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{{f5samples
{{f5samples
|id=FF:10077-102A5
|ancestors_in_anatomy_facet=UBERON:0000029,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0001062,UBERON:0002193,UBERON:0002405,UBERON:0002465,UBERON:0007023
|name=lymph node, adult, donor1
|sample_id=10077
|rna_tube_id=102A5
|rna_box=102
|rna_position=A5
|sample_cell_lot=NA
|sample_cell_catalog=NA
|sample_company=Ambion
|rna_lot_number=8060051
|rna_catalog_number=Cat:AM7894
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=30 years old adult
|sample_tissue=lymph node
|sample_donor(cell lot)=1
|sample_sex=male
|sample_age=
|sample_ethnicity=C
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=normal
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-ToTALLY-RNA-v1.0
|rna_weight_ug=50
|rna_concentration=1
|sample_note=
|profile_hcage=CNhs11788,LSID820,release009,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000029,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0001062,UBERON:0002193,UBERON:0002405,UBERON:0002465,UBERON:0007023
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=POU5F1:2.01834602736;POU2F1..3:1.897519883;SPZ1:1.7640012877;AIRE:1.63907917516;GATA4:1.62188350623;ETS1,2:1.50558849082;SPIB:1.48436970767;RXRA_VDR{dimer}:1.45561299243;FOXD3:1.43042707736;IKZF2:1.4152215341;IRF1,2:1.40812329154;ELF1,2,4:1.39615330395;SPI1:1.29054507525;TFAP4:1.26227545567;IRF7:1.2447089488;NFATC1..3:1.17533633051;AR:1.16269517551;TLX2:1.15002923632;STAT1,3:1.06597725677;T:1.0230633541;RUNX1..3:0.98770885643;RBPJ:0.955238278751;DMAP1_NCOR{1,2}_SMARC:0.884447296815;FOXO1,3,4:0.87884287215;BPTF:0.852191751102;MYFfamily:0.84261376297;NR1H4:0.840535219156;STAT2,4,6:0.831137784084;HNF4A_NR2F1,2:0.819634336269;FOX{D1,D2}:0.816380126829;SMAD1..7,9:0.816053421739;MTF1:0.788028216164;ZNF384:0.746192659038;PATZ1:0.735994117238;PRDM1:0.668653481814;FOXA2:0.653351266322;TFCP2:0.64702179794;BREu{core}:0.646573198406;PAX3,7:0.615647485292;GCM1,2:0.606618064072;HMX1:0.601584586118;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.600454003654;NKX6-1,2:0.579984225498;TGIF1:0.534506526372;TOPORS:0.515114164102;SREBF1,2:0.483747866619;MZF1:0.457526377355;SRF:0.444235475403;EP300:0.429602872304;XCPE1{core}:0.403093599691;ESR1:0.380784971966;EN1,2:0.369279056036;GATA6:0.361078855219;LMO2:0.357887098035;NKX3-2:0.314618520822;ZBTB16:0.303917918358;TBP:0.303533337876;EGR1..3:0.285317857139;ALX1:0.265818331078;MTE{core}:0.253949427835;TFAP2{A,C}:0.237809480007;SP1:0.22210150924;RREB1:0.214088280942;HAND1,2:0.203362437434;CDX1,2,4:0.200343270039;ZEB1:0.198784240756;EBF1:0.190418229325;FOX{F1,F2,J1}:0.179821716293;TEF:0.168220335147;CEBPA,B_DDIT3:0.150061903297;SNAI1..3:0.125169970793;HIF1A:0.122886227633;MYOD1:0.119332602656;MED-1{core}:0.110457692191;NR6A1:0.105798555552;PITX1..3:0.0992563960776;FOXP3:0.0973601707294;EVI1:0.0942499262344;MAZ:0.0866782487844;NANOG{mouse}:0.0786790001584;CRX:0.0637564921628;NR3C1:0.0560206483222;FOXP1:0.0428078910017;TFAP2B:0.0382235405524