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|fonse_treatment_closure=
|fonse_treatment_closure=
|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
|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
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011425
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:04, 7 March 2012


Name:small intestine, neonate N16
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
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

CNhs11114

00
10
100
1000
10000.0184
10010.0162
10020.0386
1003-0.0773
10040
10050.199
10060
1007-0.102
10081.681
1009-5.040489e-4
101-0.0723
10100
1011-0.138
10120
10130.213
1014-0.0874
1015-0.221
1016-0.13
10170
10180.336
10190
1020
10200
1021-0.0487
10220.129
10230
10240.0285
10250.695
10260
10270
10280
10290.408
1030.111
10300
1031-0.0553
10320.467
1033-0.0525
10340.187
10350
1036-0.0718
10370
10380.0374
1039-0.0755
1040
1040-0.101
10410.111



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

Jaspar motifP-value
MA0002.20.0359
MA0003.10.141
MA0004.10.885
MA0006.10.0423
MA0007.10.787
MA0009.10.31
MA0014.10.756
MA0017.15.83808e-24
MA0018.20.00708
MA0019.10.269
MA0024.10.027
MA0025.10.421
MA0027.10.629
MA0028.10.205
MA0029.10.924
MA0030.10.838
MA0031.10.513
MA0035.21.08189e-5
MA0038.10.313
MA0039.20.00439
MA0040.10.152
MA0041.10.417
MA0042.10.924
MA0043.10.0241
MA0046.12.5385e-39
MA0047.20.00819
MA0048.10.548
MA0050.19.18089e-8
MA0051.17.69406e-6
MA0052.11.02148e-4
MA0055.10.307
MA0057.10.206
MA0058.10.711
MA0059.10.829
MA0060.16.57373e-5
MA0061.10.455
MA0062.20.135
MA0065.25.67062e-14
MA0066.10.0746
MA0067.10.177
MA0068.10.254
MA0069.10.0688
MA0070.10.248
MA0071.10.56
MA0072.10.49
MA0073.10.846
MA0074.10.089
MA0076.10.0891
MA0077.10.33
MA0078.10.413
MA0079.20.493
MA0080.20.00175
MA0081.10.412
MA0083.10.703
MA0084.10.774
MA0087.10.861
MA0088.10.806
MA0090.10.711
MA0091.10.837
MA0092.10.27
MA0093.10.829
MA0099.20.0118
MA0100.10.0787
MA0101.10.827
MA0102.20.367
MA0103.19.19708e-6
MA0104.20.134
MA0105.10.202
MA0106.10.564
MA0107.10.785
MA0108.20.546
MA0111.10.933
MA0112.29.6604e-6
MA0113.10.774
MA0114.18.60702e-27
MA0115.18.8833e-11
MA0116.10.337
MA0117.10.989
MA0119.10.0411
MA0122.10.529
MA0124.10.529
MA0125.10.121
MA0131.10.378
MA0135.10.5
MA0136.10.0194
MA0137.20.738
MA0138.20.59
MA0139.10.0213
MA0140.10.0316
MA0141.11.6646e-4
MA0142.10.19
MA0143.10.118
MA0144.10.144
MA0145.10.00953
MA0146.10.245
MA0147.10.191
MA0148.15.56287e-5
MA0149.10.0255
MA0150.10.935
MA0152.10.224
MA0153.11.97305e-31
MA0154.10.0129
MA0155.10.12
MA0156.10.155
MA0157.10.8
MA0159.10.00169
MA0160.10.016
MA0162.10.238
MA0163.10.00536
MA0164.10.83
MA0258.10.00939
MA0259.10.246



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

Novel motifP-value
10.19
100.21
1000.855
1010.853
1020.785
1030.195
1040.865
1050.468
1060.00706
1070.0161
1080.748
1090.0552
110.16
1100.262
1110.0364
1120.0258
1130.497
1140.0512
1150.557
1160.283
1170.404
1180.36
1190.146
120.875
1200.731
1210.939
1220.572
1230.229
1240.878
1250.276
1260.073
1270.38
1280.0434
1290.42
130.00414
1300.826
1310.0373
1320.481
1330.556
1340.548
1350.829
1360.135
1370.506
1380.333
1390.0579
140.779
1400.555
1410.146
1420.611
1430.327
1440.547
1450.0834
1460.193
1470.275
1480.14
1490.301
150.171
1500.241
1510.447
1520.0358
1530.681
1540.554
1550.185
1560.824
1570.682
1580.681
1590.477
1600.209
1610.41
1620.951
1630.489
1640.112
1650.455
1660.732
1670.907
1680.965
1690.00605
170.0732
180.0919
190.0676
20.192
200.696
210.939
220.278
230.212
240.599
250.892
260.00812
270.576
280.55
290.418
30.218
300.396
310.616
320.00265
330.208
340.725
350.56
360.996
370.0437
380.37
390.201
40.429
400.412
410.633
420.47
430.22
440.247
450.336
460.265
470.438
480.335
490.166
50.585
500.493
510.579
520.0552
530.948
540.698
550.533
560.359
570.996
580.5
590.0819
60.897
600.0386
610.347
620.461
630.15
640.627
650.136
660.35
670.644
680.126
690.9
70.0915
700.0316
710.0979
720.587
730.121
740.938
750.152
760.848
770.0735
780.0658
790.521
80.267
800.719
810.709
820.0765
830.568
840.355
850.0188
860.143
870.238
880.68
890.308
90.564
900.208
910.254
920.16
930.803
940.727
950.204
960.623
970.485
980.803
990.0442



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


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

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