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{{f5samples
{{f5samples
|id=FF:381-16D5
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000160,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001007,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0004119,UBERON:0004185,UBERON:0004921,UBERON:0005409,UBERON:0005423,UBERON:0007026
|name=intestine, embryo E13
|sample_id=381
|rna_tube_id=16D5
|rna_box=16
|rna_position=D5
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_dev_stage=13 days embryo
|sample_tissue=intestine
|sample_donor(cell lot)=
|sample_sex=mixture
|sample_age=
|sample_ethnicity=
|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=
|rna_sample_type=
|rna_extraction_protocol=
|rna_weight_ug=
|rna_concentration=
|sample_note=
|profile_hcage=CNhs11010,LSID730,release008,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000160,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0001007,UBERON:0001062,UBERON:0001555,UBERON:0002050,UBERON:0002532,UBERON:0004119,UBERON:0004185,UBERON:0004921,UBERON:0005409,UBERON:0005423,UBERON:0007026
|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=ZNF384:2.1621153194;ZBTB16:1.74958308264;HMGA1,2:1.7259233628;FOXP1:1.71142773444;FOX{I1,J2}:1.63212972857;FOXQ1:1.5571880317;NKX3-1:1.51988687536;GATA4:1.5185519958;NKX2-1,4:1.51183333423;PAX4:1.47424998055;CDC5L:1.43930292595;DBP:1.38442425524;IKZF2:1.3576057358;EVI1:1.34716517338;NFY{A,B,C}:1.2480853097;GFI1:1.20507031628;NANOG:1.17942203766;CDX1,2,4:1.16152924657;E2F1..5:1.10889256995;MYBL2:1.09156931037;ZNF143:1.06641588204;TOPORS:1.0568983986;FOXD3:1.03646678877;TFDP1:1.01965708919;AIRE:1.00969405658;RREB1:0.990833227155;RXR{A,B,G}:0.984809379669;PDX1:0.966737140807;LHX3,4:0.924270491128;PITX1..3:0.917745122072;MZF1:0.894141047464;SRF:0.856440070122;MAZ:0.842370891021;GZF1:0.836964030517;BPTF:0.787413026801;POU1F1:0.782612210628;PATZ1:0.776025882478;OCT4_SOX2{dimer}:0.764277929218;PBX1:0.758435762552;ONECUT1,2:0.746731908888;CRX:0.744684500462;ADNP_IRX_SIX_ZHX:0.733503890318;PRRX1,2:0.727524994688;ZNF423:0.726496649796;SOX17:0.723411237764;GFI1B:0.72045977991;TEF:0.680222641844;SOX2:0.671802219452;ZNF238:0.6647623933;SOX5:0.655323024956;STAT1,3:0.64227030595;KLF4:0.634615190803;HOX{A5,B5}:0.6133856481;NANOG{mouse}:0.611479498301;HSF1,2:0.598754650355;AHR_ARNT_ARNT2:0.594868476123;NRF1:0.593495550153;GATA6:0.567752766479;UFEwm:0.551656522572;POU6F1:0.533413366979;SOX{8,9,10}:0.532907379858;GTF2I:0.506271279201;POU3F1..4:0.497708861923;BREu{core}:0.439189501023;LEF1_TCF7_TCF7L1,2:0.431603215177;HBP1_HMGB_SSRP1_UBTF:0.427856680257;TEAD1:0.421607021205;EN1,2:0.390544314147;CUX2:0.390095924891;PAX1,9:0.383854184434;PAX6:0.380685135246;XCPE1{core}:0.371837612706;PRDM1:0.365354091479;NKX6-1,2:0.3371267154;HOXA9_MEIS1:0.311298279605;MED-1{core}:0.28093853438;EP300:0.258010878656;HNF1A:0.225402026382;ZIC1..3:0.219271632583;GLI1..3:0.198147223755;HIC1:0.171459969511;HAND1,2:0.144599640586;ZFP161:0.140439878791;POU5F1:0.130661100257;T:0.129492564213;RBPJ:0.118729619281;IKZF1:0.113206546614;NR3C1:0.102610328997;NR6A1:0.100654099445;FOXM1:0.0849987344422;MYB:0.0820702799674;STAT5{A,B}:0.0784258203812;FOXP3:0.0779549666706;HMX1:0.0695938181414;FOX{F1,F2,J1}:0.0380900641426;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.032770247405;ELK1,4_GABP{A,B1}:0.0273779123809;TFAP2B:0.0221427503179;HIF1A:-0.0204313295562;ZNF148:-0.0309110130207;EGR1..3:-0.051460960222;ATF6:-0.0602194301239;FOXL1:-0.061787284351;ALX4:-0.071789681696;YY1:-0.0726648674165;IRF7:-0.078600594816;ATF2:-0.0868064709532;SP1:-0.0896837303115;FOX{D1,D2}:-0.105119269826;EBF1:-0.110678477927;RFX1:-0.124907634295;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.130243151943;ELF1,2,4:-0.140575813489;PAX8:-0.145184834032;RFX2..5_RFXANK_RFXAP:-0.15220988583;NKX3-2:-0.187674757427;MTE{core}:-0.202296360218;SPIB:-0.207076610141;GTF2A1,2:-0.21933744031;FOXA2:-0.222499258211;HNF4A_NR2F1,2:-0.225346366772;TLX1..3_NFIC{dimer}:-0.228907062892;REST:-0.23242368758;POU2F1..3:-0.250224331201;PAX5:-0.272968110851;NKX2-3_NKX2-5:-0.276551537222;TFCP2:-0.30017316937;TFAP2{A,C}:-0.35699076757;DMAP1_NCOR{1,2}_SMARC:-0.380579925742;NHLH1,2:-0.385160780173;SPI1:-0.385172287111;RUNX1..3:-0.390929994911;TBP:-0.410860114259;MEF2{A,B,C,D}:-0.448453471596;TGIF1:-0.455319671989;TFAP4:-0.462251539302;TLX2:-0.480776255035;JUN:-0.483506975098;SPZ1:-0.484407972337;VSX1,2:-0.492532290225;SNAI1..3:-0.493208744057;NKX2-2,8:-0.505060765849;RORA:-0.505531076858;LMO2:-0.530614826965;ETS1,2:-0.545140444127;ZBTB6:-0.552154265028;NFKB1_REL_RELA:-0.554788100945;ATF4:-0.555409376642;IRF1,2:-0.561102026408;ARID5B:-0.564802077825;NFATC1..3:-0.592134758386;SMAD1..7,9:-0.602627277445;GCM1,2:-0.606650362174;CREB1:-0.637038676553;ZEB1:-0.644185306153;HLF:-0.663375974009;SREBF1,2:-0.668892703682;MTF1:-0.686671593657;RXRA_VDR{dimer}:-0.718456532843;ESRRA:-0.718609206028;ATF5_CREB3:-0.723798556807;bHLH_family:-0.730700364881;FOXN1:-0.776011693827;MYFfamily:-0.78061756936;FOXO1,3,4:-0.785719753764;HES1:-0.830002213109;TAL1_TCF{3,4,12}:-0.83866977559;AR:-0.902371208289;NFE2:-0.919151655036;FOS_FOS{B,L1}_JUN{B,D}:-0.926776681231;ALX1:-0.933587156123;FOSL2:-0.935434784256;MYOD1:-0.947962033848;NR5A1,2:-0.950989464508;NR1H4:-0.951033437399;TBX4,5:-0.953688281946;BACH2:-0.976331995712;ESR1:-0.999699564532;MAFB:-1.00382346825;NFIL3:-1.00985624411;TP53:-1.0457907096;STAT2,4,6:-1.08407848217;CEBPA,B_DDIT3:-1.09852766369;PAX2:-1.09921421548;NFIX:-1.10426679814;HOX{A4,D4}:-1.20198082;NFE2L1:-1.2904153866;NFE2L2:-1.47237796115;PPARG:-1.60962043909
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:381-16D5
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011330
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011330
|name=intestine, embryo E13
