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{{f5samples
{{f5samples
|id=FF:372-23H2
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000468,UBERON:0000479,UBERON:0000922,UBERON:0001062
|name=whole body, embryo E13
|sample_id=372
|rna_tube_id=23H2
|rna_box=23
|rna_position=H2
|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=whole body
|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=CNhs10512,LSID649,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:0000465,UBERON:0000468,UBERON:0000479,UBERON:0000922,UBERON:0001062
|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=
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|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:372-23H2
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011326
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011326
|name=whole body, embryo E13
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs10512,LSID649,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=23
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=H2
|rna_rin=
|rna_sample_type=
|rna_tube_id=23H2
|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=372
|sample_note=
|sample_sex=mixture
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=whole body
|top_motifs=SOX{8,9,10}:1.87341066433;PRRX1,2:1.78567327886;SOX2:1.77622876165;VSX1,2:1.77061130574;MZF1:1.67079686944;NFY{A,B,C}:1.62935997949;GFI1:1.5613625676;RREB1:1.53827669919;SOX5:1.53671083952;LEF1_TCF7_TCF7L1,2:1.42382631219;GATA6:1.35773003942;PAX1,9:1.33742711969;NANOG:1.33266050279;HOXA9_MEIS1:1.308598835;PATZ1:1.25170996912;ZNF143:1.24594311435;NKX2-3_NKX2-5:1.1704543275;MYBL2:1.16966355141;ZNF384:1.14442998238;OCT4_SOX2{dimer}:1.13468610769;SOX17:1.13157436477;TFDP1:1.08835306976;MAZ:1.06594410348;ADNP_IRX_SIX_ZHX:1.03438384521;PRDM1:1.03314992038;HOX{A5,B5}:1.02555576382;GZF1:0.998499642292;NKX2-1,4:0.987634269635;ZNF238:0.94886216682;POU5F1:0.929961181982;BREu{core}:0.921485790824;GFI1B:0.920075593194;PAX6:0.919360934456;GTF2I:0.918177719352;TGIF1:0.916432840697;CUX2:0.914474251876;FOXD3:0.90225596939;NRF1:0.88925884068;LHX3,4:0.871317935591;HOX{A4,D4}:0.818271252213;NKX3-2:0.817868378792;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.811664465457;DBP:0.811135958971;NHLH1,2:0.805706135973;POU3F1..4:0.799537010965;AHR_ARNT_ARNT2:0.795633613694;STAT5{A,B}:0.785936325932;MED-1{core}:0.778332008411;NANOG{mouse}:0.776825928872;E2F1..5:0.773779143242;MTE{core}:0.763900522494;PBX1:0.762292683698;EN1,2:0.757359767227;HSF1,2:0.748031208646;ONECUT1,2:0.744117348488;GATA4:0.718746066421;FOXP1:0.698531198895;XCPE1{core}:0.68641054229;PITX1..3:0.680735716397;HIC1:0.651271663245;NKX3-1:0.636689586329;EP300:0.626358976811;KLF4:0.616980533806;HBP1_HMGB_SSRP1_UBTF:0.552434398581;ATF2:0.543964573733;GTF2A1,2:0.530698951742;EGR1..3:0.527605034657;MYFfamily:0.520968059588;ZFP161:0.504762911371;TFAP2B:0.488892432237;CDC5L:0.472535894401;SMAD1..7,9:0.472366300512;YY1:0.470662731438;TFAP4:0.444237532056;NKX6-1,2:0.441678889493;TAL1_TCF{3,4,12}:0.428809909721;FOX{I1,J2}:0.428769596927;CDX1,2,4:0.399824143832;ZNF423:0.375399910929;FOXP3:0.372796369338;HIF1A:0.360689364221;TBP:0.359138545255;TBX4,5:0.351837