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|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=T:3.95107121191;RXRA_VDR{dimer}:3.33232660221;SNAI1..3:2.38075136347;NFE2L2:2.25028837356;HOX{A5,B5}:2.23719961499;IRF7:2.22801202517;TFCP2:2.2165960431;ZNF148:2.1894777403;HMX1:2.12212313416;HAND1,2:2.10527968346;MYOD1:2.03154838418;FOXA2:1.90864675757;FOXL1:1.87483675489;TP53:1.84264960061;PAX8:1.82568624089;CDX1,2,4:1.80851866862;BACH2:1.7851918981;TBP:1.7748177059;ARID5B:1.7515179993;ZEB1:1.71417960182;SRF:1.63005981534;ZIC1..3:1.61204371649;STAT5{A,B}:1.60769278784;FOS_FOS{B,L1}_JUN{B,D}:1.56025992746;FOX{F1,F2,J1}:1.51728378055;NR1H4:1.38525937719;NKX3-2:1.37272894331;TBX4,5:1.3570992215;FOSL2:1.32498778036;NFE2:1.31657296256;FOXO1,3,4:1.30632210475;NKX6-1,2:1.16738300738;EBF1:1.16605390347;NR5A1,2:1.12047770308;TOPORS:1.10604305929;FOXP1:1.02963769748;TFAP4:0.90450149091;ESRRA:0.878157965619;IKZF1:0.852613722998;CDC5L:0.844086423861;LMO2:0.815245757884;NFIX:0.786754811395;TLX1..3_NFIC{dimer}:0.65112355978;HNF1A:0.62899007063;TEF:0.626880314731;AR:0.624897980332;ESR1:0.619244148742;SMAD1..7,9:0.615321047581;FOX{D1,D2}:0.567827541557;CRX:0.505801979644;PAX1,9:0.485726475638;MYBL2:0.46318589152;PPARG:0.441895644278;MAFB:0.435286464644;HNF4A_NR2F1,2:0.411767333433;NKX3-1:0.397885531144;TLX2:0.374710318925;RBPJ:0.366265017019;LHX3,4:0.365671231449;GATA6:0.335042524952;POU6F1:0.333132061193;SPZ1:0.312979389635;POU5F1:0.305327525585;EN1,2:0.296508264659;ATF6:0.26880559433;FOXN1:0.249944129303;HLF:0.241103735376;XCPE1{core}:0.240171978172;FOX{I1,J2}:0.230731311897;IKZF2:0.227353604699;MYFfamily:0.222060906527;FOXM1:0.199594236123;UFEwm:0.17701086291;GCM1,2:0.147690026608;DBP:0.13518168812;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.0931237617143;ZBTB6:0.0771414683617;bHLH_family:-0.0167510771623;CEBPA,B_DDIT3:-0.0187073044073;GTF2I:-0.0454090061678;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.0554776889284;NR3C1:-0.0598529144263;ADNP_IRX_SIX_ZHX:-0.0699419394456;HOX{A4,D4}:-0.071313236457;NKX2-3_NKX2-5:-0.100029138681;ETS1,2:-0.126293537501;ZNF423:-0.13859068996;NKX2-2,8:-0.141013469096;TEAD1:-0.144590866651;SP1:-0.178461421728;PBX1:-0.180881741125;MEF2{A,B,C,D}:-0.19804888784;BPTF:-0.200101774278