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{{f5samples
{{f5samples
|id=FF:1384-42G1
|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, neonate N30
|sample_id=1384
|rna_tube_id=42G1
|rna_box=42
|rna_position=G1
|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=30 days neonate
|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=CNhs11131,LSID735,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=HNF4A_NR2F1,2:2.66062231774;NR6A1:2.46763213275;SNAI1..3:2.06954973451;ARID5B:2.05890474347;ZEB1:1.93200179128;FOXM1:1.89880019561;HNF1A:1.79011395117;DMAP1_NCOR{1,2}_SMARC:1.75148582182;NR1H4:1.7438605031;RXRA_VDR{dimer}:1.56294258275;CDX1,2,4:1.48221603085;JUN:1.44867511335;IRF1,2:1.41107603419;ESRRA:1.34164414277;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.31765788152;NKX6-1,2:1.21151476019;TBX4,5:1.15074675955;POU1F1:1.14488932593;FOSL2:1.12000469219;ATF6:1.07671325114;FOX{D1,D2}:0.888838862923;FOXO1,3,4:0.874816154257;TLX1..3_NFIC{dimer}:0.83184702492;ZNF148:0.813740841502;PDX1:0.783170420017;GTF2A1,2:0.747666018728;XCPE1{core}:0.726750222391;RBPJ:0.725443329464;NFIX:0.721503561086;AR:0.710265131445;SP1:0.687828729427;FOXN1:0.666441314441;FOX{I1,J2}:0.641140507638;LMO2:0.62464269892;MYBL2:0.584810422071;NR5A1,2:0.583033238534;MYOD1:0.582266912201;T:0.576501234775;FOXA2:0.544646660994;bHLH_family:0.52748592737;TBP:0.505877527843;ETS1,2:0.492887066768;SRF:0.471371642909;FOS_FOS{B,L1}_JUN{B,D}:0.436615028172;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.435070444388;PAX8:0.401265115808;FOXQ1:0.376770707827;ADNP_IRX_SIX_ZHX:0.374651018914;TFCP2:0.368516579259;GATA6:0.357124112817;GZF1:0.326948190176;TP53:0.315439811546;FOXP1:0.315404767234;TLX2:0.273187691705;YY1:0.239562210109;HAND1,2:0.175448062413;TFAP4:0.163070386299;PITX1..3:0.139654883382;STAT2,4,6:0.100448255732;EVI1:0.0960465547585;HBP1_HMGB_SSRP1_UBTF:0.0252425023559;ELF1,2,4:0.00725726330963;SPZ1:0.00286652433332;IRF7:-0.0108438471904;NKX3-2:-0.0657038210782;ZBTB6:-0.0710602811629;SPI1:-0.07487333251;TOPORS:-0.0847406656008;NFE2L2:-0.167613572688;REST:-0.174654232814;CDC5L:-0.176991330069;BACH2:-0.182519991446;NFKB1_REL_RELA:-0.185306937983;POU2F1..3:-0.189529866803;PBX1:-0.197495002508;ATF5_CREB3:-0.215016765366;TEAD1:-0.218410949029;MAZ:-0.220441674237;ESR1:-0.248991023596;ELK1,4_GABP{A,B1}:-0.262102646248;BPTF:-0.268674295701;EBF1:-0.273079759796;SPIB:-0.278924042473;PPARG:-0.292034596161;OCT4_SOX2{dimer}:-0.308491688626;HMX1:-0.311390756589;MYFfamily:-0.314449070745;HMGA1,2:-0.323486937981;ZBTB16:-0.324028769916;STAT1,3:-0.34484932741;NKX2-1,4:-0.364871488629;AIRE:-0.366971442258;NFE2:-0.371516436764;GFI1:-0.382982710404;GCM1,2:-0.39298214221;GLI1..3:-0.397102573495;DBP:-0.397907412928;STAT5{A,B}:-0.40249958395;RUNX1..3:-0.403268581785;HLF:-0.40863449316;NKX2-2,8:-0.419682342185;NFY{A,B,C}:-0.456813218669;NANOG:-0.464511016452;GTF2I:-0.48604672205;POU6F1:-0.497018698577;MED-1{core}:-0.51226062108;MAFB:-0.521347858436;FOX{F1,F2,J1}:-0.52367934218;E2F1..5:-0.525343586948;MTF1:-0.525600196942;RFX2..5_RFXANK_RFXAP:-0.552356072188;CUX2:-0.555363426111;MYB:-0.56384160504;HIC1:-0.580819996324;LEF1_TCF7_TCF7L1,2:-0.586694259135;TFAP2B:-0.587405817726;UFEwm:-0.592245897279;CREB1:-0.601575978101;GFI1B:-0.605373225651;POU5F1:-0.609479649822;ALX4:-0.616228242117;TEF:-0.642667238971;FOXL1:-0.66113816882;ZNF238:-0.669508860286;LHX3,4:-0.676898668502;PRRX1,2:-0.690899375532;VSX1,2:-0.691917278327;NR3C1:-0.703400155076;CEBPA,B_DDIT3:-0.71172324011;EP300:-0.721800827103;TAL1_TCF{3,4,12}:-0.728217354797