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{{f5samples
{{f5samples
|id=FF:10610-108F7
|F5samples=
|name=small cell gastrointestinal carcinoma cell line:ECC10
|ancestors_in_anatomy_facet=
|sample_id=10610
|rna_tube_id=108F7
|rna_box=108
|rna_position=F7
|sample_cell_lot=
|sample_cell_catalog=RCB0983
|sample_company=RIKEN Bioresource centre
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=stomach
|sample_donor(cell lot)=
|sample_sex=unknown
|sample_age=unknown
|sample_ethnicity=J
|rna_rin=
|rna_od260/230=2.13
|rna_od260/280=2.13
|sample_cell_type=unclassifiable
|sample_cell_line=ECC10
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_experimental_condition=
|sample_disease=small cell gastrointestinal carcinoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=98.754
|rna_concentration=1.31672
|sample_note=
|profile_hcage=CNhs11736,LSID819,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: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=
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:162,DOID:305,DOID:3119,DOID:4
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:162,DOID:305,DOID:3119,DOID:4
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:0101120,FF:0101533
|fonse_cell_line=FF:0101120,FF:0101533
|fonse_cell_line_closure=FF:0101120,FF:0101533
|fonse_cell_line_closure=FF:0101120,FF:0101533
Line 66: Line 34:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=ONECUT1,2:3.14935770402;VSX1,2:3.14580869437;LEF1_TCF7_TCF7L1,2:2.76139589715;PITX1..3:2.50106487963;IKZF2:2.42282378477;BPTF:2.30279448467;NANOG:2.15727535231;POU6F1:2.00476787876;SOX{8,9,10}:1.83407093294;TEF:1.78244042092;RREB1:1.78038289067;ZBTB16:1.77148711479;FOXP1:1.75504310739;YY1:1.74327808963;RFX2..5_RFXANK_RFXAP:1.73465904265;GATA4:1.68843110377;HOX{A6,A7,B6,B7}:1.67445397745;FOXM1:1.57393569697;TOPORS:1.57080561851;XCPE1{core}:1.56553941665;NFY{A,B,C}:1.54847330889;ZNF143:1.49689900131;EN1,2:1.46308064267;SNAI1..3:1.45970826161;SP1:1.45358440132;POU1F1:1.44300940079;MED-1{core}:1.42853189097;GFI1:1.41556608509;RFX1:1.40441444951;E2F1..5:1.39303344561;NRF1:1.36450481898;FOXD3:1.35993098313;ZEB1:1.33687774892;LMO2:1.33627123575;LHX3,4:1.32817596576;NKX6-1,2:1.28919868928;PAX8:1.26223967203;ARID5B:1.24528927762;ZFP161:1.21068669216;ATF4:1.19098052618;NKX2-3_NKX2-5:1.12154145678;ELK1,4_GABP{A,B1}:1.09650879339;PAX1,9:1.08649934613;SOX2:1.04699879911;PATZ1:1.01339795102;FOXL1:1.00075728813;CDC5L:0.919602578194;T:0.853064468532;TFAP2B:0.853006276794;CUX2:0.808085980655;RORA:0.751221450157;AIRE:0.744745031871;FOX{F1,F2,J1}:0.738763737935;ATF5_CREB3:0.722330657934;BREu{core}:0.709946164234;EVI1:0.709552144122;NKX3-1:0.708993058548;RBPJ:0.698966255162;ESRRA:0.66242798038;TFDP1:0.6555520903;ZBTB6:0.642150821944;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.635666973705;FOXO1,3,4:0.596249527017;MTE{core}:0.57950450796;HOX{A4,D4}:0.579469753594;STAT1,3:0.559980860116;HBP1_HMGB_SSRP1_UBTF:0.551765608255;CREB1:0.54606057077;MAZ:0.545438050675;ADNP_IRX_SIX_ZHX:0.544936464859;DBP:0.52798836292;REST:0.499745504424;ATF2:0.481739083566;TAL1_TCF{3,4,12}:0.472605692049;PBX1:0.456586925719;KLF4:0.448503853083;EGR1..3:0.445041943353;SOX17:0.415822875993;FOX{I1,J2}:0.413331714051;PRDM1:0.409647093256;MYB:0.378085472245;PRRX1,2:0.375873564212;POU5F1:0.367776761061;FOX{D1,D2}:0.365422398238;MZF1:0.334237309821;PAX5:0.333861243851;bHLH_family:0.316558638762;JUN:0.305555875232;PAX4:0.280826868094;NHLH1,2:0.266713694703;NFE2L1:0.244598033962;PAX3,7:0.225088062961;SOX5:0.219479571469;PDX1:0.19056464758;TLX2:0.149919686264;FOXA2:0.148753341219;HIC1:0.118488442312;UFEwm:0.116636796323;ZIC1..3:0.0977617094267;MYFfamily:0.0872202303822;MTF1:0.0807465775581;GTF2I:0.0609911799368;MYOD1:0.0605215343894;NR5A1,2:0.0603723426738;FOXN1:0.0307856648495;POU2F1..3:0.0176771026473;CDX1,2,4:-0.0105837785596;TLX1..3_NFIC{dimer}:-0.014314337329;ALX1:-0.0461875649459;SREBF1,2:-0.0809987502003;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.101321826055;ZNF423:-0.138135491616;FOXQ1:-0.191857368386;NKX2-1,4:-0.206268169761;NFIX:-0.26217465806;RXR{A,B,G}:-0.308213681522;HNF1A:-0.353889745653;GFI1B:-0.367265875681;SPIB:-0.368315055874;CRX:-0.382567907527;TFAP2{A,C}:-0.39776344525;STAT5{A,B}:-0.416810118886;HNF4A_NR2F1,2:-0.440712950744;AHR_ARNT_ARNT2:-0.455344343825;GATA6:-0.463250307086;NFE2:-0.499915620295;TBP:-0.504531753443;ZNF384:-0.517530276091;PAX2:-0.518386687333;HOX{A5,B5}:-0.525311754478;NR1H4:-0.529377277906;GZF1:-0.567282053128;OCT4_SOX2{dimer}:-0.571874564354;TFCP2:-0.575994240946;TP53:-0.580047829349;GTF2A1,2:-0.604444327384;ZNF148:-0.621775644493;HSF1,2:-0.631081226631;SPI1:-0.650456741844;RXRA_VDR{dimer}:-0.660387784649;RUNX1..3:-0.679476655985;EP300:-0.684286344887;MEF2{A,B,C,D}:-0.707217277871;BACH2:-0.715847642284;TGIF1:-0.734651362412;FOSL2:-0.745585904365;HAND1,2:-0.746635181305;ESR1:-0.748740412101;FOS_FOS{B,L1}_JUN{B,D}:-0.750186227972;ELF1,2,4:-0.757872329126;MYBL2:-0.766558457532;AR:-0.77429588698;NFKB1_REL_RELA:-0.789356758201;HOXA9_MEIS1:-0.800731259036;MAFB:-0.801693277092;EBF1:-0.801925520262;FOXP3:-0.815382141235;ZNF238:-0.849149320851;XBP1:-0.851179562676;DMAP1_NCOR{1,2}_SMARC:-0.894168618892;SRF:-0.903643270106;ALX4:-0.926938503661;POU3F1..4:-1.0175601788;IKZF1:-1.03183990274;CEBPA,B_DDIT3:-1.04869406452;HLF:-1.10706088775;NKX2-2,8:-1.12777896598;NR6A1:-1.15294411704;HMGA1,2:-1.17953170577;TEAD1:-1.18900145662;NKX3-2:-1.23618422357;NFIL3:-1.25353890389;PAX6:-1.33768851632;NANOG{mouse}:-1.38124047891;PPARG:-1.38482795816;ETS1,2:-1.40183204533;HIF1A:-1.46289007647;IRF7:-1.47124071993;IRF1,2:-1.47213334592;ATF6:-1.4972477308;SPZ1:-1.52802403775;TFAP4:-1.5476769454;NR3C1:-1.56229465657;GLI1..3:-1.56846961692;GCM1,2:-1.56925032108;SMAD1..7,9:-1.7775044852;NFE2L2:-1.8644028415;STAT2,4,6:-1.86606202685;HES1:-1.99180081341;NFATC1..3:-2.27422582727;TBX4,5:-2.27765278209;HMX1:-2.33513621681
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10610-108F7
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100297;;FF:0101533
|is_a=EFO:0002091;;FF:0000003;;FF:0000210;;FF:0100297;;FF:0101533