;GZF1:0.0361640600132;SOX5:0.0113210386535;KLF4:-0.0043920240724;NFKB1_REL_RELA:-0.00592377392409;ALX4:-0.017586104597;ZFP161:-0.0335147943783;NR5A1,2:-0.035057984518;MAFB:-0.0436461049361;HMGA1,2:-0.0479979557375;GFI1B:-0.0888065984712;GTF2I:-0.0913270029585;PAX6:-0.0955031032286;LHX3,4:-0.107955558023;GLI1..3:-0.112192094485;POU6F1:-0.117795137736;ZNF148:-0.128923816106;PAX5:-0.130880347598;HIC1:-0.140666266302;ATF6:-0.144986074917;IKZF1:-0.178262784177;AHR_ARNT_ARNT2:-0.186189797116;UFEwm:-0.198773458079;ZNF423:-0.202269414291;OCT4_SOX2{dimer}:-0.2137709928;ATF2:-0.256511832505;TLX1..3_NFIC{dimer}:-0.268455576419;NFIL3:-0.271196306562;HNF1A:-0.278663387891;TAL1_TCF{3,4,12}:-0.290227139284;ATF4:-0.329027970745;REST:-0.343570419609;RXR{A,B,G}:-0.361225534464;ZNF238:-0.36235000287;PPARG:-0.391626838195;ADNP_IRX_SIX_ZHX:-0.426066054943;CREB1:-0.451199621571;HES1:-0.468243294498;LEF1_TCF7_TCF7L1,2:-0.474103720337;VSX1,2:-0.479387294941;RFX2..5_RFXANK_RFXAP:-0.490274638925;PAX2:-0.535650997891;MEF2{A,B,C,D}:-0.539163924166;HLF:-0.547452609723;NFE2L1:-0.568041966493;DBP:-0.612664881829;ATF5_CREB3:-0.61726129727;NFE2L2:-0.620138997294;GTF2A1,2:-0.622316459456;NHLH1,2:-0.630278720051;HBP1_HMGB_SSRP1_UBTF:-0.650865672468;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.660581123005;NFY{A,B,C}:-0.680965934756;YY1:-0.694360847594;FOXN1:-0.697885057068;SOX2:-0.702209203817;TFDP1:-0.704945880004;TEAD1:-0.711836077872;ZNF143:-0.717909490183;CUX2:-0.71976054987;E2F1..5:-0.74634415564;FOX{I1,J2}:-0.747193167653;NKX2-3_NKX2-5:-0.760405228841;POU1F1:-0.772687977315;FOXL1:-0.779108462809;PAX1,9:-0.786074884251;FOXQ1:-0.789075640626;MYBL2:-0.813589955819;FOS_FOS{B,L1}_JUN{B,D}:-0.838405698642;NFE2:-0.848985971919;SOX{8,9,10}:-0.862131913841;NKX2-2,8:-0.863920331795;MYB:-0.866039712997;SOX17:-0.900385670638;RORA:-0.914264958916;ZBTB6:-0.921976877101;NKX2-1,4:-0.925608820732;PBX1:-0.931750778254;JUN:-0.934185248077;BACH2:-0.948567084385;ELK1,4_GABP{A,B1}:-0.949089191928;STAT5{A,B}:-0.950866097982;FOXM1:-0.951280161065;XBP1:-0.9695278933;NRF1:-0.986228069917;FOSL2:-1.02862769676;HOX{A4,D4}:-1.03962135623;bHLH_family:-1.0461548323;POU3F1..4:-1.04781315883;PRRX1,2:-1.1174605262;GFI1:-1.15594362719;ZIC1..3:-1.15950985941;HOX{A6,A7,B6,B7}:-1.20981480483;PDX1:-1.25458246678;TP53:-1.26243351672;CDC5L:-1.29277566681;HOX{A5,B5}:-1.32452206548;NANOG:-1.33994876445;RFX1:-1.47258944438;ARID5B:-1.48445243127;ESRRA:-1.5861666854;ONECUT1,2:-1.67568138891;HSF1,2:-1.67678483182;NKX3-1:-1.75376597429;NFIX:-1.84595975809;PAX8:-1.96006051725;TBX4,5:-2.18200195131;PAX4:-2.18522943695;HOXA9_MEIS1:-2.22606484692
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:10077-102A5
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010077
|is_a=EFO:0002091;;FF:0000004;;FF:0000210;;FF:0010077
|name=lymph node, adult, donor1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11788,LSID820,release009,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=102
|rna_catalog_number=Cat:AM7894
|rna_concentration=1