263926;POU2F1..3:0.333140571184;IKZF1:0.331355248786;RBPJ:0.326274692102;SP1:0.319615744153;PAX5:0.316466581372;TLX2:0.315039117813;MTF1:0.314747406507;PAX4:0.307093227222;POU6F1:0.305631541715;MAFB:0.304660875222;TEAD1:0.300781397927;ZBTB6:0.298147783809;ZNF148:0.291024773752;TOPORS:0.281621256553;CRX:0.280171468917;RFX1:0.264742012256;FOXN1:0.264329993785;REST:0.259217983045;IKZF2:0.256912240385;HMX1:0.253634719355;HES1:0.244596937792;ZIC1..3:0.232410588594;SRF:0.23053265093;HMGA1,2:0.164013695389;UFEwm:0.15599126576;FOXL1:0.15072477768;JUN:0.137433844696;FOXA2:0.130238719813;RXR{A,B,G}:0.127552878334;ATF6:0.122254638779;TLX1..3_NFIC{dimer}:0.112928923044;MEF2{A,B,C,D}:0.081821921288;ZBTB16:0.0805812952105;GLI1..3:0.0758550687602;ELK1,4_GABP{A,B1}:0.0728310195173;FOX{F1,F2,J1}:0.0464797157336;NR6A1:0.0255686601686;GCM1,2:0.00814128106226;RFX2..5_RFXANK_RFXAP:-0.0140061313849;TFAP2{A,C}:-0.0243239649644;STAT1,3:-0.0353547922451;PAX8:-0.040733398979;MYB:-0.0478540751881;HNF1A:-0.0991320523284;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.118262316619;TFCP2:-0.136778447857;ATF5_CREB3:-0.151638814127;LMO2:-0.152606032239;SPZ1:-0.156181964551;POU1F1:-0.200577163644;PDX1:-0.202989228795;T:-0.216082441105;EVI1:-0.226308879095;ATF4:-0.242070275688;PAX2:-0.247032817946;NR3C1:-0.266330640722;SNAI1..3:-0.292638785652;ELF1,2,4:-0.300489523558;NFATC1..3:-0.331796376277;NFE2:-0.334911071805;SPIB:-0.341422589391;TEF:-0.356411473852;ARID5B:-0.363928609535;RORA:-0.365033106364;HNF4A_NR2F1,2:-0.374991927497;MYOD1:-0.378821607514;RUNX1..3:-0.396438620406;NFIX:-0.399298673098;CREB1:-0.401762127983;SPI1:-0.404060315131;BPTF:-0.437225294853;ESR1:-0.437312967374;AIRE:-0.467813369088;NFE2L2:-0.50595701835;FOXM1:-0.509742825693;NFKB1_REL_RELA:-0.584573055399;NFIL3:-0.608460119344;bHLH_family:-0.609698221229;NFE2L1:-0.618988843964;PPARG:-0.630586225819;RXRA_VDR{dimer}:-0.639015579145;DMAP1_NCOR{1,2}_SMARC:-0.64700225312;TP53:-0.66489223693;ALX1:-0.674802401646;NR5A1,2:-0.677033658313;ZEB1:-0.681325745586;ETS1,2:-0.692229719632;SREBF1,2:-0.701385496414;HLF:-0.719765379442;FOS_FOS{B,L1}_JUN{B,D}:-0.771083468888;CEBPA,B_DDIT3:-0.89388834527;FOSL2:-0.898439026506;EBF1:-0.907737243602;BACH2:-0.953965752483;ESRRA:-0.963378136565;IRF7:-0.971665978204;AR:-0.985967470151;FOXQ1:-0.992153458359;IRF1,2:-1.0226722961;HAND1,2:-1.08512848032;NKX2-2,8:-1.09915295977;FOX{D1,D2}:-1.11924854473;STAT2,4,6:-1.12244739896;ALX4:-1.15284783267;FOXO1,3,4:-1.47584990636;NR1H4:-1.5813512996
}}
}}

Revision as of 15:34, 21 March 2012


Name:whole body, 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
tissuewhole body
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

CNhs10512



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: CNhs10512



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: CNhs10512



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: CNhs10512


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)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000479 (tissue)
0000922 (embryo)
0001062 (anatomical entity)

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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:372-23H2&oldid=729016"