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{{f5samples
{{f5samples
|id=FF:976-16D8
|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 E15
|sample_id=976
|rna_tube_id=16D8
|rna_box=16
|rna_position=D8
|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=15 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=CNhs10602,LSID654,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=GFI1:1.680843985;ZNF238:1.40382928843;GZF1:1.34783780103;MYBL2:1.18600479308;NFY{A,B,C}:1.15570200101;FOX{I1,J2}:1.09212632107;SRF:1.05548673558;MAZ:0.989245809122;NANOG:0.988745632541;PDX1:0.988689018662;E2F1..5:0.960149953916;TLX2:0.951493013826;CDX1,2,4:0.92010223409;ZNF423:0.905818828489;HNF1A:0.892285278004;ZNF143:0.838113241766;XCPE1{core}:0.837093478571;ADNP_IRX_SIX_ZHX:0.831543787064;TOPORS:0.812995214432;RREB1:0.781754113604;TFDP1:0.765567051099;EP300:0.765150421649;ZNF148:0.740988315177;PAX1,9:0.737045945326;NKX2-1,4:0.727890006025;RBPJ:0.68205409247;ATF6:0.664845440624;ZNF384:0.654924111357;SOX17:0.648013864693;HNF4A_NR2F1,2:0.64187247537;PATZ1:0.630168686759;GATA6:0.596672934777;MZF1:0.57931279474;GTF2I:0.549726638222;DBP:0.543317763228;GFI1B:0.525431368357;HBP1_HMGB_SSRP1_UBTF:0.518377915013;PBX1:0.518335730357;TEAD1:0.511683018127;SP1:0.494885644396;PRRX1,2:0.491378669123;NANOG{mouse}:0.484766783689;LHX3,4:0.477304517375;ZIC1..3:0.476175504;HMGA1,2:0.471354434932;SNAI1..3:0.468145261193;STAT1,3:0.448563282189;BREu{core}:0.443745265647;PAX6:0.434130904324;ONECUT1,2:0.433921651527;NKX3-2:0.423864918744;RXR{A,B,G}:0.397915471645;SOX{8,9,10}:0.396653216326;TFCP2:0.392816453445;LEF1_TCF7_TCF7L1,2:0.392422300798;SOX2:0.380439704595;HIC1:0.380336159506;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.373130350141;T:0.370882586022;FOXA2:0.367520484053;TLX1..3_NFIC{dimer}:0.36651996692;ZEB1:0.328642082407;HMX1:0.328052181279;CUX2:0.31544644221;HIF1A:0.313080457022;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.311080037282;SPZ1:0.29026718807;MED-1{core}:0.278717963256;AHR_ARNT_ARNT2:0.259556835983;ATF2:0.252682647894;CRX:0.249236047934;NRF1:0.248840702632;TBX4,5:0.224486292656;IKZF2:0.215173810421;OCT4_SOX2{dimer}:0.212395563713;TBP:0.212186417341;GATA4:0.200615432003;EBF1:0.190173953511;HOX{A5,B5}:0.18695314574;IKZF1:0.185284338658;VSX1,2:0.184456815715;bHLH_family:0.183278041882;FOXM1:0.182889736193;FOXQ1:0.178450250684;TFAP2B:0.173390955716;PAX8:0.170674420263;PRDM1:0.163397484754;GLI1..3:0.163198935033;POU6F1:0.155562623463;FOXD3:0.1446012295;POU3F1..4:0.14404989432;GCM1,2:0.143837487302;EN1,2:0.121456039775;NR6A1:0.121342610729;FOX{F1,F2,J1}:0.105009018402;NKX3-1:0.100245149193;HAND1,2:0.0979566862866;HSF1,2:0.0923521896963;ELF1,2,4:0.0720743754009;FOX{D1,D2}:0.0719249864844;SMAD1..7,9:0.066129615503;FOXN1:0.061612840295;ELK1,4_GABP{A,B1}:0.0528886979551;CDC5L:0.0444582665978;TFAP4:0.0426711667956;ZFP161:0.0223906519723;ETS1,2:0.0105464195885;EGR1..3:0.00110556785341;ESRRA:-0.0171291955281;FOS_FOS{B,L1}_JUN{B,D}:-0.0209038376516;GTF2A1,2:-0.0297660018334;TFAP2{A,C}:-0.0455226511356;ALX4:-0.0526857688379;PITX1..3:-0.0677885042478;MYB:-0.0738727687594;NFIX:-0.0751430649263;NKX2-3_NKX2-5:-0.0787156518043;KLF4:-0.0842320876838;MTF1:-0.0887730662655;REST:-0.0959211366121;SPIB:-0.103047361767;MTE{core}:-0.103778234951;NHLH1,2:-0.108179509952;STAT5{A,B}:-0.126902655076;FOSL2:-0.12743353554;ZBTB16:-0.128441133136;MYOD1:-0.128496138578;NFKB1_REL_RELA:-0.137129988509;JUN:-0.151031305475;EVI1:-0.165192841838;RXRA_VDR{dimer}:-0.173140262167;SOX5:-0.179700357358;DMAP1_NCOR{1,2}_SMARC:-0.180759010845;TEF:-0.192079467626;LMO2:-0.199287881289;RFX1:-0.206625043101;TGIF1:-0.207484121288;TP53:-0.215090074965;RUNX1..3:-0.220362705632;AIRE:-0.224463133354;POU2F1..3:-0.24709441402;MYFfamily:-0.256541112787;AR:-0.269833224703;ESR1:-0.27407981195;YY1:-0.279019054642;MEF2{A,B,C,D}:-0.28097727602;SPI1:-0.300092042833;PAX5:-0.305043175062;POU5F1:-0.318623682379;ARID5B:-0.32702505899;NFATC1..3:-0.333658201467;NR3C1:-0.354838855892;HOXA9_MEIS1:-0.358023620854;SREBF1,2:-0.368640189369;RFX2..5_RFXANK_RFXAP:-0.399787372842;FOXP1:-0.413251521073;ZBTB6:-0.425730607894;NKX2-2,8:-0.427131009514;ATF5_CREB3:-0.443119876879;UFEwm:-0.45073389404;FOXL1:-0.468445037327;HLF:-0.49113605636;IRF1,2:-0.495470699311;PAX2:-0.504270329828;ATF4:-0.509223258328;NR1H4:-0.54353063466;CREB1:-0.550087192009;PAX4:-0.589704075664;BACH2:-0.596475404851;MAFB:-0.615056894633;IRF7:-0.617910646688;FOXO1,3,4:-0.619712080206;STAT2,4,6:-0.621792528099;TAL1_TCF{3,4,12}:-0.656437394091;NR5A1,2:-0.659152801519;RORA:-0.67074586376;CEBPA,B_DDIT3:-0.714032502194;POU1F1:-0.718688514449;BPTF:-0.77852957579;HES1:-0.781215046833;NFE2L1:-0.815091942687;NFE2L2:-0.844354500594;NFE2:-0.853557596689;PPARG:-1.00553121349;ALX1:-1.02666965022;HOX{A4,D4}:-1.03280405436;NKX6-1,2:-1.09507768421;FOXP3:-1.24196444063;NFIL3:-1.24301256631
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:976-16D8
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011441
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011441
|name=intestine, embryo E15
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs10602,LSID654,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=D8
|rna_rin=
|rna_sample_type=
|rna_tube_id=16D8
|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=15 days embryo
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=976
|sample_note=
|sample_sex=mixture
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=intestine
|top_motifs=GFI1:1.680843985;ZNF238:1.40382928843;GZF1:1.34783780103;MYBL2:1.18600479308;NFY{A,B,C}:1.15570200101;FOX{I1,J2}:1.09212632107;SRF:1.05548673558;MAZ:0.989245809122;NANOG:0.988745632541;PDX1:0.988689018662;E2F1..5:0.960149953916;TLX2:0.951493013826;CDX1,2,4:0.92010223409;ZNF423:0.905818828489;HNF1A:0.892285278004;ZNF143:0.838113241766;XCPE1{core}:0.837093478571;ADNP_IRX_SIX_ZHX:0.831543787064;TOPORS:0.812995214432;RREB1:0.781754113604;TFDP1:0.765567051099;EP300:0.765150421649;ZNF148:0.740988315177;PAX1,9:0.737045945326;NKX2-1,4:0.727890006025;RBPJ:0.68205409247;ATF6:0.664845440624;ZNF384:0.654924111357;SOX17:0.648013864693;HNF4A_NR2F1,2:0.64187247537;PATZ1:0.630168686759;GATA6:0.596672934777;MZF1:0.57931279474;GTF2I:0.549726638222;DBP:0.543317763228;GFI1B:0.525431368357;HBP1_HMGB_SSRP1_UBTF:0.518377915013;PBX1:0.518335730357;TEAD1:0.511683018127;SP1:0.494885644396;PRRX1,2:0.491378669123;NANOG{mouse}:0.484766783689;LHX3,4:0.477304517375;ZIC1..3:0.476175504;HMGA1,2:0.471354434932;SNAI1..3:0.468145261193;STAT1,3:0.448563282189;BREu{core}:0.443745265647;PAX6:0.434130904324;ONECUT1,2:0.433921651527;NKX3-2:0.423864918744;RXR{A,B,G}:0.397915471645;SOX{8,9,10}:0.396653216326;TFCP2:0.392816453445;LEF1_TCF7_TCF7L1,2:0.392422300798;SOX2:0.380439704595;HIC1:0.380336159506;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.373130350141;T:0.370882586022;FOXA2:0.367520484053;TLX1..3_NFIC{dimer}:0.36651996692;ZEB1:0.328642082407;HMX1:0.328052181279;CUX2:0.31544644221;HIF1A:0.