;ONECUT1,2:-0.733534910797;PAX5:-0.739773922231;ATF4:-0.740895700107;ZFP161:-0.749558197593;ATF2:-0.760381998282;PAX4:-0.760387984233;EGR1..3:-0.794057741491;TGIF1:-0.79798707416;SMAD1..7,9:-0.803295132661;MEF2{A,B,C,D}:-0.803757169113;HOXA9_MEIS1:-0.809565321996;ZNF423:-0.813835690588;ZNF384:-0.843964274085;NFIL3:-0.844011475789;PAX2:-0.850425805122;NKX2-3_NKX2-5:-0.854072974731;NHLH1,2:-0.866564107526;IKZF2:-0.884307990646;ZIC1..3:-0.891807508443;SREBF1,2:-0.896990861476;FOXD3:-0.898063211017;BREu{core}:-0.936720922172;AHR_ARNT_ARNT2:-0.942113790671;HOX{A5,B5}:-0.952933906168;IKZF1:-0.965046206829;RORA:-0.975066254896;PAX6:-1.00516918654;RFX1:-1.00576398948;PRDM1:-1.00984659223;ZNF143:-1.01579386436;NFATC1..3:-1.02445316031;EN1,2:-1.04020419412;MTE{core}:-1.04831964843;RXR{A,B,G}:-1.05135959911;RREB1:-1.05228158271;SOX17:-1.06620430157;HIF1A:-1.10255580797;HES1:-1.11531168828;PATZ1:-1.11614434928;NRF1:-1.1247756346;MZF1:-1.14726481406;CRX:-1.1670984892;NKX3-1:-1.20571079851;SOX5:-1.29654572582;SOX2:-1.29670928931;TFDP1:-1.30363766625;PAX1,9:-1.31924498614;HOX{A4,D4}:-1.3414894424;KLF4:-1.34478783376;NFE2L1:-1.35418994096;SOX{8,9,10}:-1.35872479423;GATA4:-1.37077098065;TFAP2{A,C}:-1.39110412508;POU3F1..4:-1.44315662084;FOXP3:-1.448854842;ALX1:-1.67782556292;HSF1,2:-1.93020080378;NANOG{mouse}:-1.98562396457
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:1384-42G1
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011481
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011481
|name=intestine, neonate N30
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11131,LSID735,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=42
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=G1
|rna_rin=
|rna_sample_type=
|rna_tube_id=42G1
|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=30 days neonate
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=1384
|sample_note=
|sample_sex=mixture
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=intestine
|top_motifs=HNF4A_NR2F1,2:2.66062231774;NR6A1:2.46763213275;SNAI1..3:2.06954973451;ARID5B:2.05890474347;ZEB1:1.93200179128;FOXM1:1.89880019561;HNF1A:1.79011395117;DMAP1_NCOR{1,2}_SMARC:1.75148582182;NR1H4:1.7438605031;RXRA_VDR{dimer}:1.56294258275;CDX1,2,4:1.48221603085;JUN:1.44867511335;IRF1,2:1.41107603419;ESRRA:1.34164414277;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.31765788152;NKX6-1,2:1.21151476019;TBX4,5:1.15074675955;POU1F1:1.14488932593;FOSL2:1.12000469219;ATF6:1.07671325114;FOX{D1,D2}:0.888838862923;FOXO1,3,4:0.874816154257;TLX1..3_NFIC{dimer}:0.83184702492;ZNF148:0.813740841502;PDX1:0.783170420017;GTF2A1,2:0.747666018728;XCPE1{core}:0.726750222391;RBPJ:0.725443329464;NFIX:0.721503561086;AR:0.710265131445;SP1:0.687828729427;FOXN1:0.666441314441;FOX{I1,J2}:0.641140507638;LMO2:0.62464269892;MYBL2:0.584810422071;NR5A1,2:0.583033238534;MYOD1:0.582266912201;T:0.576501234775;FOXA2:0.544646660994;bHLH_family:0.52748592737;TBP:0.505877527843;ETS1,2:0.492887066768;SRF:0.471371642909;FOS_FOS{B,L1}_JUN{B,D}:0.436615028172;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.435070444388;PAX8:0.401265115808;FOXQ1:0.376770707827;ADNP_IRX_SIX_ZHX:0.374651018914;TFCP2:0.368516579259;GATA6:0.357124112817;GZF1:0.326948190176;TP53:0.315439811546;FOXP1:0.315404767234;TLX2:0.273187691705;YY1:0.239562210109;HAND1,2:0.175448062413;TFAP4:0.163070386299;PITX1..3:0.139654883382;STAT2,4,6:0.100448255732;EVI1:0.0960465547585;HBP1_HMGB_SSRP1_UBTF:0.0252425023559;ELF1,2,4:0.00725726330963;SPZ1:0.00286652433332;IRF7:-0.0108438471904;