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{{f5samples
{{f5samples
|id=FF:761-6B4
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000468,UBERON:0000479,UBERON:0001062
|name=whole body, neonate N10
|sample_id=761
|rna_tube_id=6B4
|rna_box=6
|rna_position=B4
|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=10 days neonate
|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=CNhs10518,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: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:761-6B4
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011420
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011420
|name=whole body, neonate N10
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs10518,LSID649,release008,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=6
|rna_catalog_number=
|rna_concentration=
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=B4
|rna_rin=
|rna_sample_type=
|rna_tube_id=6B4
|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=10 days neonate
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=761
|sample_note=
|sample_sex=mixture
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=whole body
|top_motifs=MEF2{A,B,C,D}:2.80323910383;FOXL1:2.72468084339;TBP:2.47606531534;ESR1:2.2433557508;SMAD1..7,9:2.20985432401;HOX{A4,D4}:2.20495899248;TFAP4:2.13592758709;TLX2:1.94807032519;TFCP2:1.91300412354;GCM1,2:1.70515688105;NFE2L2:1.70159875066;ZNF238:1.66602352621;NFATC1..3:1.66068905205;TFAP2{A,C}:1.58905909781;GLI1..3:1.52432422895;NKX2-3_NKX2-5:1.51051223567;EBF1:1.50129678498;TAL1_TCF{3,4,12}:1.46770968639;SOX5:1.44543554135;NR5A1,2:1.35337656013;FOSL2:1.30556586257;FOXP3:1.29607807461;ZNF148:1.29595107254;MAFB:1.29320512701;TOPORS:1.29223790227;TGIF1:1.27710959651;STAT2,4,6:1.22827755255;SRF:1.21066375291;MYFfamily:1.21041108672;TLX1..3_NFIC{dimer}:1.17244341913;MYOD1:1.14473076544;SOX{8,9,10}:1.14221378804;NHLH1,2:1.12470227594;HES1:1.10864112159;RXRA_VDR{dimer}:1.10293844155;TEAD1:1.08219124716;PAX1,9:1.02916651666;GFI1:0.957963622087;RXR{A,B,G}:0.933063802209;NR3C1:0.930698855749;EP300:0.884640029966;MYBL2:0.824743845232;MTF1:0.805007064923;ATF6:0.800055514575;GTF2A1,2:0.781441130419;NFE2L1:0.752719247282;ESRRA:0.735284898356;IKZF1:0.658133237052;HSF1,2:0.639159317767;PPARG:0.628854369099;GATA6:0.609188070029;ALX4:0.607860826218;TP53:0.59948501821;RORA:0.585734695703;CEBPA,B_DDIT3:0.582942685641;KLF4:0.581816751212;MAZ:0.580198421903;PAX5:0.565113970601;FOS_FOS{B,L1}_JUN{B,D}:0.529783316323;GFI1B:0.517386894328;FOXQ1:0.494074883555;PATZ1:0.493163602032;SP1:0.476686051157;XCPE1{core}:0.474131716993;PRDM1:0.469553718445;HIC1:0.452432253473;HLF:0.444738186271;FOXA2:0.419192342001;GTF2I:0.404422504369;NFE2:0.398360449629;HIF1A:0.398312381944;YY1:0.391583452498;ALX1:0.34379148953;SPZ1:0.339504372265;RUNX1..3:0.33064269021;LEF1_TCF7_TCF7L1,2:0.324705649786;CRX:0.324081649535;LMO2:0.322427521787;PBX1:0.317288311439;IRF7:0.316463990561;SPIB:0.290663452512;ZIC1..3:0.288409942086;SPI1:0.278859218893;FOX{I1,J2}:0.267351280936;BACH2:0.252679082507;DMAP1_NCOR{1,2}_SMARC:0.247747467