|name=small cell gastrointestinal carcinoma cell line:ECC10
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11736,LSID819,release009,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=108
|rna_catalog_number=
|rna_concentration=1.31672
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=2.13
|rna_od260/280=2.13
|rna_position=F7
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=108F7
|rna_weight_ug=98.754
|sample_age=unknown
|sample_cell_catalog=RCB0983
|sample_cell_line=ECC10
|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=small cell gastrointestinal carcinoma
|sample_donor(cell lot)=
|sample_ethnicity=J
|sample_experimental_condition=
|sample_id=10610
|sample_note=
|sample_sex=unknown
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=stomach
|top_motifs=ONECUT1,2:3.14935770402;VSX1,2:3.14580869437;LEF1_TCF7_TCF7L1,2:2.76139589715;PITX1..3:2.50106487963;IKZF2:2.42282378477;BPTF:2.30279448467;NANOG:2.15727535231;POU6F1:2.00476787876;SOX{8,9,10}:1.83407093294;TEF:1.78244042092;RREB1:1.78038289067;ZBTB16:1.77148711479;FOXP1:1.75504310739;YY1:1.74327808963;RFX2..5_RFXANK_RFXAP:1.73465904265;GATA4:1.68843110377;HOX{A6,A7,B6,B7}:1.67445397745;FOXM1:1.57393569697;TOPORS:1.57080561851;XCPE1{core}:1.56553941665;NFY{A,B,C}:1.54847330889;ZNF143:1.49689900131;EN1,2:1.46308064267;SNAI1..3:1.45970826161;SP1:1.45358440132;POU1F1:1.44300940079;MED-1{core}:1.42853189097;GFI1:1.41556608509;RFX1:1.40441444951;E2F1..5:1.39303344561;NRF1:1.36450481898;FOXD3:1.35993098313;ZEB1:1.33687774892;LMO2:1.33627123575;LHX3,4:1.32817596576;NKX6-1,2:1.28919868928;PAX8:1.26223967203;ARID5B:1.24528927762;ZFP161:1.21068669216;ATF4:1.19098052618;NKX2-3_NKX2-5:1.12154145678;ELK1,4_GABP{A,B1}:1.09650879339;PAX1,9:1.08649934613;SOX2:1.04699879911;PATZ1:1.01339795102;FOXL1:1.00075728813;CDC5L:0.919602578194;T:0.853064468532;TFAP2B:0.853006276794;CUX2:0.808085980655;RORA:0.751221450157;AIRE:0.744745031871;FOX{F1,F2,J1}:0.738763737935;ATF5_CREB3:0.722330657934;BREu{core}:0.709946164234;EVI1:0.709552144122;NKX3-1:0.708993058548;RBPJ:0.698966255162;ESRRA:0.66242798038;TFDP1:0.6555520903;ZBTB6:0.642150821944;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.635666973705;FOXO1,3,4:0.596249527017;MTE{core}:0.57950450796;HOX{A4,D4}:0.579469753594;STAT1,3:0.559980860116;HBP1_HMGB_SSRP1_UBTF:0.551765608255;CREB1:0.54606057077;MAZ:0.545438050675;ADNP_IRX_SIX_ZHX:0.544936464859;DBP:0.52798836292;REST:0.499745504424;ATF2:0.481739083566;TAL1_TCF{3,4,12}:0.472605692049;PBX1:0.456586925719;KLF4:0.448503853083;EGR1..3:0.445041943353;SOX17:0.415822875993;FOX{I1,J2}:0.413331714051;PRDM1:0.409647093256;MYB:0.378085472245;PRRX1,2:0.375873564212;POU5F1:0.367776761061;FOX{D1,D2}:0.365422398238;MZF1:0.334237309821;PAX5:0.333861243851;bHLH_family:0.316558638762;JUN:0.305555875232;PAX4:0.280826868094;NHLH1,2:0.266713694703;NFE2L1:0.244598033962;PAX3,7:0.225088062961;SOX5:0.219479571469;PDX1:0.19056464758;TLX2:0.149919686264;FOXA2:0.148753341219;HIC1:0.118488442312;UFEwm:0.116636796323