;IRF1,2:-0.233124687038;REST:-0.258066084499;KLF4:-0.29765935127;PITX1..3:-0.318264660738;NKX2-1,4:-0.345653092087;GTF2A1,2:-0.361743599103;STAT2,4,6:-0.378215990107;RUNX1..3:-0.385674281399;RFX2..5_RFXANK_RFXAP:-0.39420562335;PAX4:-0.400098219713;HMGA1,2:-0.401659068024;DMAP1_NCOR{1,2}_SMARC:-0.407232076685;PAX5:-0.411836139993;NANOG:-0.416597590873;STAT1,3:-0.439845929578;ELF1,2,4:-0.457603970332;NFKB1_REL_RELA:-0.459478936313;PRRX1,2:-0.469707145636;TFAP2{A,C}:-0.476664096622;HIC1:-0.517673458359;ZNF238:-0.530609243532;LEF1_TCF7_TCF7L1,2:-0.542555657238;POU1F1:-0.600425229473;EP300:-0.61702473628;RREB1:-0.637554828592;AIRE:-0.645397829562;PATZ1:-0.65416055826;ONECUT1,2:-0.684993354723;GZF1:-0.690478537246;ALX4:-0.695198966297;POU2F1..3:-0.712906353562;NR6A1:-0.715742909922;YY1:-0.717117173819;TAL1_TCF{3,4,12}:-0.721773244665;NFATC1..3:-0.745185711174;PRDM1:-0.76817765712;RFX1:-0.774834139372;TGIF1:-0.775236836512;MAZ:-0.780714333697;HIF1A:-0.781431605138;MTF1:-0.786888260754;ZBTB16:-0.801805156064;OCT4_SOX2{dimer}:-0.820202924458;FOXQ1:-0.823361582986;SPI1:-0.827443615954;MYB:-0.87339806376;VSX1,2:-0.908760819368;HOXA9_MEIS1:-0.915857076415;ATF5_CREB3:-0.94358746501;GFI1B:-0.950762659004;ELK1,4_GABP{A,B1}:-0.953111408052;NANOG{mouse}:-0.954868430335;GLI1..3:-0.95978701868;MED-1{core}:-0.970936923751;SREBF1,2:-0.974145578161;ALX1:-0.980562486276;NHLH1,2:-0.998917940313;ATF4:-1.0129586373;SPIB:-1.01440863082;PAX6:-1.0198808067;NFIL3:-1.03481970868;TFAP2B:-1.03925731863;SOX17:-1.03931595484;HBP1_HMGB_SSRP1_UBTF:-1.05415722198;ATF2:-1.07513090584;JUN:-1.08083908202;NFE2L1:-1.08371031419;BREu{core}:-1.14488722717;CREB1:-1.15783775534;EGR1..3:-1.24272896712;GATA4:-1.25511194619;SOX2:-1.27635903891;HSF1,2:-1.27868009296;EVI1:-1.29872379171;E2F1..5:-1.32856253419;PDX1:-1.35838394473;AHR_ARNT_ARNT2:-1.37480733266;HES1:-1.39657127764;CUX2:-1.48861951313;SOX5:-1.48889690099;GFI1:-1.54355243561;FOXD3:-1.56386868416;MZF1:-1.56553285252;RORA:-1.6060720145;ZNF143:-1.65587363755;ZFP161:-1.6649733068;POU3F1..4:-1.71081599513;NRF1:-1.84819259199;ZNF384:-1.91281202902;NFY{A,B,C}:-1.96432986565;PAX2:-2.01174996146;SOX{8,9,10}:-2.09124708055;FOXP3:-2.09627893747;MTE{core}:-2.20268273019;RXR{A,B,G}:-2.26758961046;TFDP1:-2.42990252583