313080457022;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.311080037282;SPZ1:0.29026718807;MED-1{core}:0.278717963256;AHR_ARNT_ARNT2:0.259556835983;ATF2:0.252682647894;CRX:0.249236047934;NRF1:0.248840702632;TBX4,5:0.224486292656;IKZF2:0.215173810421;OCT4_SOX2{dimer}:0.212395563713;TBP:0.212186417341;GATA4:0.200615432003;EBF1:0.190173953511;HOX{A5,B5}:0.18695314574;IKZF1:0.185284338658;VSX1,2:0.184456815715;bHLH_family:0.183278041882;FOXM1:0.182889736193;FOXQ1:0.178450250684;TFAP2B:0.173390955716;PAX8:0.170674420263;PRDM1:0.163397484754;GLI1..3:0.163198935033;POU6F1:0.155562623463;FOXD3:0.1446012295;POU3F1..4:0.14404989432;GCM1,2:0.143837487302;EN1,2:0.121456039775;NR6A1:0.121342610729;FOX{F1,F2,J1}:0.105009018402;NKX3-1:0.100245149193;HAND1,2:0.0979566862866;HSF1,2:0.0923521896963;ELF1,2,4:0.0720743754009;FOX{D1,D2}:0.0719249864844;SMAD1..7,9:0.066129615503;FOXN1:0.061612840295;ELK1,4_GABP{A,B1}:0.0528886979551;CDC5L:0.0444582665978;TFAP4:0.0426711667956;ZFP161:0.0223906519723;ETS1,2:0.0105464195885;EGR1..3:0.00110556785341;ESRRA:-0.0171291955281;FOS_FOS{B,L1}_JUN{B,D}:-0.0209038376516;GTF2A1,2:-0.0297660018334;TFAP2{A,C}:-0.0455226511356;ALX4:-0.0526857688379;PITX1..3:-0.0677885042478;MYB:-0.0738727687594;NFIX:-0.0751430649263;NKX2-3_NKX2-5:-0.0787156518043;KLF4:-0.0842320876838;MTF1:-0.0887730662655;REST:-0.0959211366121;SPIB:-0.103047361767;MTE{core}:-0.103778234951;NHLH1,2:-0.108179509952;STAT5{A,B}:-0.126902655076;FOSL2:-0.12743353554;ZBTB16:-0.128441133136;MYOD1:-0.128496138578;NFKB1_REL_RELA:-0.137129988509;JUN:-0.151031305475;EVI1:-0.165192841838;RXRA_VDR{dimer}:-0.173140262167;SOX5:-0.179700357358;DMAP1_NCOR{1,2}_SMARC:-0.180759010845;TEF:-0.192079467626;LMO2:-0.199287881289;RFX1:-0.206625043101;TGIF1:-0.207484121288;TP53:-0.215090074965;RUNX1..3:-0.220362705632;AIRE:-0.224463133354;POU2F1..3:-0.24709441402;MYFfamily:-0.256541112787;AR:-0.269833224703;ESR1:-0.27407981195;YY1:-0.279019054642;MEF2{A,B,C,D}:-0.28097727602;SPI1:-0.300092042833;PAX5:-0.305043175062;POU5F1:-0.318623682379;ARID5B:-0.32702505899;NFATC1..3:-0.333658201467;NR3C1:-0.354838855892;HOXA9_MEIS1:-0.358023620854;SREBF1,2:-0.368640189369;RFX2..5_RFXANK_RFXAP:-0.399787372842;FOXP1:-0.413251521073;ZBTB6:-0.425730607894;NKX2-2,8:-0.427131009514;ATF5_CREB3:-0.443119876879;UFEwm:-0.45073389404;FOXL1:-0.468445037327;HLF:-0.49113605636;IRF1,2:-0.495470699311;PAX2:-0.504270329828;ATF4:-0.509223258328;NR1H4:-0.54353063466;CREB1:-0.550087192009;PAX4:-0.589704075664;BACH2:-0.596475404851;MAFB:-0.615056894633;IRF7:-0.617910646688;FOXO1,3,4:-0.619712080206;STAT2,4,6:-0.621792528099;TAL1_TCF{3,4,12}:-0.656437394091;NR5A1,2:-0.659152801519;RORA:-0.67074586376;CEBPA,B_DDIT3:-0.714032502194;POU1F1:-0.718688514449;BPTF:-0.77852957579;HES1:-0.781215046833;NFE2L1:-0.815091942687;NFE2L2:-0.844354500594;NFE2:-0.853557596689;PPARG:-1.00553121349;ALX1:-1.02666965022;HOX{A4,D4}:-1.03280405436;NKX6-1,2:-1.09507768421;FOXP3:-1.24196444063;NFIL3:-1.24301256631
}}
}}

Revision as of 15:37, 21 March 2012


Name:intestine, embryo E15
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 stage15 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

CNhs10602



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: CNhs10602



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: CNhs10602



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: CNhs10602


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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