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{{f5samples
{{f5samples
|id=FF:10492-107B6
|F5samples=
|name=transitional-cell carcinoma cell line:JMSU1
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000119,UBERON:0000465,UBERON:0000468,UBERON:0000479,UBERON:0000483,UBERON:0000486,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0004119,UBERON:0005423,UBERON:0005910,UBERON:0005911
|sample_id=10492
|rna_tube_id=107B6
|rna_box=107
|rna_position=B6
|sample_cell_lot=
|sample_cell_catalog=RCB2227
|sample_company=RIKEN Bioresource centre
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=bladder
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=75
|sample_ethnicity=unknown
|rna_rin=
|rna_od260/230=2.06
|rna_od260/280=2.07
|sample_cell_type=unclassifiable
|sample_cell_line=JMSU1
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_experimental_condition=
|sample_disease=transitional-cell carcinoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=49.59375
|rna_concentration=1.98375
|sample_note=
|profile_hcage=CNhs11261,LSID758,release008,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:0000061,UBERON:0000119,UBERON:0000465,UBERON:0000468,UBERON:0000479,UBERON:0000483,UBERON:0000486,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0004119,UBERON:0005423,UBERON:0005910,UBERON:0005911
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,DOID:305,DOID:4
|ancestors_in_disease_facet=DOID:0050687,DOID:14566,DOID:162,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=HIF1A:2.07117755363;bHLH_family:1.97317584864;NKX2-1,4:1.83752597816;PITX1..3:1.82771282409;FOXQ1:1.75164944084;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.48510085906;E2F1..5:1.35523424264;MYB:1.35090401408;AIRE:1.2301506833;NKX6-1,2:1.15225074608;NKX3-1:1.12627029136;ZNF384:1.03066465365;FOXP1:1.01862918748;PDX1:0.983695344002;NFY{A,B,C}:0.970026747997;PPARG:0.954037696546;CDX1,2,4:0.915563389541;NKX2-2,8:0.836745354092;BREu{core}:0.83660251887;ZBTB16:0.690066311784;HBP1_HMGB_SSRP1_UBTF:0.680354694868;ELK1,4_GABP{A,B1}:0.667500230729;CDC5L:0.663343933415;IRF7:0.652070474381;TFDP1:0.622429171331;NRF1:0.585096058815;AHR_ARNT_ARNT2:0.581653769529;GFI1:0.574599888878;PAX3,7:0.574170945224;TEF:0.573329043052;MYOD1:0.571201323198;ARID5B:0.569502080707;FOXA2:0.539427014254;EVI1:0.523840797813;YY1:0.502217115135;ZNF143:0.490673606529;LHX3,4:0.47750981808;TEAD1:0.474589759014;FOXD3:0.465765649662;PBX1:0.44861467548;SP1:0.447806016695;HOXA9_MEIS1:0.404675919759;TAL1_TCF{3,4,12}:0.403865776003;HOX{A4,D4}:0.397145901006;IRF1,2:0.370735909172;NKX3-2:0.353240007434;TBX4,5:0.344756583188;FOXM1:0.321628287897;STAT5{A,B}:0.314285277762;FOXN1:0.313370122308;HSF1,2:0.302180920538;ZFP161:0.29957883493;NFKB1_REL_RELA:0.285679045705;UFEwm:0.273126196484;ZIC1..3:0.269307266086;XBP1:0.254828065436;POU1F1:0.247427763311;ATF5_CREB3:0.240414972835;HES1:0.217238451479;PAX4:0.201419211644;RREB1:0.196491238022;NR6A1:0.192384447429;EN1,2:0.183192156321;POU3F1..4:0.178423237935;HNF4A_NR2F1,2:0.177347528903;CEBPA,B_DDIT3:0.174926981114;KLF4:0.170258052237;RFX1:0.147976477939;