FF:395-14B1: Difference between revisions
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{{f5samples | {{f5samples | ||
| | |ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000468,UBERON:0000479,UBERON:0000922,UBERON:0001062 | ||
|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
| | |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= | ||
|has_quality= | |has_quality= | ||
|id=FF:395-14B1 | |||
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011333 | |is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011333 | ||
|name=whole body, embryo E14 | |||
|namespace=FANTOM5 | |namespace=FANTOM5 | ||
|part_of= | |part_of= | ||
|profile_cagescan=,,, | |||
|profile_hcage=CNhs10519,LSID649,release008,COMPLETED | |||
|profile_rnaseq=,,, | |||
|profile_srnaseq=,,, | |||
|rna_box=14 | |||
|rna_catalog_number= | |||
|rna_concentration= | |||
|rna_extraction_protocol= | |||
|rna_lot_number= | |||
|rna_od260/230= | |||
|rna_od260/280= | |||
|rna_position=B1 | |||
|rna_rin= | |||
|rna_sample_type= | |||
|rna_tube_id=14B1 | |||
|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=14 days embryo | |||
|sample_disease= | |||
|sample_donor(cell lot)= | |||
|sample_ethnicity= | |||
|sample_experimental_condition= | |||
|sample_id=395 | |||
|sample_note= | |||
|sample_sex=mixture | |||
|sample_species=Mouse (Mus musculus) | |||
|sample_strain=C57BL/6J | |||
|sample_tissue=whole body | |||
|top_motifs=FOXL1:1.66996773276;PAX1,9:1.65485229188;ZNF423:1.60185290511;NANOG{mouse}:1.52488342711;GATA6:1.50026370319;NKX2-3_NKX2-5:1.36608057585;RREB1:1.35300656011;SMAD1..7,9:1.34779740125;HOX{A4,D4}:1.31146004352;SOX{8,9,10}:1.19941720528;NFY{A,B,C}:1.1324969034;MZF1:1.12238824107;PATZ1:1.11298906094;OCT4_SOX2{dimer}:1.05690486617;GFI1:1.05579907472;EP300:1.0481726741;TBP:1.01784142529;PBX1:1.01218027003;TGIF1:0.983799150015;HSF1,2:0.983278962992;PRRX1,2:0.979432075494;CUX2:0.927072840691;HOXA9_MEIS1:0.926769294156;ONECUT1,2:0.913132529234;POU5F1:0.908829165674;MAZ:0.9021018025;PAX6:0.884414780452;E2F1..5:0.878718987457;SOX2:0.865955984368;LHX3,4:0.818484464789;FOX{F1,F2,J1}:0.812927896033;KLF4:0.769737823956;ZNF238:0.768457695275;BREu{core}:0.766689587849;ZNF148:0.746050738041;NKX3-2:0.735661183994;TFAP4:0.734309600077;NHLH1,2:0.734232622416;GTF2I:0.72627193007;TFCP2:0.711932704679;ADNP_IRX_SIX_ZHX:0.710910399337;SOX5:0.703002207447;TFDP1:0.702177264752;MYBL2:0.695508305205;VSX1,2:0.693575225665;LEF1_TCF7_TCF7L1,2:0.660545155321;SOX17:0.645826949592;TBX4,5:0.643883626793;NANOG:0.631279895999;MED-1{core}:0.621626529551;SRF:0.61821484043;ZNF143:0.611451782152;GZF1:0.609926541305;MYFfamily:0.598401272591;AHR_ARNT_ARNT2:0.574564709542;NRF1:0.546934289196;EN1,2:0.53544954341;ZNF384:0.518602731043;MEF2{A,B,C,D}:0.516000164394;HIC1:0.507151440625;MAFB:0.501450552858;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.459063298952;EGR1..3:0.422648214866;T:0.415793127818;NKX2-1,4:0.414815937767;FOXA2:0.413277156079;TLX1..3_NFIC{dimer}:0.40996198913;MTF1:0.405513614766;EBF1:0.396043797416;ZFP161:0.394725596716;HBP1_HMGB_SSRP1_UBTF:0.393930813112;DBP:0.380645162577;POU2F1..3:0.37921925989;MYOD1:0.379029073246;PRDM1:0.372782782063;XCPE1{core}:0.369193264819;GFI1B:0.368315607657;TFAP2B:0.359379725129;ZIC1..3:0.350286610621;TOPORS:0.346824602432;TFAP2{A,C}:0.343961368135;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.342711863904;FOXM1:0.342533725057;POU6F1:0.33341370124;HOX{A5,B5}:0.321248042474;RFX1:0.30