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11010,LSID730,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=16
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=D5
|rna_rin=
|rna_sample_type=
|rna_tube_id=16D5
|rna_weight_ug=
|sample_age=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=
|sample_description=
|sample_dev_stage=13 days embryo
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=381
|sample_note=
|sample_sex=mixture
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=intestine
|top_motifs=ZNF384:2.1621153194;ZBTB16:1.74958308264;HMGA1,2:1.7259233628;FOXP1:1.71142773444;FOX{I1,J2}:1.63212972857;FOXQ1:1.5571880317;NKX3-1:1.51988687536;GATA4:1.5185519958;NKX2-1,4:1.51183333423;PAX4:1.47424998055;CDC5L:1.43930292595;DBP:1.38442425524;IKZF2:1.3576057358;EVI1:1.34716517338;NFY{A,B,C}:1.2480853097;GFI1:1.20507031628;NANOG:1.17942203766;CDX1,2,4:1.16152924657;E2F1..5:1.10889256995;MYBL2:1.09156931037;ZNF143:1.06641588204;TOPORS:1.0568983986;FOXD3:1.03646678877;TFDP1:1.01965708919;AIRE:1.00969405658;RREB1:0.990833227155;RXR{A,B,G}:0.984809379669;PDX1:0.966737140807;LHX3,4:0.924270491128;PITX1..3:0.917745122072;MZF1:0.894141047464;SRF:0.856440070122;MAZ:0.842370891021;GZF1:0.836964030517;BPTF:0.787413026801;POU1F1:0.782612210628;PATZ1:0.776025882478;OCT4_SOX2{dimer}:0.764277929218;PBX1:0.758435762552;ONECUT1,2:0.746731908888;CRX:0.744684500462;ADNP_IRX_SIX_ZHX:0.733503890318;PRRX1,2:0.727524994688;ZNF423:0.726496649796;SOX17:0.723411237764;GFI1B:0.72045977991;TEF:0.680222641844;SOX2:0.671802219452;ZNF238:0.6647623933;SOX5:0.655323024956;STAT1,3:0.64227030595;KLF4:0.634615190803;HOX{A5,B5}:0.6133856481;NANOG{mouse}:0.611479498301;HSF1,2:0.598754650355;AHR_ARNT_ARNT2:0.594868476123;NRF1:0.593495550153;GATA6:0.567752766479;UFEwm:0.551656522572;POU6F1:0.533413366979;SOX{8,9,10}:0.532907379858;GTF2I:0.506271279201;POU3F1..4:0.497708861923;BREu{core}:0.439189501023;LEF1_TCF7_TCF7L1,2:0.431603215177;HBP1_HMGB_SSRP1_UBTF:0.427856680257;TEAD1:0.421607021205;EN1,2:0.390544314147;CUX2:0.390095924891;PAX1,9:0.383854184434;PAX6:0.380685135246;XCPE1{core}:0.371837612706;PRDM1:0.365354091479;NKX6-1,2:0.3371267154;HOXA9_MEIS1:0.311298279605;MED-1{core}:0.28093853438;EP300:0.258010878656;HNF1A:0.225402026382;ZIC1..3:0.219271632583;GLI1..3:0.198147223755;HIC1:0.171459969511;HAND1,2:0.144599640586;ZFP161:0.140439878791;POU5F1:0.130661100257;T:0.129492564213;RBPJ:0.118729619281;IKZF1:0.113206546614;NR3C1:0.102610328997;NR6A1:0.100654099445;FOXM1:0.0849987344422;MYB:0.0820702799674;STAT5{A,B}:0.0784258203812;FOXP3:0.0779549666706;HMX1:0.0695938181414;FOX{F1,F2,J1}:0.0380900641426;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.032770247405;ELK1,4_GABP{A,B1}:0.0273779123809;TFAP2B:0.0221427503179;HIF1A:-0.0204313295562;ZNF148:-0.0309110130207;EGR1..3:-0.051460960222;ATF6:-0.0602194301239;FOXL1:-0.061787284351;ALX4:-0.071789681696;YY1:-0.0726648674165;IRF7:-0.078600594816;ATF2:-0.0868064709532;SP1:-