672;RREB1:0.24458727361;PAX2:0.24006667197;SREBF1,2:0.237799490082;MTE{core}:0.233478645614;STAT5{A,B}:0.186110615242;ETS1,2:0.178205264117;NR1H4:0.171204727348;UFEwm:0.148804870144;VSX1,2:0.136537284073;TFAP2B:0.135902212097;HMGA1,2:0.126494148817;AR:0.123260863627;EN1,2:0.093912414872;HMX1:0.0896004064106;PDX1:0.0743148773323;MZF1:0.0655682518132;TBX4,5:0.0571134419723;FOXO1,3,4:0.0520125325742;NR6A1:0.0197210710121;GATA4:0.0129181380287;POU3F1..4:0.00203304528926;NFIL3:-0.005117094985;NKX2-2,8:-0.0211067389043;REST:-0.0233686684871;IRF1,2:-0.0244318619339;POU5F1:-0.027977462379;ZNF423:-0.0357569815057;POU2F1..3:-0.0771069247004;NFKB1_REL_RELA:-0.0810517803638;ZNF143:-0.0821965557977;ELF1,2,4:-0.085644613349;NKX3-2:-0.0928423275228;HBP1_HMGB_SSRP1_UBTF:-0.0944845052777;IKZF2:-0.112593896668;E2F1..5:-0.120851597821;FOX{F1,F2,J1}:-0.121671363584;NANOG{mouse}:-0.121822615294;EVI1:-0.136694479445;T:-0.143560217044;NKX2-1,4:-0.15328672953;JUN:-0.156523191962;ZFP161:-0.165166924088;ATF2:-0.18365394511;ZBTB6:-0.196718485877;EGR1..3:-0.217014698799;HOXA9_MEIS1:-0.232190567364;NANOG:-0.232395069508;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.27256277422;MED-1{core}:-0.326008583104;SOX2:-0.339199432212;SOX17:-0.36698232171;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.376405580598;FOX{D1,D2}:-0.378281622971;ATF4:-0.384834730705;PITX1..3:-0.390513067031;CDC5L:-0.406248824278;PRRX1,2:-0.412568508485;HNF4A_NR2F1,2:-0.426607727516;bHLH_family:-0.439112082428;ZNF384:-0.439856759627;HOX{A5,B5}:-0.4442957746;MYB:-0.451983548648;ARID5B:-0.495226030114;BREu{core}:-0.49878689591;POU6F1:-0.498995077124;HNF1A:-0.515677026114;LHX3,4:-0.522415682626;NRF1:-0.523280863556;RFX1:-0.528299385598;CUX2:-0.529691589305;PAX8:-0.555104176871;RFX2..5_RFXANK_RFXAP:-0.562664379562;RBPJ:-0.578033079071;HAND1,2:-0.58013047477;NFY{A,B,C}:-0.592028891047;DBP:-0.594272815287;ATF5_CREB3:-0.599629772239;POU1F1:-0.631508106767;FOXM1:-0.688686850916;TEF:-0.716846063983;SNAI1..3:-0.748978068609;GZF1:-0.761334356603;AHR_ARNT_ARNT2:-0.788260366886;NKX3-1:-0.791075641707;TFDP1:-0.794000718577;ZEB1:-0.856894907041;PAX6:-0.894967752471;PAX4:-0.912921155951;FOXP1:-0.969288184802;OCT4_SOX2{dimer}:-0.97129757895;CREB1:-1.01713215188;NFIX:-1.01871816744;AIRE:-1.14860198871;ELK1,4_GABP{A,B1}:-1.20488981648;ADNP_IRX_SIX_ZHX:-1.27675756429;FOXD3:-1.28134194755;FOXN1:-1.29079430229;STAT1,3:-1.33236730547;NKX6-1,2:-1.36228821431;CDX1,2,4:-1.52092002853;ZBTB16:-1.56603721766;BPTF:-1.69274181558;ONECUT1,2:-1.78540902025
}}
}}

Revision as of 15:36, 21 March 2012


Name:whole body, neonate N10
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 stage10 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
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

CNhs10518



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: CNhs10518



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: CNhs10518



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: CNhs10518


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)
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