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-ToTALLY-RNA-v1.0
|rna_lot_number=8060051
|rna_od260/230=
|rna_od260/280=
|rna_position=A5
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=102A5
|rna_weight_ug=50
|sample_age=
|sample_cell_catalog=NA
|sample_cell_line=
|sample_cell_lot=NA
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Ambion
|sample_description=
|sample_dev_stage=30 years old adult
|sample_disease=normal
|sample_donor(cell lot)=1
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=10077
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=lymph node
|top_motifs=POU5F1:2.01834602736;POU2F1..3:1.897519883;SPZ1:1.7640012877;AIRE:1.63907917516;GATA4:1.62188350623;ETS1,2:1.50558849082;SPIB:1.48436970767;RXRA_VDR{dimer}:1.45561299243;FOXD3:1.43042707736;IKZF2:1.4152215341;IRF1,2:1.40812329154;ELF1,2,4:1.39615330395;SPI1:1.29054507525;TFAP4:1.26227545567;IRF7:1.2447089488;NFATC1..3:1.17533633051;AR:1.16269517551;TLX2:1.15002923632;STAT1,3:1.06597725677;T:1.0230633541;RUNX1..3:0.98770885643;RBPJ:0.955238278751;DMAP1_NCOR{1,2}_SMARC:0.884447296815;FOXO1,3,4:0.87884287215;BPTF:0.852191751102;MYFfamily:0.84261376297;NR1H4:0.840535219156;STAT2,4,6:0.831137784084;HNF4A_NR2F1,2:0.819634336269;FOX{D1,D2}:0.816380126829;SMAD1..7,9:0.816053421739;MTF1:0.788028216164;ZNF384:0.746192659038;PATZ1:0.735994117238;PRDM1:0.668653481814;FOXA2:0.653351266322;TFCP2:0.64702179794;BREu{core}:0.646573198406;PAX3,7:0.615647485292;GCM1,2:0.606618064072;HMX1:0.601584586118;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.600454003654;NKX6-1,2:0.579984225498;TGIF1:0.534506526372;TOPORS:0.515114164102;SREBF1,2:0.483747866619;MZF1:0.457526377355;SRF:0.444235475403;EP300:0.429602872304;XCPE1{core}:0.403093599691;ESR1:0.380784971966;EN1,2:0.369279056036;GATA6:0.361078855219;LMO2:0.357887098035;NKX3-2:0.314618520822;ZBTB16:0.303917918358;TBP:0.303533337876;EGR1..3:0.285317857139;ALX1:0.265818331078;MTE{core}:0.253949427835;TFAP2{A,C}:0.237809480007;SP1:0.22210150924;RREB1:0.214088280942;HAND1,2:0.203362437434;CDX1,2,4:0.200343270039;ZEB1:0.198784240756;EBF1:0.190418229325;FOX{F1,F2,J1}:0.179821716293;TEF:0.168220335147;CEBPA,B_DDIT3:0.150061903297;SNAI1..3:0.125169970793;HIF1A:0.122886227633;MYOD1:0.119332602656;MED-1{core}:0.110457692191;NR6A1:0.105798555552;PITX1..3:0.0992563960776;FOXP3:0.0973601707294;EVI1:0.0942499262344;MAZ:0.0866782487844;NANOG{mouse}:0.0786790001584;CRX:0.0637564921628;NR3C1:0.0560206483222;FOXP1:0.0428078910017;TFAP2B:0.0382235405524;GZF1:0.0361640600132;SOX5:0.0113210386535;KLF4:-0.0043920240724;NFKB1_REL_RELA:-0.00592377392409;ALX4:-0.017586104597;ZFP161:-0.0335147943783;NR5A1,2:-0.035057984518;MAFB:-0.0436461049361;HMGA1,2:-0.0479979557375;GFI1B:-0.0888065984712;GTF2I:-0.0913270029585;PAX6:-0.0955031032286;LHX3,4:-0.107955558023;GLI1..3:-0.112192094485;POU6F1:-0.117795137736;ZNF148:-0.128923816106;PAX5:-0.130880347598;HIC1:-0.140666266302;ATF6:-0.144986074917;IKZF1:-0.178262784177;AHR_ARNT_ARNT2:-0.186189797116;UFEwm:-0.198773458079;ZNF423