TCF7_TCF7L1,2:2.19703770575;bHLH_family:2.14861616564;FOX{F1,F2,J1}:1.86324120674;NFY{A,B,C}:1.66870148087;NR6A1:1.53232542716;ONECUT1,2:1.47765464728;E2F1..5:1.47592317324;ELK1,4_GABP{A,B1}:1.23872793575;NR1H4:1.23461280756;ADNP_IRX_SIX_ZHX:1.22934199989;ZNF143:1.22412043089;YY1:1.20862518294;EN1,2:1.06665004701;SOX{8,9,10}:1.06174733679;PBX1:1.04782136736;AIRE:0.98829447571;GFI1:0.98484139588;NRF1:0.920649391277;NR5A1,2:0.874768753787;SNAI1..3:0.856303376606;PAX3,7:0.837744510058;RORA:0.79861321017;NKX3-2:0.771750133057;TOPORS:0.759765491852;MYB:0.697958246999;SOX2:0.683448595365;LHX3,4:0.662898727197;ZEB1:0.65942116707;CEBPA,B_DDIT3:0.613502778284;RXRA_VDR{dimer}:0.586732412275;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.575912015516;FOXM1:0.567846136374;ALX4:0.497064052524;ESRRA:0.47231716769;FOX{D1,D2}:0.450645710745;PITX1..3:0.425379426971;TP53:0.423384381828;TFDP1:0.410184480164;EBF1:0.344287564557;MYOD1:0.329055318413;HIC1:0.324836155651;AR:0.320502696575;XCPE1{core}:0.300921503577;FOXD3:0.299343646739;HLF:0.253034137309;NFIL3:0.247875662216;POU6F1:0.19377342825;PPARG:0.181084785694;ELF1,2,4:0.157234911242;CUX2:0.151659047194;FOXP1:0.150339252802;STAT5{A,B}:0.118364349087;DBP:0.111274202656;PAX4:0.102549210155;MTE{core}:0.0843819045578;GATA6:0.0704830260118;SP1:0.0676730424047;MAZ:0.0574476049822;ZFP161:0.0432753769729;BREu{core}:0.034747475777;NKX3-1:0.0288551279048;UFEwm:-0.00115933343807;SOX5:-0.00375613758848;RBPJ:-0.0136885623597;TFCP2:-0.028940951366;TFAP2{A,C}:-0.0526428295901;ARID5B:-0.059325773711;SREBF1,2:-0.0727296082073;PAX2:-0.0964500460761;FOXQ1:-0.0971982231484;SOX17:-0.0997918067386;EVI1:-0.135058742636;T:-0.136089760285;CDC5L:-0.141628942961;PAX1,9:-0.1440933795;VSX1,2:-0.14497351687;TBX4,5:-0.152203793972;RXR{A,B,G}:-0.156010726229;NFKB1_REL_RELA:-0.16415423961;KLF4:-0.165227177282;STAT2,4,6:-0.165517342186;HOXA9_MEIS1:-0.189971082165;MED-1{core}:-0.205918083093;AHR_ARNT_ARNT2:-0.214634109497;LMO2:-0.233844518225;GLI1..3:-0.235065286609;PATZ1:-0.237935863777;TEAD1:-0.259816226482;POU3F1..4:-0.261919752527;ATF5_CREB3:-0.292632998736;MTF1:-0.303324225714;HOX{A5,B5}:-0.343292041025;STAT1,3:-0.346937591822;TLX1..3_NFIC{dimer}:-0.361979596959;TAL1_TCF{3,4,12}:-0.378302518924;ATF6:-0.385324785709;FOXN1:-0.389810556209;FOSL2:-0.404244924148;BPTF:-0.41064733055;ZNF148:-0.418390428381;NFE2:-0.421036518576;ESR1:-0.444171029788;CREB1:-0.447163137058;ZNF423:-0.449556038679;IRF7:-0.455765145368;DMAP1_NCOR{1,2}_SMARC:-0.45683060099;HOX{A4,D4}:-0.459790075376;HOX{A6,A7,B6,B7}:-0.467895264854;FOXO1,3,4:-0.470025126306;IKZF2:-0.474506016029;HES1:-0.50934388326;OCT4_SOX2{dimer}:-0.509672867534;POU2F1..3:-0.51370714317;REST:-0.521637185438;NKX6-1,2:-0.539231323858;NKX2-3_NKX2-5:-0.54144901116;IRF1,2:-0.550938756496;GTF2A1,2:-0.554792862096;FOS_FOS{B,L1}_JUN{B,D}:-0.559606984292;GATA4:-0.571006511047;NFE2L2:-0.572