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|top_motifs=HNF4A_NR2F1,2:2.62816392383;NR6A1:2.62277976578;ARID5B:2.21803687763;RXRA_VDR{dimer}:1.94863117154;FOXM1:1.93155852366;SNAI1..3:1.80483872213;ZEB1:1.79727265148;DMAP1_NCOR{1,2}_SMARC:1.7428916467;POU1F1:1.66020947999;HNF1A:1.62090348726;TBX4,5:1.60551486418;IRF1,2:1.54616117115;NR1H4:1.4857705697;ESRRA:1.39136208363;CDX1,2,4:1.3717755399;JUN:1.29437432447;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.25158104392;TLX1..3_NFIC{dimer}:1.1385716009;NKX6-1,2:1.04560848469;RBPJ:1.02230257577;T:0.926872380662;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.893169715178;MYBL2:0.851865579832;ATF6:0.828545802862;PDX1:0.783581481064;STAT2,4,6:0.734350982862;AR:0.720924551191;MYOD1:0.683787267721;ZNF148:0.681222007612;XCPE1{core}:0.668415368374;SPZ1:0.647241744847;SRF:0.610089998646;LMO2:0.5793310954;GTF2A1,2:0.5772895675;ESR1:0.548682945465;EVI1:0.476787419132;NKX3-2:0.473272045694;FOSL2:0.44925407541;HAND1,2:0.43531728501;NFIX:0.396363962777;GATA6:0.39091925595;SP1:0.381215700122;ETS1,2:0.373260252237;ZNF423:0.359395537993;GLI1..3:0.340825307404;EBF1:0.307391831626;UFEwm:0.304458023416;FOXP1:0.282598668046;NR5A1,2:0.282280781459;FOXN1:0.274716228961;TBP:0.256430622264;PITX1..3:0.235641892718;TFAP4:0.216713055406;IRF7:0.210769924738;TOPORS:0.209161064054;TP53:0.192735297582;FOXA2:0.188453645598;FOX{D1,D2}:0.187655104153;FOS_FOS{B,L1}_JUN{B,D}:0.162926161062;TFCP2:0.1484905778;FOXO1,3,4:0.134701091146;ADNP_IRX_SIX_ZHX:0.130154909119;SPI1:0.107926200918;MAZ:0.102736856554;PPARG:0.0797308659947;FOX{I1,J2}:0.043033342929;ZBTB6:0.0312172362446;EN1,2:0.0244777906971;NKX2-1,4:0.024158110959;TEAD1:0.0179320223659;ELF1,2,4:-0.0129477634362;NFKB1_REL_RELA:-0.0308763776266;STAT1,3:-0.0925874211039;PAX8:-0.0926295667149;SPIB:-0.0934036923591;CDC5L:-0.136949663935;GZF1:-0.145026573745;LEF1_TCF7_TCF7L1,2:-0.173512936345;REST:-0.177371620609;bHLH_family:-0.18932567508;STAT5{A,B}:-0.192928552404;ATF5_CREB3:-0.21586693183;PBX1:-0.258433108116;CEBPA,B_DDIT3:-0.263715403433;BACH2:-0.291034204682;ZNF238:-0.299555581363;MYFfamily:-0.308545614078;HMGA1,2:-0.312372019043;TLX2:-0.32569593211;RUNX1..3:-0.331928602791;GFI1:-0.35031973055;TFAP2B:-0.373632879916;TEF:-0.378300185733;E2F1..5:-0.385016315254;GTF2I:-0.409641566042;HIC1:-0.430874987132;TAL1_TCF{3,4,12}:-0.455030092968;YY1:-0.458181292561;AIRE:-0.483421182274;ELK1,4_GABP{A,B1}:-0.493689410229;POU2F1..3:-0.500963236451;MTF1:-0.509709148731;DBP:-0.523143321214;IKZF1:-0.528462262485;MYB:-0.533099171402;MAFB:-0.533525902307;NANOG:-0.5364070227;BPTF:-0.53977185818;FOXQ1:-0.539988126125;PRDM1:-0.542009093019;ZIC1..3:-0.543508356991;VSX1,2:-0.556897664912;PAX5:-0.558024738746;NKX3-1:-0.5582685154;ALX4:-0.559428315926;HES1:-0.559789079039;NFE2L1:-0.563056167527;CUX2:-0.569148459083;MED-1{core}:-0.57447723969;HIF1A:-0.580524190272;EP300:-0.593984365096;CREB1:-0.595775628803;HMX1:-0.622752131155;ZFP161:-0.629920339198;PAX4:-0.63134489466;HLF:-0.639859351501;NR3C1:-0.640380340298;FOXL1:-0.653638240905;POU6F1:-0.657336025382;NKX2-2,8:-0.669919396453;MTE{core}:-0.671119615977;ONECUT1,2:-0.675937189818;OCT4_SOX2{dimer}:-0.678334589728;ATF2:-0.682672786298;KLF4:-0.687384273979;TFAP2{A,C}:-0.700483118903;HBP1_HMGB_SSRP1_UBTF:-0.703780684323;IKZF2:-0.707059021069;PATZ1:-0.717683638275;HOXA9_MEIS1:-0.718502965158;ZNF384:-0.723614650991;GATA4:-0.737095225717;PAX2:-0.745803890579;SMAD1..7,9:-0.770216850383;FOX{F1,F2,J1}:-0.800381759933;EGR1..3:-0.805294107921;ZBTB16:-0.830554850173;GCM1,2:-0.833826201195;TGIF1:-0.833962175743;RFX2..5_RFXANK_RFXAP:-0.840878599562;MEF2{A,B,C,D}:-0.845902113361;GFI1B:-0.853965337857;TFDP1:-0.85626106046;BREu{core}:-0.863057150931;SREBF1,2:-0.867505091983;NFE2:-0.87744461125;POU5F1:-0.877998981931;CRX:-0.89802319246;MZF1:-0.899450884378;PAX6:-0.912119242676;RREB1:-0.917071029819;PRRX1,2:-0.936176155375;NFIL3:-0.936578778161;FOXD3:-0.954644085443;RORA:-0.955531225558;PAX1,9:-0.971450627424;NFATC1..3:-0.971800427191;LHX3,4:-0.991455799442;NFY{A,B,C}:-1.00259909263;SOX17:-1.01630454554;RFX1:-1.03266408103;NFE2L2:-1.03863854698;AHR_ARNT_ARNT2:-1.06331182967;ATF4:-1.0978962747;NKX2-3_NKX2-5:-1.16390784596;RXR{A,B,G}:-1.18348094681;POU3F1..4:-1.20746699746;NHLH1,2:-1.23315031852;ZNF143:-1.28510432851;NRF1:-1.2861858851;SOX{8,9,10}:-1.31070687027;NANOG{mouse}:-1.36497108174;SOX5:-1.36917188535;SOX2:-1.4333534124;FOXP3:-1.44562612466;ALX1:-1.47029726668;HSF1,2:-1.56401454998;HOX{A5,B5}:-1.61374263012;HOX{A4,D4}:-1.73573295994
}}
}}

Revision as of 15:20, 15 February 2012


Name:small intestine, neonate N16, 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
tissuesmall intestine
dev stage16 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

CNhs11114



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: CNhs11114



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: CNhs11114



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: CNhs11114


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)
0000062 (organ)
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)
0002108 (small intestine)
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