ADNP_IRX_SIX_ZHX:0.141767331015;SNAI1..3:0.134620629763;FOS_FOS{B,L1}_JUN{B,D}:0.134483709571;FOXL1:0.129140870356;RXRA_VDR{dimer}:0.125070005735;ZBTB6:0.115393715041;CUX2:0.107127425453;RBPJ:0.0925240537995;RXR{A,B,G}:0.0898039987668;GFI1B:0.0794786450709;ONECUT1,2:0.0792565074716;FOXO1,3,4:0.0643732485212;IKZF2:0.0583683968026;FOXP3:0.0546083304683;SREBF1,2:0.0371281495484;DMAP1_NCOR{1,2}_SMARC:0.0309271361938;MZF1:0.0259682231547;ATF4:0.000175594846128;EBF1:-0.00238297117965;GTF2A1,2:-0.00639818273022;TOPORS:-0.0127722961734;PAX8:-0.0247688347448;MTF1:-0.0280089635862;BPTF:-0.028594718048;FOX{D1,D2}:-0.0297108988283;BACH2:-0.0297622667543;TBP:-0.0366415741001;GATA4:-0.0440576478132;ZNF148:-0.049285665736;FOSL2:-0.0514971318227;NFE2:-0.0625489091837;TLX2:-0.0654779516967;STAT2,4,6:-0.0703873538637;HOX{A5,B5}:-0.0749198584648;HOX{A6,A7,B6,B7}:-0.0790566557842;LMO2:-0.0927152778947;EP300:-0.107962271245;T:-0.116067346583;TLX1..3_NFIC{dimer}:-0.130761324543;MEF2{A,B,C,D}:-0.136396319818;TFAP2{A,C}:-0.151973025786;HLF:-0.153271625392;RUNX1..3:-0.161733412249;DBP:-0.172041878855;POU5F1:-0.176797872444;NR3C1:-0.177775280255;CRX:-0.183590513012;PATZ1:-0.184996707509;CREB1:-0.187972163951;NR1H4:-0.202158969107;HNF1A:-0.218374043621;RFX2..5_RFXANK_RFXAP:-0.230789554531;MED-1{core}:-0.2351415792;ALX1:-0.237978732238;POU2F1..3:-0.24157097285;SOX17:-0.242212064653;FOX{I1,J2}:-0.246567636517;XCPE1{core}:-0.267332946895;MAZ:-0.271557268437;TFAP2B:-0.27961600147;ZEB1:-0.28085456009;ZNF423:-0.284332695714;PAX5:-0.289434227218;ALX4:-0.290224781166;HIC1:-0.291078025915;LEF1_TCF7_TCF7L1,2:-0.294457009238;POU6F1:-0.298980422259;RORA:-0.300833617994;GTF2I:-0.303226692338;ELF1,2,4:-0.304154768259;NFE2L2:-0.312925378004;PAX1,9:-0.315764980437;MYBL2:-0.318898333599;ATF2:-0.323320883926;GZF1:-0.32774959833;NKX2-3_NKX2-5:-0.33081842122;NFIX:-0.334663184373;SOX5:-0.335640677952;SRF:-0.339409536108;PRDM1:-0.35302336497;FOX{F1,F2,J1}:-0.365027646002;PRRX1,2:-0.365642073737;TP53:-0.368589731144;MYFfamily:-0.36886997195;REST:-0.381522529861;OCT4_SOX2{dimer}:-0.389859199863;MTE{core}:-0.396423092219;NR5A1,2:-0.411185165679;ATF6:-0.421438793875;ESR1:-0.439601203753;PAX6:-0.493752658875;PAX2:-0.495161462166;IKZF1:-0.498081838604;SPIB:-0.506587600494;ESRRA:-0.507492138385;NANOG:-0.510368513569;HMGA1,2:-0.526822199576;MAFB:-0.528391510211;GLI1..3:-0.586056105326;SPI1:-0.635907513;TFCP2:-0.641165789239;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.670048340134;STAT1,3:-0.67272905764;NHLH1,2:-0.679165606217;GATA6:-0.711256230414;SOX{8,9,10}:-0.720830922755;HAND1,2:-0.798129006678;ETS1,2:-0.845709791156;NFE2L1:-0.865229141237;NFATC1..3:-0.871611522362;VSX1,2:-0.8738693268;JUN:-0.901183481395;NFIL3:-1.05180094055;GCM1,2:-1.05255939261;EGR1..3:-1.06036560375;SOX2:-1.18058680782;AR:-1.18571007094;ZNF238:-1.20353697584;TFAP4:-1.22980667054;TGIF1:-1.32247842907;NANOG{mouse}:-1.38971323245;HMX1:-1.55180752939;SMAD1..7,9:-1.88379582268;SPZ1:-1.99815042805
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10492-107B6
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102869