NKX3-2:-0.0657038210782;ZBTB6:-0.0710602811629;SPI1:-0.07487333251;TOPORS:-0.0847406656008;NFE2L2:-0.167613572688;REST:-0.174654232814;CDC5L:-0.176991330069;BACH2:-0.182519991446;NFKB1_REL_RELA:-0.185306937983;POU2F1..3:-0.189529866803;PBX1:-0.197495002508;ATF5_CREB3:-0.215016765366;TEAD1:-0.218410949029;MAZ:-0.220441674237;ESR1:-0.248991023596;ELK1,4_GABP{A,B1}:-0.262102646248;BPTF:-0.268674295701;EBF1:-0.273079759796;SPIB:-0.278924042473;PPARG:-0.292034596161;OCT4_SOX2{dimer}:-0.308491688626;HMX1:-0.311390756589;MYFfamily:-0.314449070745;HMGA1,2:-0.323486937981;ZBTB16:-0.324028769916;STAT1,3:-0.34484932741;NKX2-1,4:-0.364871488629;AIRE:-0.366971442258;NFE2:-0.371516436764;GFI1:-0.382982710404;GCM1,2:-0.39298214221;GLI1..3:-0.397102573495;DBP:-0.397907412928;STAT5{A,B}:-0.40249958395;RUNX1..3:-0.403268581785;HLF:-0.40863449316;NKX2-2,8:-0.419682342185;NFY{A,B,C}:-0.456813218669;NANOG:-0.464511016452;GTF2I:-0.48604672205;POU6F1:-0.497018698577;MED-1{core}:-0.51226062108;MAFB:-0.521347858436;FOX{F1,F2,J1}:-0.52367934218;E2F1..5:-0.525343586948;MTF1:-0.525600196942;RFX2..5_RFXANK_RFXAP:-0.552356072188;CUX2:-0.555363426111;MYB:-0.56384160504;HIC1:-0.580819996324;LEF1_TCF7_TCF7L1,2:-0.586694259135;TFAP2B:-0.587405817726;UFEwm:-0.592245897279;CREB1:-0.601575978101;GFI1B:-0.605373225651;POU5F1:-0.609479649822;ALX4:-0.616228242117;TEF:-0.642667238971;FOXL1:-0.66113816882;ZNF238:-0.669508860286;LHX3,4:-0.676898668502;PRRX1,2:-0.690899375532;VSX1,2:-0.691917278327;NR3C1:-0.703400155076;CEBPA,B_DDIT3:-0.71172324011;EP300:-0.721800827103;TAL1_TCF{3,4,12}:-0.728217354797;ONECUT1,2:-0.733534910797;PAX5:-0.739773922231;ATF4:-0.740895700107;ZFP161:-0.749558197593;ATF2:-0.760381998282;PAX4:-0.760387984233;EGR1..3:-0.794057741491;TGIF1:-0.79798707416;SMAD1..7,9:-0.803295132661;MEF2{A,B,C,D}:-0.803757169113;HOXA9_MEIS1:-0.809565321996;ZNF423:-0.813835690588;ZNF384:-0.843964274085;NFIL3:-0.844011475789;PAX2:-0.850425805122;NKX2-3_NKX2-5:-0.854072974731;NHLH1,2:-0.866564107526;IKZF2:-0.884307990646;ZIC1..3:-0.891807508443;SREBF1,2:-0.896990861476;FOXD3:-0.898063211017;BREu{core}:-0.936720922172;AHR_ARNT_ARNT2:-0.942113790671;HOX{A5,B5}:-0.952933906168;IKZF1:-0.965046206829;RORA:-0.975066254896;PAX6:-1.00516918654;RFX1:-1.00576398948;PRDM1:-1.00984659223;ZNF143:-1.01579386436;NFATC1..3:-1.02445316031;EN1,2:-1.04020419412;MTE{core}:-1.04831964843;RXR{A,B,G}:-1.05135959911;RREB1:-1.05228158271;SOX17:-1.06620430157;HIF1A:-1.10255580797;HES1:-1.11531168828;PATZ1:-1.11614434928;NRF1:-1.1247756346;MZF1:-1.14726481406;CRX:-1.1670984892;NKX3-1:-1.20571079851;SOX5:-1.29654572582;SOX2:-1.29670928931;TFDP1:-1.30363766625;PAX1,9:-1.31924498614;HOX{A4,D4}:-1.3414894424;KLF4:-1.34478783376;NFE2L1:-1.35418994096;SOX{8,9,10}:-1.35872479423;GATA4:-1.37077098065;TFAP2{A,C}:-1.39110412508;POU3F1..4:-1.44315662084;FOXP3:-1.448854842;ALX1:-1.67782556292;HSF1,2:-1.93020080378;NANOG{mouse}:-1.98562396457
}}
}}

Revision as of 15:31, 21 March 2012


Name:intestine, neonate N30
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 stage30 days neonate
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
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
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

CNhs11131



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: CNhs11131



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: CNhs11131



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: CNhs11131


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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