0.0896837303115;FOX{D1,D2}:-0.105119269826;EBF1:-0.110678477927;RFX1:-0.124907634295;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.130243151943;ELF1,2,4:-0.140575813489;PAX8:-0.145184834032;RFX2..5_RFXANK_RFXAP:-0.15220988583;NKX3-2:-0.187674757427;MTE{core}:-0.202296360218;SPIB:-0.207076610141;GTF2A1,2:-0.21933744031;FOXA2:-0.222499258211;HNF4A_NR2F1,2:-0.225346366772;TLX1..3_NFIC{dimer}:-0.228907062892;REST:-0.23242368758;POU2F1..3:-0.250224331201;PAX5:-0.272968110851;NKX2-3_NKX2-5:-0.276551537222;TFCP2:-0.30017316937;TFAP2{A,C}:-0.35699076757;DMAP1_NCOR{1,2}_SMARC:-0.380579925742;NHLH1,2:-0.385160780173;SPI1:-0.385172287111;RUNX1..3:-0.390929994911;TBP:-0.410860114259;MEF2{A,B,C,D}:-0.448453471596;TGIF1:-0.455319671989;TFAP4:-0.462251539302;TLX2:-0.480776255035;JUN:-0.483506975098;SPZ1:-0.484407972337;VSX1,2:-0.492532290225;SNAI1..3:-0.493208744057;NKX2-2,8:-0.505060765849;RORA:-0.505531076858;LMO2:-0.530614826965;ETS1,2:-0.545140444127;ZBTB6:-0.552154265028;NFKB1_REL_RELA:-0.554788100945;ATF4:-0.555409376642;IRF1,2:-0.561102026408;ARID5B:-0.564802077825;NFATC1..3:-0.592134758386;SMAD1..7,9:-0.602627277445;GCM1,2:-0.606650362174;CREB1:-0.637038676553;ZEB1:-0.644185306153;HLF:-0.663375974009;SREBF1,2:-0.668892703682;MTF1:-0.686671593657;RXRA_VDR{dimer}:-0.718456532843;ESRRA:-0.718609206028;ATF5_CREB3:-0.723798556807;bHLH_family:-0.730700364881;FOXN1:-0.776011693827;MYFfamily:-0.78061756936;FOXO1,3,4:-0.785719753764;HES1:-0.830002213109;TAL1_TCF{3,4,12}:-0.83866977559;AR:-0.902371208289;NFE2:-0.919151655036;FOS_FOS{B,L1}_JUN{B,D}:-0.926776681231;ALX1:-0.933587156123;FOSL2:-0.935434784256;MYOD1:-0.947962033848;NR5A1,2:-0.950989464508;NR1H4:-0.951033437399;TBX4,5:-0.953688281946;BACH2:-0.976331995712;ESR1:-0.999699564532;MAFB:-1.00382346825;NFIL3:-1.00985624411;TP53:-1.0457907096;STAT2,4,6:-1.08407848217;CEBPA,B_DDIT3:-1.09852766369;PAX2:-1.09921421548;NFIX:-1.10426679814;HOX{A4,D4}:-1.20198082;NFE2L1:-1.2904153866;NFE2L2:-1.47237796115;PPARG:-1.60962043909
}}
}}

Revision as of 15:34, 21 March 2012


Name:intestine, embryo E13
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueintestine
dev stage13 days embryo
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
Download raw sequence, BAM & CTSS
CollapseMm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
CollapseMm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} 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

CNhs11010



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: CNhs11010



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: CNhs11010



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: CNhs11010


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
0000061 (anatomical structure)
0000160 (intestine)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)

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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