202202087;RBPJ:0.296587887015;HES1:0.29531206662;NFE2L1:0.286122525504;FOXD3:0.284888739862;TAL1_TCF{3,4,12}:0.281685290758;HNF1A:0.279201904878;NFIX:0.274930243235;GLI1..3:0.269908311203;RORA:0.257946213456;TEAD1:0.223559989429;ATF2:0.206861321555;JUN:0.188947546109;TLX2:0.182367824591;PDX1:0.167725966257;UFEwm:0.16535466018;MTE{core}:0.143713186584;GCM1,2:0.136407227356;IKZF2:0.126917508932;NFE2L2:0.126257665643;REST:0.122692270856;POU3F1..4:0.120889033378;RFX2..5_RFXANK_RFXAP:0.116168467169;MYB:0.107488390675;LMO2:0.105244701393;HMX1:0.0984049906459;HIF1A:0.084537283167;PAX2:0.0658704240611;ZBTB6:0.057127620108;STAT5{A,B}:0.0560391958389;EVI1:0.0515348360605;IKZF1:0.042327304269;NKX3-1:0.0388397495307;NFATC1..3:0.0290970151438;HNF4A_NR2F1,2:0.0234613496625;CDC5L:0.000326751293077;HMGA1,2:0.000194585955411;RUNX1..3:-0.00845139077689;SP1:-0.0143352325665;ALX1:-0.0200178313814;SNAI1..3:-0.0265229642188;STAT1,3:-0.0331533341811;CEBPA,B_DDIT3:-0.0352114244261;GTF2A1,2:-0.0362929115039;YY1:-0.0399490236469;ATF4:-0.0642177238157;NFE2:-0.0724339618789;PAX5:-0.0857685959583;NR3C1:-0.102695441594;ATF6:-0.111455505624;ATF5_CREB3:-0.135947237182;GATA4:-0.140093292392;BACH2:-0.149129643672;HAND1,2:-0.184444199731;HLF:-0.213282722917;PPARG:-0.214808539446;bHLH_family:-0.221049540241;PITX1..3:-0.237736410669;AIRE:-0.26614828625;CREB1:-0.271934960979;CDX1,2,4:-0.277041163453;FOSL2:-0.281278421758;ELK1,4_GABP{A,B1}:-0.283111770443;TP53:-0.293282455761;ARID5B:-0.294804598768;FOS_FOS{B,L1}_JUN{B,D}:-0.295008906252;PAX8:-0.323071074042;TEF:-0.347569272657;NR5A1,2:-0.365866419487;PAX4:-0.370874581804;DMAP1_NCOR{1,2}_SMARC:-0.384727013846;ESRRA:-0.406041762285;FOX{D1,D2}:-0.421822190205;RXRA_VDR{dimer}:-0.436777637454;SPI1:-0.448188090463;CRX:-0.462893349795;AR:-0.468431614673;FOXP3:-0.487211401125;IRF7:-0.488035566772;SPIB:-0.488256839221;NFKB1_REL_RELA:-0.492658216114;ESR1:-0.507492912587;RXR{A,B,G}:-0.51081141906;ELF1,2,4:-0.513317247468;NFIL3:-0.535484126512;ZEB1:-0.544303601139;NKX6-1,2:-0.564633766684;STAT2,4,6:-0.577213678973;FOXN1:-0.604671275774;ETS1,2:-0.60500228992;ALX4:-0.655377457604;NR6A1:-0.665675805437;FOXQ1:-0.671055131466;SPZ1:-0.680474676038;FOX{I1,J2}:-0.850963543807;IRF1,2:-0.907315967897;ZBTB16:-0.958178137645;POU1F1:-0.967723502707;NKX2-2,8:-0.979559998467;FOXO1,3,4:-0.990598428091;SREBF1,2:-1.04458628017;NR1H4:-1.05046405578;FOXP1:-1.18678322172;BPTF:-1.50615994155 | |||
}} | }} |
Revision as of 15:34, 21 March 2012
Name: | whole body, embryo E14 |
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Species: | Mouse (Mus musculus) |
Library ID: | {{{library_id}}} |
Sample type: | {{{sample_category}}} |
Genomic View: | UCSC |
CAGEd-oPOSSUM: | link |
Additional information | ||||||||||||||||||||||||||||
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Sample information
RNA information
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Download raw sequence, BAM & CTSS | ||||||||||||
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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
CNhs10519
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: CNhs10519
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: CNhs10519
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: CNhs10519
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000004 tissue sample
FF:0000103 mouse sample
FF:0011333 mouse whole body- embryo E14 sample
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