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102869
|name=transitional-cell carcinoma cell line:JMSU1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11261,LSID758,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=107
|rna_catalog_number=
|rna_concentration=1.98375
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.06
|rna_od260/280=2.07
|rna_position=B6
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=107B6
|rna_weight_ug=49.59375
|sample_age=75
|sample_cell_catalog=RCB2227
|sample_cell_line=JMSU1
|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=transitional-cell carcinoma
|sample_donor(cell lot)=
|sample_ethnicity=unknown
|sample_experimental_condition=
|sample_id=10492
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=bladder
|top_motifs=HIF1A:2.07117755363;bHLH_family:1.97317584864;NKX2-1,4:1.83752597816;PITX1..3:1.82771282409;FOXQ1:1.75164944084;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.48510085906;E2F1..5:1.35523424264;MYB:1.35090401408;AIRE:1.2301506833;NKX6-1,2:1.15225074608;NKX3-1:1.12627029136;ZNF384:1.03066465365;FOXP1:1.01862918748;PDX1:0.983695344002;NFY{A,B,C}:0.970026747997;PPARG:0.954037696546;CDX1,2,4:0.915563389541;NKX2-2,8:0.836745354092;BREu{core}:0.83660251887;ZBTB16:0.690066311784;HBP1_HMGB_SSRP1_UBTF:0.680354694868;ELK1,4_GABP{A,B1}:0.667500230729;CDC5L:0.663343933415;IRF7:0.652070474381;TFDP1:0.622429171331;NRF1:0.585096058815;AHR_ARNT_ARNT2:0.581653769529;GFI1:0.574599888878;PAX3,7:0.574170945224;TEF:0.573329043052;MYOD1:0.571201323198;ARID5B:0.569502080707;FOXA2:0.539427014254;EVI1:0.523840797813;YY1:0.502217115135;ZNF143:0.490673606529;LHX3,4:0.47750981808;TEAD1:0.474589759014;FOXD3:0.465765649662;PBX1:0.44861467548;SP1:0.447806016695;HOXA9_MEIS1:0.404675919759;TAL1_TCF{3,4,12}:0.403865776003;HOX{A4,D4}:0.397145901006;IRF1,2:0.370735909172;NKX3-2:0.353240007434;TBX4,5:0.344756583188;FOXM1:0.321628287897;STAT5{A,B}:0.314285277762;FOXN1:0.313370122308;HSF1,2:0.302180920538;ZFP161:0.29957883493;NFKB1_REL_RELA:0.285679045705;UFEwm:0.273126196484;ZIC1..3:0.269307266086;XBP1:0.254828065436;POU1F1:0.247427763311;ATF5_CREB3:0.240414972835;HES1:0.217238451479;PAX4:0.201419211644;RREB1:0.196491238022;NR6A1:0.192384447429;EN1,2:0.183192156321;POU3F1..4:0.178423237935;HNF4A_NR2F1,2:0.177347528903;CEBPA,B_DDIT3:0.174926981114;KLF4:0.170258052237;RFX1:0.147976477939;ADNP_IRX_SIX_ZHX:0.141767331015;SNAI1..3:0.134620629763;FOS_FOS{B,L1}_JUN{B,D}:0.134483709571;FOXL1:0.129140870356;RXRA_VDR{dimer}:0.125070005735;ZBTB6:0.115393715041;CUX2:0.107127425453;RBPJ:0.0925240537995;RXR{A,B,G}:0.0898039987668;GFI1B:0.0794786450709;ONECUT1,2:0.0792565074716;FOXO1,3,4:0.0643732485212;IKZF2:0.0583683968026;FOXP3:0.0546083304683;SREBF1,2:0.0371281495484;DMAP1_NCOR{1,2}_SMARC:0.0309271361938;MZF1:0.0259682231547;ATF4:0.000175594846128;EBF1:-0.00238297117965;GTF2A1,2:-0.00639818273022;TOPORS:-0.0127722961734;PAX8:-0.0247688347448;MTF1:-0.0280089635862;BPTF:-0.028594718048;FOX{D1,D2}:-0.0297108988283;BACH2:-0.0297622667543;TBP:-0.0366415741001;GATA4:-0.0440576478132;ZNF148:-0.049285665736;FOSL2:-0.0514