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(Created page with "{{f5samples |id=FF:13297-142H3 |name=trophoblast stem cell line B1 differentiation, day00, biol_rep1 |sample_id=13297 |rna_tube_id=142H3 |rna_box=142 |rna_position=H3 |...")
 
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|top_motifs=BACH2:1.39587627061;PAX1,9:1.37832172921;AIRE:1.37727350279;PAX8:1.36561497692;HIF1A:1.32795327226;ELK1,4_GABP{A,B1}:1.28779952338;E2F1..5:1.25486518153;ZNF143:1.19287070415;NFE2:1.09153059985;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.04462916555;TP53:1.03992106893;ALX1:0.964340480251;HES1:0.921786351708;NRF1:0.910595465873;NFY{A,B,C}:0.903531790729;NFE2L1:0.851744733323;FOXP3:0.786839049289;PPARG:0.775160349623;ZBTB16:0.77300515957;STAT5{A,B}:0.599190260861;ONECUT1,2:0.592037543885;ZEB1:0.54252062426;TFDP1:0.517334601265;TEF:0.468667021712;MYB:0.467940782354;HSF1,2:0.456916860674;bHLH_family:0.442321666005;PDX1:0.409438394736;ZNF148:0.38669134856;FOS_FOS{B,L1}_JUN{B,D}:0.378353180518;NANOG:0.372412360702;RXR{A,B,G}:0.271638888269;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.256219904764;POU3F1..4:0.252126907544;XCPE1{core}:0.248088597071;PITX1..3:0.246360477426;SP1:0.23494386156;FOSL2:0.224994998689;HOXA9_MEIS1:0.214573521053;ATF4:0.199620997627;EVI1:0.180241495625;ELF1,2,4:0.172041352371;EN1,2:0.166476568123;SNAI1..3:0.164256496525;NFKB1_REL_RELA:0.155984648737;CDX1,2,4:0.145929177857;PAX2:0.14319509029;LHX3,4:0.139554377502;CREB1:0.131356172127;YY1:0.123618019557;UFEwm:0.12057794794;POU1F1:0.0598387667793;ESRRA:0.0425420780733;NKX3-1:0.0205766277759;TEAD1:-0.000613732519324;JUN:-0.0054589247946;GZF1:-0.018751981377;TFAP2{A,C}:-0.0460664676124;POU2F1..3:-0.0513577084104;HMX1:-0.0550700991314;STAT1,3:-0.0570715024802;ZIC1..3:-0.074866529948;FOXQ1:-0.097622722712;RORA:-0.127737863888;OCT4_SOX2{dimer}:-0.140642731869;MYOD1:-0.186982495725;RFX1:-0.189534697142;AHR_ARNT_ARNT2:-0.199866288997;HLF:-0.210149681759;ARID5B:-0.227299089291;SOX17:-0.233606725403;MTE{core}:-0.239033010128;FOXO1,3,4:-0.240978171793;LEF1_TCF7_TCF7L1,2:-0.25911627729;RUNX1..3:-0.262360644531;RFX2..5_RFXANK_RFXAP:-0.278287107073;TFCP2:-0.285388306024;PRRX1,2:-0.293403534854;FOXM1:-0.299099522891;SREBF1,2:-0.302987528111;T:-0.317825281281;CEBPA,B_DDIT3:-0.337216112843;RXRA_VDR{dimer}:-0.340878381202;ALX4:-0.349869624691;NKX2-3_NKX2-5:-0.363500152509;CRX:-0.368796608928;NFE2L2:-0.389470253139;HAND1,2:-0.393514586652;NANOG{mouse}:-0.396699026948;FOX{F1,F2,J1}:-0.401223094936;ZNF384:-0.402098798845;ATF5_CREB3:-0.403703585014;HNF4A_NR2F1,2:-0.407868686869;KLF4:-0.413734875979;SPIB:-0.416996233809;EGR1..3:-0.420082414766;NKX3-2:-0.425561668336;ADNP_IRX_SIX_ZHX:-0.440926844812;VSX1,2:-0.454867944449;ETS1,2:-0.46113508128;BREu{core}:-0.476969442403;TBP:-0.479172456179;REST:-0.484894198288;TFAP2B:-0.500435134852;HIC1:-0.506096694794;IKZF2:-0.519362177062;ESR1:-0.548270216638;IKZF1:-0.5553096861;