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|top_motifs=HNF4A_NR2F1,2:1.96046446143;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.86739970724;HNF1A:1.47459817942;ESRRA:1.35045284726;PDX1:1.34846376521;SREBF1,2:1.26301938913;ATF6:1.22953251441;MYBL2:1.19862521038;ZNF423:1.16658418045;GZF1:1.14911292266;SNAI1..3:1.11398221191;GFI1:1.01390172308;XCPE1{core}:0.970665290228;CDX1,2,4:0.969006126412;NFIX:0.848353883456;SRF:0.836311267054;TOPORS:0.814722545511;FOXM1:0.778624921923;NR6A1:0.768804757802;TLX1..3_NFIC{dimer}:0.709102019086;ZEB1:0.692651071621;ZNF238:0.648293583632;NFY{A,B,C}:0.643668556089;TLX2:0.630030114458;ZNF148:0.622008862701;DMAP1_NCOR{1,2}_SMARC:0.608735237602;RXRA_VDR{dimer}:0.598481696126;MAZ:0.589445285175;NANOG:0.588816232337;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.506211679936;LEF1_TCF7_TCF7L1,2:0.479054037113;SP1:0.468811087164;ADNP_IRX_SIX_ZHX:0.455378949257;TBX4,5:0.41331335929;GATA6:0.412602417501;HIF1A:0.401985887264;NKX2-1,4:0.386889813362;RBPJ:0.383087832058;TFAP4:0.321880583731;ESR1:0.317546287609;GTF2I:0.272502512501;STAT1,3:0.268281529642;FOXA2:0.267360033739;PAX6:0.251541906221;ETS1,2:0.247047437155;PRRX1,2:0.245591831414;CUX2:0.233802128066;TEAD1:0.21933208804;GTF2A1,2:0.189963300659;TFCP2:0.184183389343;POU6F1:0.182311772723;EVI1:0.180727445412;TBP:0.174808537039;RXR{A,B,G}:0.174782715985;NKX3-1:0.162381335193;E2F1..5:0.155618717714;EP300:0.154614456446;RREB1:0.143594937698;VSX1,2:0.140086564525;HMGA1,2:0.139074685909;PAX2:0.138405570828;LMO2:0.137702392733;FOXQ1:0.135212603323;FOX{D1,D2}:0.135192905063;IKZF2:0.131975396581;GFI1B:0.112916051029;ELF1,2,4:0.111550530463;AR:0.097364026128;NANOG{mouse}:0.0938187295026;ARID5B:0.0728760642143;FOX{I1,J2}:0.0675340508524;HIC1:0.0402351237973;PATZ1:0.0360972666796;T:0.0301704811793;REST:0.0179577082468;CDC5L:0.0129818391004;TP53:0.00995925039542;IKZF1:0.00837630522564;FOXN1:0.00671964651892;STAT2,4,6:0.00122982500114;TFDP1:-0.00466891306488;FOSL2:-0.0066354710463;IRF1,2:-0.0169028431502;NR1H4:-0.0210201262121;NKX3-2:-0.0263179758678;ALX4:-0.0267580685482;HMX1:-0.0323824900445;MYOD1:-0.0342810312293;DBP:-0.0383149730198;ZNF143:-0.0553571461912;ZNF384:-0.0594445163762;ONECUT1,2:-0.0752371587519;EBF1:-0.10435079662;GLI1..3:-0.109371477655;POU1F1:-0.109709435631;LHX3,4:-0.116962582496;SMAD1..7,9:-0.131075785324;HBP1_HMGB_SSRP1_UBTF:-0.139392079489;NR5A1,2:-0.144350324503;NFKB1_REL_RELA:-0.150299074051;SPIB:-0.156593014511;PAX8:-0.16427308949;PBX1:-0.170951877816;PAX1,9:-0.173276928011;FOS_FOS{B,L1}_JUN{B,D}:-0.180766975356;SOX17:-0.190031412281;BREu{core}:-0.201158929341;ELK1,4_GABP{A,B1}:-0.202074366642;SPZ1:-0.212915263601;PPARG:-0.215974918016;FOX{F1,F2,J1}:-0.218121359535;bHLH_family:-0.22723227301;AIRE:-0.228857893354;ZBTB6:-0.235438214357;MZF1:-0.240007751605;MED-1{core}:-0.254208466867;FOXP1:-0.258791717206;GCM1,2:-0.268982358311;SPI1:-0.293166677466;IRF7:-0.294526583509;ATF2:-0.295570401257;AHR_ARNT_ARNT2:-0.297578235486;HAND1,2:-0.300575140447;POU3F1..4:-0.306437942823;KLF4:-0.313565484926;MYFfamily:-0.323949478106;OCT4_SOX2{dimer}:-0.349550185386;BPTF:-0.360659834303;GATA4:-0.373919610433;HES1:-0.377608716162;ATF5_CREB3:-0.379377032861;TFAP2B:-0.388401008593;SOX5:-0.391891791623;NKX2-3_NKX2-5:-0.392777813743;ZIC1..3:-0.397072186327;FOXL1:-0.398999932185;MYB:-0.403870570353;SOX2:-0.411081502378;SOX{8,9,10}:-0.413208082893;MTF1:-0.421743486959;NRF1:-0.432398554212;HLF:-0.432399213773;RUNX1..3:-0.434225965247;PRDM1:-0.445070196783;PAX4:-0.452345928962;YY1:-0.467987813741;ZFP161:-0.474845554097;JUN:-0.47720063329;STAT5{A,B}:-0.477958412434;FOXD3:-0.479276233961;RFX1:-0.483442223027;CREB1:-0.507778418116;EN1,2:-0.511506250298;POU2F1..3:-0.512019362757;FOXO1,3,4:-0.525153034161;EGR1..3:-0.53444419991;CEBPA,B_DDIT3:-0.542707978342;ZBTB16:-0.572885017979;TFAP2{A,C}:-0.573214122038;TGIF1:-0.574459783734;NHLH1,2:-0.610327926076;MEF2{A,B,C,D}:-0.611126852218;RORA:-0.626041860439;MTE{core}:-0.637069522816;PAX5:-0.646667947254;TEF:-0.672143439255;CRX:-0.673258727914;PITX1..3:-0.698616749528;NKX2-2,8:-0.705869836918;MAFB:-0.741917384962;UFEwm:-0.756810073934;NFE2:-0.7662788409;NFE2L2:-0.766655566304;NKX6-1,2:-0.769190894485;HOXA9_MEIS1:-0.787385087508;BACH2:-0.787512182853;TAL1_TCF{3,4,12}:-0.795377919054;ATF4:-0.815400009139;NR3C1:-0.858846200494;NFATC1..3:-0.865463773529;HSF1,2:-0.902124309072;RFX2..5_RFXANK_RFXAP:-0.937910247808;POU5F1:-0.944341569092;HOX{A5,B5}:-0.97125195644;FOXP3:-1.08912162224;NFE2L1:-1.15024304607;NFIL3:-1.43763966688;ALX1:-1.45218749499;HOX{A4,D4}:-1.65678469178
}}
}}

Revision as of 15:19, 15 February 2012


Name:intestine, embryo E17, 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 stage17 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
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
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

CNhs10582



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: CNhs10582



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: CNhs10582



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: CNhs10582


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

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