|top_motifs=T:3.95107121191;RXRA_VDR{dimer}:3.33232660221;SNAI1..3:2.38075136347;NFE2L2:2.25028837356;HOX{A5,B5}:2.23719961499;IRF7:2.22801202517;TFCP2:2.2165960431;ZNF148:2.1894777403;HMX1:2.12212313416;HAND1,2:2.10527968346;MYOD1:2.03154838418;FOXA2:1.90864675757;FOXL1:1.87483675489;TP53:1.84264960061;PAX8:1.82568624089;CDX1,2,4:1.80851866862;BACH2:1.7851918981;TBP:1.7748177059;ARID5B:1.7515179993;ZEB1:1.71417960182;SRF:1.63005981534;ZIC1..3:1.61204371649;STAT5{A,B}:1.60769278784;FOS_FOS{B,L1}_JUN{B,D}:1.56025992746;FOX{F1,F2,J1}:1.51728378055;NR1H4:1.38525937719;NKX3-2:1.37272894331;TBX4,5:1.3570992215;FOSL2:1.32498778036;NFE2:1.31657296256;FOXO1,3,4:1.30632210475;NKX6-1,2:1.16738300738;EBF1:1.16605390347;NR5A1,2:1.12047770308;TOPORS:1.10604305929;FOXP1:1.02963769748;TFAP4:0.90450149091;ESRRA:0.878157965619;IKZF1:0.852613722998;CDC5L:0.844086423861;LMO2:0.815245757884;NFIX:0.786754811395;TLX1..3_NFIC{dimer}:0.65112355978;HNF1A:0.62899007063;TEF:0.626880314731;AR:0.624897980332;ESR1:0.619244148742;SMAD1..7,9:0.615321047581;FOX{D1,D2}:0.567827541557;CRX:0.505801979644;PAX1,9:0.485726475638;MYBL2:0.46318589152;PPARG:0.441895644278;MAFB:0.435286464644;HNF4A_NR2F1,2:0.411767333433;NKX3-1:0.397885531144;TLX2:0.374710318925;RBPJ:0.366265017019;LHX3,4:0.365671231449;GATA6:0.335042524952;POU6F1:0.333132061193;SPZ1:0.312979389635;POU5F1:0.305327525585;EN1,2:0.296508264659;ATF6:0.26880559433;FOXN1:0.249944129303;HLF:0.241103735376;XCPE1{core}:0.240171978172;FOX{I1,J2}:0.230731311897;IKZF2:0.227353604699;MYFfamily:0.222060906527;FOXM1:0.199594236123;UFEwm:0.17701086291;GCM1,2:0.147690026608;DBP:0.13518168812;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.0931237617143;ZBTB6:0.0771414683617;bHLH_family:-0.0167510771623;CEBPA,B_DDIT3:-0.0187073044073;GTF2I:-0.0454090061678;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.0554776889284;NR3C1:-0.0598529144263;ADNP_IRX_SIX_ZHX:-0.0699419394456;HOX{A4,D4}:-0.071313236457;NKX2-3_NKX2-5:-0.100029138681;ETS1,2:-0.126293537501;ZNF423:-0.13859068996;NKX2-2,8:-0.141013469096;TEAD1:-0.144590866651;SP1:-0.178461421728;PBX1:-0.180881741125;MEF2{A,B,C,D}:-0.19804888784;BPTF:-0.200101774278;IRF1,2:-0.233124687038;REST:-0.258066084499;KLF4:-0.29765935127;PITX1..3:-0.318264660738;NKX