HOX{A4,D4}:-0.558972457128;NFATC1..3:-0.562968367388;ZFP161:-0.570453972623;MAZ:-0.576789521236;FOXN1:-0.577737696795;NKX2-2,8:-0.589677220379;SOX{8,9,10}:-0.59369345823;NFIX:-0.594584543302;HNF1A:-0.59699259541;CUX2:-0.613251861454;SPI1:-0.617346291311;CDC5L:-0.619601482488;EBF1:-0.619902386608;IRF1,2:-0.625972006806;MEF2{A,B,C,D}:-0.630320956416;TBX4,5:-0.633712666581;EP300:-0.649160499415;GFI1:-0.664988435055;MED-1{core}:-0.673491430731;FOX{D1,D2}:-0.677714677664;STAT2,4,6:-0.717293890854;GATA6:-0.724017921503;RREB1:-0.736053808892;MZF1:-0.736564684719;PAX4:-0.737693067417;FOXA2:-0.76415728685;ZBTB6:-0.766955285308;ATF2:-0.780580713386;PATZ1:-0.786876276683;NKX2-1,4:-0.789320610688;POU6F1:-0.791610401172;SPZ1:-0.79232706454;GFI1B:-0.806050887229;SOX2:-0.806529989659;GATA4:-0.830056442664;POU5F1:-0.830974253808;TLX2:-0.83392438315;SRF:-0.838991096124;NR5A1,2:-0.865999692263;FOXL1:-0.870076149512;ZNF423:-0.876642982997;BPTF:-0.894618639586;PAX6:-0.94656890043;HMGA1,2:-0.952616149345;NKX6-1,2:-0.960004086616;NFIL3:-0.962329932503;NR1H4:-0.98697132039;FOX{I1,J2}:-1.00019770148;FOXD3:-1.00140350546;SOX5:-1.00331834607;LMO2:-1.03044403273;DMAP1_NCOR{1,2}_SMARC:-1.04386297761;TOPORS:-1.045699673;TFAP4:-1.06462514412;AR:-1.06906863586;HOX{A5,B5}:-1.08050669796;GCM1,2:-1.08522439015;NHLH1,2:-1.09357996633;DBP:-1.11442946627;PBX1:-1.12893840537;ZNF238:-1.14520566653;GTF2A1,2:-1.15390903684;IRF7:-1.15530261442;GTF2I:-1.19763043583;HBP1_HMGB_SSRP1_UBTF:-1.24187010385;MTF1:-1.25360182191;MAFB:-1.26794223288;FOXP1:-1.3145125963;NR3C1:-1.33062537351;GLI1..3:-1.34388723408;TAL1_TCF{3,4,12}:-1.34460245194;PAX5:-1.39892936531;TGIF1:-1.41135115052;RBPJ:-1.48917875103;MYFfamily:-1.53095093211;PRDM1:-1.62140914281;NR6A1:-1.68024928342;ATF6:-1.69709596547;SMAD1..7,9:-1.72022919973;MYBL2:-1.75105649845;TLX1..3_NFIC{dimer}:-1.85586221429
}}
}}

Revision as of 15:21, 15 February 2012


Name:trophoblast stem cell line B1 differentiation, day00, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexfemale
ageNA
cell typeSELECT CELL TYPE
cell lineNA
companyNA
collaborationHirohiko Kodeki(RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberB1 +d0
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

CNhs13526



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: CNhs13526



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: CNhs13526



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: CNhs13526


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000255 (eukaryotic cell)
0000349 (extraembryonic cell)
0000351 (trophoblast cell)
0000548 (animal cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000358 (blastocyst)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000922 (embryo)
0001062 (anatomical entity)
0002050 (embryonic structure)
0005423 (developing anatomical structure)

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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