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|top_motifs=GZF1:1.85010041054;HNF4A_NR2F1,2:1.63527921;PDX1:1.44661625918;HNF1A:1.41661358767;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.37797786652;GFI1:1.1839618278;CDX1,2,4:1.14268707193;ATF6:1.04247688044;ESRRA:1.00190535895;SNAI1..3:1.00130892971;TOPORS:0.960884111614;MYBL2:0.944567258139;NKX2-1,4:0.844748696709;ZNF423:0.835487253574;FOXM1:0.831642751669;SRF:0.817617613215;ZNF238:0.796920788966;XCPE1{core}:0.791594309367;ADNP_IRX_SIX_ZHX:0.779462013365;NR6A1:0.764433492956;TLX2:0.733938596707;NFY{A,B,C}:0.709720451724;SREBF1,2:0.649389739364;MAZ:0.629584209401;ZEB1:0.597281073296;NANOG:0.59113867299;TLX1..3_NFIC{dimer}:0.55509937387;RXR{A,B,G}:0.487191277065;E2F1..5:0.481002598877;ZNF148:0.479216258574;LEF1_TCF7_TCF7L1,2:0.458470678168;RXRA_VDR{dimer}:0.435899133734;GATA6:0.424333225624;RBPJ:0.418461288136;FOX{I1,J2}:0.412789347065;SP1:0.392062201323;GFI1B:0.377468136918;bHLH_family:0.337979947008;NFIX:0.337047368279;HIF1A:0.327706906295;GTF2I:0.319631018516;FOXQ1:0.317439505646;HMX1:0.308711973672;TEAD1:0.306126396063;FOXA2:0.28726253168;CUX2:0.273887372416;STAT1,3:0.272624967575;PATZ1:0.264597704431;FOXN1:0.258690212447;DMAP1_NCOR{1,2}_SMARC:0.247852950505;NKX3-2:0.240352852344;PRRX1,2:0.233466745712;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.232899732943;RREB1:0.228580617468;TFDP1:0.228009233177;T:0.224957288776;ONECUT1,2:0.224051527664;HMGA1,2:0.195626646793;IKZF2:0.180391421611;LHX3,4:0.179106102709;EP300:0.177500391861;TFCP2:0.168856174876;ZNF384:0.163778525339;BREu{core}:0.163093911468;ETS1,2:0.158969037886;HAND1,2:0.1541596979;FOSL2:0.145096776317;HIC1:0.135193909969;TFAP4:0.12370169967;EBF1:0.123111475154;AHR_ARNT_ARNT2:0.115572874104;ZIC1..3:0.10997802182;HBP1_HMGB_SSRP1_UBTF:0.0965970790041;ZNF143:0.0890819686793;LMO2:0.0844313067829;OCT4_SOX2{dimer}:0.0844048810389;FOX{D1,D2}:0.0839970955905;ESR1:0.0725327629844;ELF1,2,4:0.0663615364494;YY1:0.0650026310583;DBP:0.0275489008578;VSX1,2:0.0261190783965;TP53:0.0215152016573;TBP:0.0200549579671;PAX8:0.0136275864678;PBX1:0.0108116046449;POU3F1..4:0.00400123808893;SOX17:-0.00764709245535;REST:-0.0159801177532;MYOD1:-0.0201343694027;IKZF1:-0.0226504144101;MTF1:-0.0247570551072;TBX4,5:-0.02919049084;GTF2A1,2:-0.0539617182964;ARID5B:-0.060360365139;AIRE:-0.0626584301151;FOX{F1,F2,J1}:-0.0665313381459;EVI1:-0.0701628323359;NKX2-3_NKX2-5:-0.0796741656191;POU6F1:-0.0878217723422;GCM1,2:-0.0883178369879;MZF1:-0.0999995512474;TEF:-0.115601085463;MED-1{core}:-0.115676707041;PAX6:-0.121067657196;ATF2:-0.123337526723;PRDM1:-0.138967822008;IRF7:-0.161578268842;SOX5:-0.167822304706;FOXO1,3,4:-0.17129846385;NFKB1_REL_RELA:-0.183698638852;HOXA9_MEIS1:-0.184559160382;ZBTB6:-0.204158210242;GLI1..3:-0.205641910427;CDC5L:-0.212048348872;SOX{8,9,10}:-0.214065435647;SOX2:-0.220930582067;SPIB:-0.228219935322;AR:-0.228246673736;FOS_FOS{B,L1}_JUN{B,D}:-0.231867157652;FOXD3:-0.235234363193;TFAP2B:-0.235754406994;SPZ1:-0.250230236076;BPTF:-0.252653844996;MYB:-0.260070033277;ZFP161:-0.264395429101;IRF1,2:-0.273164246167;ALX4:-0.287758392943;NR5A1,2:-0.290903811031;SMAD1..7,9:-0.293108191508;GATA4:-0.294590425187;ELK1,4_GABP{A,B1}:-0.295954590912;STAT2,4,6:-0.29824441798;FOXP1:-0.317200999883;TFAP2{A,C}:-0.327291417561;RUNX1..3:-0.335048515281;KLF4:-0.336709570243;PITX1..3:-0.337626348828;EGR1..3:-0.340801832654;ZBTB16:-0.370480064653;NRF1:-0.371429173297;SPI1:-0.374267102623;POU2F1..3:-0.385800727604;ATF5_CREB3:-0.390829181497;NR1H4:-0.39084102573;RFX1:-0.401194866606;PAX1,9:-0.42381772707;NANOG{mouse}:-0.426328148514;TGIF1:-0.428522593681;JUN:-0.464925331946;NKX3-1:-0.468237523353;MYFfamily:-0.483872774009;CEBPA,B_DDIT3:-0.493419834157;CRX:-0.493635062916;PAX4:-0.514577974612;PAX2:-0.524835218493;POU1F1:-0.537922641674;MTE{core}:-0.543953038253;HLF:-0.554666657203;NFATC1..3:-0.555121343032;HES1:-0.561720752895;PAX5:-0.562329725284;NR3C1:-0.574929540903;NKX2-2,8:-0.580647536755;HSF1,2:-0.58067775993;NHLH1,2:-0.581944483204;RFX2..5_RFXANK_RFXAP:-0.585292902054;CREB1:-0.593269071289;EN1,2:-0.593660169317;MAFB:-0.602484878005;MEF2{A,B,C,D}:-0.623515887087;UFEwm:-0.656988119463;POU5F1:-0.662130612674;PPARG:-0.682990561212;STAT5{A,B}:-0.686710999211;HOX{A5,B5}:-0.720530301201;NFE2:-0.730082912719;BACH2:-0.78001802248;ALX1:-0.799469518441;FOXL1:-0.840502236306;RORA:-0.849179587919;NFE2L2:-0.874203532307;ATF4:-0.989088370877;FOXP3:-1.06687534548;NKX6-1,2:-1.11918545336;NFE2L1:-1.12094179891;TAL1_TCF{3,4,12}:-1.25071219769;NFIL3:-1.5677003174;HOX{A4,D4}:-1.57047923999
}}
}}

Revision as of 15:19, 15 February 2012


Name:intestine, embryo E16, biol_rep1
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 stage16 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

CNhs10585



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: CNhs10585



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: CNhs10585



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: CNhs10585


FANTOM5 (FF) ontology


Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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