143578382;NANOG{mouse}:-0.584195857887;BACH2:-0.596434522525;POU5F1:-0.598747557707;PAX5:-0.598789630056;NR3C1:-0.614164326561;RFX2..5_RFXANK_RFXAP:-0.625690901673;CDX1,2,4:-0.630608083756;ATF4:-0.637273290144;FOXP3:-0.638749043053;EGR1..3:-0.641133517395;ZBTB16:-0.644252011753;TBP:-0.6488505454;IKZF1:-0.654981581328;PDX1:-0.656384877817;SPI1:-0.659815756185;ATF2:-0.660971287191;SPIB:-0.66265416194;PAX8:-0.663390241483;XBP1:-0.663461946158;RREB1:-0.672884714426;ALX1:-0.676959472369;NFIX:-0.706670308976;TFAP2B:-0.738307727604;MYBL2:-0.740243696716;SRF:-0.787934317686;NHLH1,2:-0.78864316682;HSF1,2:-0.793263623152;MEF2{A,B,C,D}:-0.803685989872;RFX1:-0.842381476787;NKX2-2,8:-0.847533213266;GTF2I:-0.851049930485;JUN:-0.851634836205;HMGA1,2:-0.85549949622;HAND1,2:-0.857144696788;MYFfamily:-0.876758402729;RUNX1..3:-0.888916293547;GCM1,2:-0.891126046233;ZBTB6:-0.943957369801;CRX:-1.00956012356;ETS1,2:-1.04814527658;ZIC1..3:-1.0537545522;POU1F1:-1.0574304188;TFAP4:-1.05945828406;MAFB:-1.05979860937;NKX2-1,4:-1.06799278697;GFI1B:-1.07202974465;PRDM1:-1.0785146347;NFE2L1:-1.08347923675;ZNF384:-1.09271843507;FOX{I1,J2}:-1.1022475061;PAX6:-1.14364054218;SPZ1:-1.1457298066;EP300:-1.1475564127;MZF1:-1.21280396701;PRRX1,2:-1.26983335219;NFATC1..3:-1.28640399381;NANOG:-1.32158074644;TGIF1:-1.41415422759;ZNF238:-1.44425329126;TEF:-1.53566371064;HBP1_HMGB_SSRP1_UBTF:-1.60651166154;GZF1:-1.66471205192;TLX2:-1.74346414584;SMAD1..7,9:-1.77536123114;HIF1A:-1.79732203238;FOXL1:-1.93984636463;HMX1:-1.94158043128
}}
}}

Revision as of 14:15, 21 March 2012


Name:hepatocellular carcinoma cell line: HepG2 ENCODE, biol_rep3
Species:
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Additional information
Sample information
strainNA
tissueliver
dev stageNA
sexmale
age15
cell typehepatocyte
cell lineHepG2
companyNA
collaborationCarrie Davis (Cold spring Harbor Laboratories)
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



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)
0000255 (eukaryotic cell)
0000548 (animal cell)

DOID: Disease
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
305 (carcinoma)
4 (disease)
7 (disease of anatomical entity)

UBERON: Anatomy
0000015 (anatomical boundary)
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002100 (trunk)
0002107 (liver)
0002330 (exocrine system)
0002365 (exocrine gland)
0002368 (endocrine gland)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002530 (gland)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0003894 (liver primordium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0006235 (foregut-midgut junction)
0006925 (digestive gland)
0007026 (primitive gut)
0008835 (hepatic diverticulum)
0008836 (liver bud)
0009142 (entire embryonic mesenchyme)

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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:10820-111C1&oldid=726921"