:-0.202269414291;OCT4_SOX2{dimer}:-0.2137709928;ATF2:-0.256511832505;TLX1..3_NFIC{dimer}:-0.268455576419;NFIL3:-0.271196306562;HNF1A:-0.278663387891;TAL1_TCF{3,4,12}:-0.290227139284;ATF4:-0.329027970745;REST:-0.343570419609;RXR{A,B,G}:-0.361225534464;ZNF238:-0.36235000287;PPARG:-0.391626838195;ADNP_IRX_SIX_ZHX:-0.426066054943;CREB1:-0.451199621571;HES1:-0.468243294498;LEF1_TCF7_TCF7L1,2:-0.474103720337;VSX1,2:-0.479387294941;RFX2..5_RFXANK_RFXAP:-0.490274638925;PAX2:-0.535650997891;MEF2{A,B,C,D}:-0.539163924166;HLF:-0.547452609723;NFE2L1:-0.568041966493;DBP:-0.612664881829;ATF5_CREB3:-0.61726129727;NFE2L2:-0.620138997294;GTF2A1,2:-0.622316459456;NHLH1,2:-0.630278720051;HBP1_HMGB_SSRP1_UBTF:-0.650865672468;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.660581123005;NFY{A,B,C}:-0.680965934756;YY1:-0.694360847594;FOXN1:-0.697885057068;SOX2:-0.702209203817;TFDP1:-0.704945880004;TEAD1:-0.711836077872;ZNF143:-0.717909490183;CUX2:-0.71976054987;E2F1..5:-0.74634415564;FOX{I1,J2}:-0.747193167653;NKX2-3_NKX2-5:-0.760405228841;POU1F1:-0.772687977315;FOXL1:-0.779108462809;PAX1,9:-0.786074884251;FOXQ1:-0.789075640626;MYBL2:-0.813589955819;FOS_FOS{B,L1}_JUN{B,D}:-0.838405698642;NFE2:-0.848985971919;SOX{8,9,10}:-0.862131913841;NKX2-2,8:-0.863920331795;MYB:-0.866039712997;SOX17:-0.900385670638;RORA:-0.914264958916;ZBTB6:-0.921976877101;NKX2-1,4:-0.925608820732;PBX1:-0.931750778254;JUN:-0.934185248077;BACH2:-0.948567084385;ELK1,4_GABP{A,B1}:-0.949089191928;STAT5{A,B}:-0.950866097982;FOXM1:-0.951280161065;XBP1:-0.9695278933;NRF1:-0.986228069917;FOSL2:-1.02862769676;HOX{A4,D4}:-1.03962135623;bHLH_family:-1.0461548323;POU3F1..4:-1.04781315883;PRRX1,2:-1.1174605262;GFI1:-1.15594362719;ZIC1..3:-1.15950985941;HOX{A6,A7,B6,B7}:-1.20981480483;PDX1:-1.25458246678;TP53:-1.26243351672;CDC5L:-1.29277566681;HOX{A5,B5}:-1.32452206548;NANOG:-1.33994876445;RFX1:-1.47258944438;ARID5B:-1.48445243127;ESRRA:-1.5861666854;ONECUT1,2:-1.67568138891;HSF1,2:-1.67678483182;NKX3-1:-1.75376597429;NFIX:-1.84595975809;PAX8:-1.96006051725;TBX4,5:-2.18200195131;PAX4:-2.18522943695;HOXA9_MEIS1:-2.22606484692
}}
}}

Revision as of 14:01, 21 March 2012


Name:lymph node, adult, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuelymph node
dev stage30 years old adult
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyAmbion
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number8060051
catalog numberCat:AM7894
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-ToTALLY-RNA-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: CNhs11788



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: CNhs11788



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: CNhs11788


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

UBERON: Anatomy
0000029 (lymph node)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0001062 (anatomical entity)
0002193 (hemolymphoid system)
0002405 (immune system)
0002465 (lymphoid system)
0007023 (adult organism)

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