971318227;NFE2:-0.0625489091837;TLX2:-0.0654779516967;STAT2,4,6:-0.0703873538637;HOX{A5,B5}:-0.0749198584648;HOX{A6,A7,B6,B7}:-0.0790566557842;LMO2:-0.0927152778947;EP300:-0.107962271245;T:-0.116067346583;TLX1..3_NFIC{dimer}:-0.130761324543;MEF2{A,B,C,D}:-0.136396319818;TFAP2{A,C}:-0.151973025786;HLF:-0.153271625392;RUNX1..3:-0.161733412249;DBP:-0.172041878855;POU5F1:-0.176797872444;NR3C1:-0.177775280255;CRX:-0.183590513012;PATZ1:-0.184996707509;CREB1:-0.187972163951;NR1H4:-0.202158969107;HNF1A:-0.218374043621;RFX2..5_RFXANK_RFXAP:-0.230789554531;MED-1{core}:-0.2351415792;ALX1:-0.237978732238;POU2F1..3:-0.24157097285;SOX17:-0.242212064653;FOX{I1,J2}:-0.246567636517;XCPE1{core}:-0.267332946895;MAZ:-0.271557268437;TFAP2B:-0.27961600147;ZEB1:-0.28085456009;ZNF423:-0.284332695714;PAX5:-0.289434227218;ALX4:-0.290224781166;HIC1:-0.291078025915;LEF1_TCF7_TCF7L1,2:-0.294457009238;POU6F1:-0.298980422259;RORA:-0.300833617994;GTF2I:-0.303226692338;ELF1,2,4:-0.304154768259;NFE2L2:-0.312925378004;PAX1,9:-0.315764980437;MYBL2:-0.318898333599;ATF2:-0.323320883926;GZF1:-0.32774959833;NKX2-3_NKX2-5:-0.33081842122;NFIX:-0.334663184373;SOX5:-0.335640677952;SRF:-0.339409536108;PRDM1:-0.35302336497;FOX{F1,F2,J1}:-0.365027646002;PRRX1,2:-0.365642073737;TP53:-0.368589731144;MYFfamily:-0.36886997195;REST:-0.381522529861;OCT4_SOX2{dimer}:-0.389859199863;MTE{core}:-0.396423092219;NR5A1,2:-0.411185165679;ATF6:-0.421438793875;ESR1:-0.439601203753;PAX6:-0.493752658875;PAX2:-0.495161462166;IKZF1:-0.498081838604;SPIB:-0.506587600494;ESRRA:-0.507492138385;NANOG:-0.510368513569;HMGA1,2:-0.526822199576;MAFB:-0.528391510211;GLI1..3:-0.586056105326;SPI1:-0.635907513;TFCP2:-0.641165789239;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.670048340134;STAT1,3:-0.67272905764;NHLH1,2:-0.679165606217;GATA6:-0.711256230414;SOX{8,9,10}:-0.720830922755;HAND1,2:-0.798129006678;ETS1,2:-0.845709791156;NFE2L1:-0.865229141237;NFATC1..3:-0.871611522362;VSX1,2:-0.8738693268;JUN:-0.901183481395;NFIL3:-1.05180094055;GCM1,2:-1.05255939261;EGR1..3:-1.06036560375;SOX2:-1.18058680782;AR:-1.18571007094;ZNF238:-1.20353697584;TFAP4:-1.22980667054;TGIF1:-1.32247842907;NANOG{mouse}:-1.38971323245;HMX1:-1.55180752939;SMAD1..7,9:-1.88379582268;SPZ1:-1.99815042805
}}
}}

Revision as of 14:08, 21 March 2012


Name:transitional-cell carcinoma cell line:JMSU1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebladder
dev stageNA
sexmale
age75
cell typeunclassifiable
cell lineJMSU1
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: CNhs11261



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: CNhs11261



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: CNhs11261


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)

UBERON: Anatomy
0000061 (anatomical structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000479 (tissue)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0005423 (developing anatomical structure)
0005910 (transitional epithelium)
0005911 (endo-epithelium)

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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