2-1,4:-0.345653092087;GTF2A1,2:-0.361743599103;STAT2,4,6:-0.378215990107;RUNX1..3:-0.385674281399;RFX2..5_RFXANK_RFXAP:-0.39420562335;PAX4:-0.400098219713;HMGA1,2:-0.401659068024;DMAP1_NCOR{1,2}_SMARC:-0.407232076685;PAX5:-0.411836139993;NANOG:-0.416597590873;STAT1,3:-0.439845929578;ELF1,2,4:-0.457603970332;NFKB1_REL_RELA:-0.459478936313;PRRX1,2:-0.469707145636;TFAP2{A,C}:-0.476664096622;HIC1:-0.517673458359;ZNF238:-0.530609243532;LEF1_TCF7_TCF7L1,2:-0.542555657238;POU1F1:-0.600425229473;EP300:-0.61702473628;RREB1:-0.637554828592;AIRE:-0.645397829562;PATZ1:-0.65416055826;ONECUT1,2:-0.684993354723;GZF1:-0.690478537246;ALX4:-0.695198966297;POU2F1..3:-0.712906353562;NR6A1:-0.715742909922;YY1:-0.717117173819;TAL1_TCF{3,4,12}:-0.721773244665;NFATC1..3:-0.745185711174;PRDM1:-0.76817765712;RFX1:-0.774834139372;TGIF1:-0.775236836512;MAZ:-0.780714333697;HIF1A:-0.781431605138;MTF1:-0.786888260754;ZBTB16:-0.801805156064;OCT4_SOX2{dimer}:-0.820202924458;FOXQ1:-0.823361582986;SPI1:-0.827443615954;MYB:-0.87339806376;VSX1,2:-0.908760819368;HOXA9_MEIS1:-0.915857076415;ATF5_CREB3:-0.94358746501;GFI1B:-0.950762659004;ELK1,4_GABP{A,B1}:-0.953111408052;NANOG{mouse}:-0.954868430335;GLI1..3:-0.95978701868;MED-1{core}:-0.970936923751;SREBF1,2:-0.974145578161;ALX1:-0.980562486276;NHLH1,2:-0.998917940313;ATF4:-1.0129586373;SPIB:-1.01440863082;PAX6:-1.0198808067;NFIL3:-1.03481970868;TFAP2B:-1.03925731863;SOX17:-1.03931595484;HBP1_HMGB_SSRP1_UBTF:-1.05415722198;ATF2:-1.07513090584;JUN:-1.08083908202;NFE2L1:-1.08371031419;BREu{core}:-1.14488722717;CREB1:-1.15783775534;EGR1..3:-1.24272896712;GATA4:-1.25511194619;SOX2:-1.27635903891;HSF1,2:-1.27868009296;EVI1:-1.29872379171;E2F1..5:-1.32856253419;PDX1:-1.35838394473;AHR_ARNT_ARNT2:-1.37480733266;HES1:-1.39657127764;CUX2:-1.48861951313;SOX5:-1.48889690099;GFI1:-1.54355243561;FOXD3:-1.56386868416;MZF1:-1.56553285252;RORA:-1.6060720145;ZNF143:-1.65587363755;ZFP161:-1.6649733068;POU3F1..4:-1.71081599513;NRF1:-1.84819259199;ZNF384:-1.91281202902;NFY{A,B,C}:-1.96432986565;PAX2:-2.01174996146;SOX{8,9,10}:-2.09124708055;FOXP3:-2.09627893747;MTE{core}:-2.20268273019;RXR{A,B,G}:-2.26758961046;TFDP1:-2.42990252583
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011312
|namespace=FANTOM5
|part_of=
}}
}}