;ZIC1..3:0.0977617094267;MYFfamily:0.0872202303822;MTF1:0.0807465775581;GTF2I:0.0609911799368;MYOD1:0.0605215343894;NR5A1,2:0.0603723426738;FOXN1:0.0307856648495;POU2F1..3:0.0176771026473;CDX1,2,4:-0.0105837785596;TLX1..3_NFIC{dimer}:-0.014314337329;ALX1:-0.0461875649459;SREBF1,2:-0.0809987502003;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.101321826055;ZNF423:-0.138135491616;FOXQ1:-0.191857368386;NKX2-1,4:-0.206268169761;NFIX:-0.26217465806;RXR{A,B,G}:-0.308213681522;HNF1A:-0.353889745653;GFI1B:-0.367265875681;SPIB:-0.368315055874;CRX:-0.382567907527;TFAP2{A,C}:-0.39776344525;STAT5{A,B}:-0.416810118886;HNF4A_NR2F1,2:-0.440712950744;AHR_ARNT_ARNT2:-0.455344343825;GATA6:-0.463250307086;NFE2:-0.499915620295;TBP:-0.504531753443;ZNF384:-0.517530276091;PAX2:-0.518386687333;HOX{A5,B5}:-0.525311754478;NR1H4:-0.529377277906;GZF1:-0.567282053128;OCT4_SOX2{dimer}:-0.571874564354;TFCP2:-0.575994240946;TP53:-0.580047829349;GTF2A1,2:-0.604444327384;ZNF148:-0.621775644493;HSF1,2:-0.631081226631;SPI1:-0.650456741844;RXRA_VDR{dimer}:-0.660387784649;RUNX1..3:-0.679476655985;EP300:-0.684286344887;MEF2{A,B,C,D}:-0.707217277871;BACH2:-0.715847642284;TGIF1:-0.734651362412;FOSL2:-0.745585904365;HAND1,2:-0.746635181305;ESR1:-0.748740412101;FOS_FOS{B,L1}_JUN{B,D}:-0.750186227972;ELF1,2,4:-0.757872329126;MYBL2:-0.766558457532;AR:-0.77429588698;NFKB1_REL_RELA:-0.789356758201;HOXA9_MEIS1:-0.800731259036;MAFB:-0.801693277092;EBF1:-0.801925520262;FOXP3:-0.815382141235;ZNF238:-0.849149320851;XBP1:-0.851179562676;DMAP1_NCOR{1,2}_SMARC:-0.894168618892;SRF:-0.903643270106;ALX4:-0.926938503661;POU3F1..4:-1.0175601788;IKZF1:-1.03183990274;CEBPA,B_DDIT3:-1.04869406452;HLF:-1.10706088775;NKX2-2,8:-1.12777896598;NR6A1:-1.15294411704;HMGA1,2:-1.17953170577;TEAD1:-1.18900145662;NKX3-2:-1.23618422357;NFIL3:-1.25353890389;PAX6:-1.33768851632;NANOG{mouse}:-1.38124047891;PPARG:-1.38482795816;ETS1,2:-1.40183204533;HIF1A:-1.46289007647;IRF7:-1.47124071993;IRF1,2:-1.47213334592;ATF6:-1.4972477308;SPZ1:-1.52802403775;TFAP4:-1.5476769454;NR3C1:-1.56229465657;GLI1..3:-1.56846961692;GCM1,2:-1.56925032108;SMAD1..7,9:-1.7775044852;NFE2L2:-1.8644028415;STAT2,4,6:-1.86606202685;HES1:-1.99180081341;NFATC1..3:-2.27422582727;TBX4,5:-2.27765278209;HMX1:-2.33513621681
}}
}}

Revision as of 14:11, 21 March 2012


Name:small cell gastrointestinal carcinoma cell line:ECC10
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuestomach
dev stageNA
sexunknown
ageunknown
cell typeunclassifiable
cell lineECC10
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: CNhs11736



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: CNhs11736



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: CNhs11736


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
0050686 (organ system cancer)
0050687 (cell type cancer)
14566 (disease of cellular proliferation)
162 (cancer)
305 (carcinoma)
3119 (gastrointestinal system cancer)
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

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