Revision as of 16:01, 7 March 2012


Name:stomach, adult
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuestomach
dev stageadult
sexmale
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

CNhs10503

00
10
100
1000
10000.749
10010.0714
10020.535
10030.275
10040
10050.0941
1006-0.0864
1007-0.115
10080
10090.101
101-0.105
10100
10110
10120
10130.407
10140
1015-0.187
1016-0.2
10170.761
10180.683
10190
1020
10200
1021-0.0487
10220.549
10230
10240.0265
10250.587
10260
10270
10280
10290.316
1030
10300
1031-0.256
10320.285
1033-0.0665
10340.291
10350
1036-0.2
10370
10380.0249
10390.256
1040
10400.035
10410.464



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: CNhs10503

Jaspar motifP-value
MA0002.20.114
MA0003.10.194
MA0004.10.961
MA0006.10.242
MA0007.10.233
MA0009.10.116
MA0014.10.78
MA0017.10.00795
MA0018.20.00343
MA0019.10.981
MA0024.10.0011
MA0025.10.0778
MA0027.10.643
MA0028.10.224
MA0029.10.556
MA0030.10.971
MA0031.10.56
MA0035.20.39
MA0038.10.15
MA0039.20.146
MA0040.10.176
MA0041.10.233
MA0042.10.374
MA0043.16.3758e-5
MA0046.12.335e-7
MA0047.22.07395e-4
MA0048.10.913
MA0050.10.516
MA0051.10.94
MA0052.10.899
MA0055.10.304
MA0057.10.0389
MA0058.10.822
MA0059.10.488
MA0060.18.98166e-9
MA0061.10.55
MA0062.20.0394
MA0065.20.00208
MA0066.10.117
MA0067.10.515
MA0068.10.0538
MA0069.10.176
MA0070.10.281
MA0071.10.97
MA0072.10.677
MA0073.10.714
MA0074.10.148
MA0076.10.0729
MA0077.10.537
MA0078.10.947
MA0079.20.378
MA0080.20.697
MA0081.10.0465
MA0083.10.0324
MA0084.10.548
MA0087.10.628
MA0088.10.246
MA0090.10.288
MA0091.10.347
MA0092.10.207
MA0093.10.88
MA0099.25.95523e-5
MA0100.10.301
MA0101.10.547
MA0102.20.188
MA0103.11.14931e-4
MA0104.20.825
MA0105.10.0246
MA0106.10.074
MA0107.10.588
MA0108.20.0167
MA0111.10.255
MA0112.25.02786e-6
MA0113.10.662
MA0114.10.014
MA0115.10.201
MA0116.10.0138
MA0117.10.831
MA0119.10.0667
MA0122.10.681
MA0124.10.214
MA0125.10.0546
MA0131.10.172
MA0135.10.139
MA0136.10.0406
MA0137.20.652
MA0138.20.076
MA0139.10.0412
MA0140.10.884
MA0141.10.0762
MA0142.10.873
MA0143.10.479
MA0144.10.516
MA0145.10.00529
MA0146.10.237
MA0147.10.977
MA0148.11.92768e-6
MA0149.10.0145
MA0150.10.262
MA0152.10.249
MA0153.14.29083e-6
MA0154.10.00675
MA0155.10.384
MA0156.10.144
MA0157.10.495
MA0159.10.0147
MA0160.10.492
MA0162.10.21
MA0163.10.00809
MA0164.10.783
MA0258.10.00122
MA0259.10.668



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: CNhs10503

Novel motifP-value
10.12
100.215
1000.63
1010.632
1020.373
1030.0369
1040.703
1050.425
1060.0158
1070.119
1080.678
1090.0796
110.191
1100.214
1110.0202
1120.0726
1130.966
1140.112
1150.499
1160.497
1170.31
1180.898
1190.0322
120.753
1200.441
1210.678
1220.957
1230.888
1240.884
1250.844
1260.266
1270.951
1280.0333
1290.382
130.0532
1300.651
1310.862
1320.698
1330.754
1340.667
1350.521
1360.646
1370.357
1380.531
1390.00513
140.653
1400.00623
1410.108
1420.586
1430.395
1440.144
1450.131
1460.2
1470.987
1480.229
1490.0952
150.139
1500.398
1510.339
1520.0674
1530.983
1540.947
1550.443
1562.18241e-39
1570.812
1580.626
1590.723
1600.264
1610.424
1620.736
1630.896
1640.362
1650.0796
1660.882
1670.761
1680.301
1690.00137
170.0263
180.812
190.105
20.477
200.669
210.902
220.227
230.437
240.416
250.87
260.103
270.38
280.583
290.409
30.207
300.408
310.28
320.0188
330.655
340.777
350.321
360.123
370.0415
380.745
390.278
40.0553
400.218
410.832
420.494
430.178
440.275
450.384
460.153
470.191
480.318
490.169
50.0596
500.767
510.58
520.103
530.684
540.481
550.424
560.299
570.509
580.278
590.12
60.786
600.0399
610.244
620.188
630.132
640.45
650.311
660.813
670.445
680.797
690.587
70.167
700.0103
710.0934
720.601
730.0931
740.588
750.141
760.609
770.0209
780.127
790.0987
80.0626
800.824
810.481
820.0144
830.306
840.465
850.0152
860.356
870.736
880.378
890.0271
90.465
900.532
910.149
920.133
930.366
940.969
950.383
960.0607
970.00327
980.26
990.162



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: CNhs10503


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)
0000077 (mixed endoderm/mesoderm-derived structure)
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)
0000926 (mesoderm)
0000945 (stomach)
0001007 (digestive system)
0001041 (foregut)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007023 (adult organism)
0007026 (primitive gut)
0009142 (entire embryonic mesenchyme)

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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