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|top_motifs=RXRA_VDR{dimer}:2.5833058572;ATF6:2.38476710514;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.91166093051;GCM1,2:1.82411871207;EN1,2:1.74618426627;MYOD1:1.68831878989;NR1H4:1.53803581165;SNAI1..3:1.53257520489;PAX1,9:1.46675710139;ZNF238:1.4509273026;XCPE1{core}:1.44365891338;FOXA2:1.17924733658;ZEB1:1.1545682046;ESR1:1.15260077773;TFAP4:1.15201434965;PAX6:1.14064412077;RBPJ:1.12345815415;LMO2:1.12147948373;TLX2:1.10742309575;bHLH_family:1.08746291863;TAL1_TCF{3,4,12}:1.06289860143;ZNF423:1.05670828397;ZNF148:0.950639593779;TOPORS:0.907199363708;TFCP2:0.906847913827;SPZ1:0.906764939136;TLX1..3_NFIC{dimer}:0.82809723176;ZIC1..3:0.811301159331;HIF1A:0.810493881405;GLI1..3:0.793771705935;TBP:0.788048230762;ALX4:0.773725251842;GZF1:0.770808943621;NFY{A,B,C}:0.738098822728;STAT1,3:0.693228980761;HES1:0.680437391402;NR5A1,2:0.68010880676;HNF1A:0.672528739985;PPARG:0.624507457015;PDX1:0.621813895593;FOX{F1,F2,J1}:0.565909108474;MYBL2:0.520511799002;GATA6:0.510799804574;SP1:0.493713040253;FOXM1:0.379166054265;RXR{A,B,G}:0.374189841736;BACH2:0.357218052015;MTF1:0.346731448984;HSF1,2:0.340164888304;ZNF143:0.339249842764;PATZ1:0.334946648314;NFIX:0.323167093492;EP300:0.319482770229;CEBPA,B_DDIT3:0.306375403751;HBP1_HMGB_SSRP1_UBTF:0.28895170523;GFI1:0.268913851124;SOX{8,9,10}:0.264686465301;MAZ:0.254916686364;TP53:0.247280078933;ESRRA:0.240800450672;ONECUT1,2:0.24068385619;LEF1_TCF7_TCF7L1,2:0.239437926229;HOX{A5,B5}:0.233729943545;HAND1,2:0.219363713643;ELF1,2,4:0.208289600686;SRF:0.191181744012;GTF2A1,2:0.190368705471;HMX1:0.189485537213;DBP:0.188257559427;MAFB:0.187987124152;SMAD1..7,9:0.185367147775;IKZF1:0.177365532928;TEAD1:0.151061365853;YY1:0.145924430385;STAT5{A,B}:0.145702679727;ETS1,2:0.117046510303;GTF2I:0.102822445254;HIC1:0.0990948605053;NFKB1_REL_RELA:0.0944929833302;SOX17:0.0603761434959;NKX3-2:0.0553275983205;NANOG:0.0453490792181;ARID5B:0.0251905164772;RREB1:0.0207156746119;TGIF1:7.42114810355e-05;ADNP_IRX_SIX_ZHX:-0.0190782582311;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.0224438692445;NANOG{mouse}:-0.0309290489197;ATF2:-0.0520943762013;POU2F1..3:-0.0650635876124;RFX1:-0.0777064963403;NRF1:-0.091927464608;HLF:-0.0988554529632;FOXL1:-0.104583905147;NFE2L2:-0.107628212128;NHLH1,2:-0.107762775404;ELK1,4_GABP{A,B1}:-0.109190531167;PBX1:-0.117200560332;HNF4A_NR2F1,2:-0.120883895697;T:-0.141922746694;HOX{A4,D4}:-0.14711734121;AR:-0.156094805548;MYFfamily:-0.19106601728;REST:-0.194072247302;TFAP2{A,C}:-0.194328241803;TFAP2B:-0.203091091992;ATF4:-0.211887545233;MEF2{A,B,C,D}:-0.213237817466;KLF4:-0.214097885563;MED-1{core}:-0.224412996937;FOX{D1,D2}:-0.233641004727;E2F1..5:-0.245484736063;FOS_FOS{B,L1}_JUN{B,D}:-0.247837017718;ZBTB6:-0.248826501331;PAX5:-0.250095702471;HOXA9_MEIS1:-0.25529065532;RUNX1..3:-0.270279203053;HMGA1,2:-0.280678364474;MTE{core}:-0.282264017255;CRX:-0.310272541611;SPIB:-0.315497362774;FOSL2:-0.321379010206;LHX3,4:-0.337756587581;GFI1B:-0.337848427754;NFE2:-0.356156716653;SOX2:-0.371120105133;PAX8:-0.395046040449;PRDM1:-0.399811145357;SOX5:-0.40029597873;FOXD3:-0.403144515809;TBX4,5:-0.404511870901;GATA4:-0.423393309051;FOXO1,3,4:-0.43275559727;NKX2-3_NKX2-5:-0.43280054609;UFEwm:-0.434057465215;BREu{core}:-0.434725991366;MYB:-0.463511264744;AHR_ARNT_ARNT2:-0.465084940532;NR6A1:-0.485103234959;STAT2,4,6:-0.485237550776;IKZF2:-0.501281902525;PRRX1,2:-0.525852118126;POU6F1:-0.531870870706;ATF5_CREB3:-0.535011652376;NFIL3:-0.547449826803;CDX1,2,4:-0.551245188732;EBF1:-0.5549888732;RORA:-0.557795133757;JUN:-0.566334413291;CUX2:-0.57778209184;SPI1:-0.579271298698;MZF1:-0.584764571658;NFATC1..3:-0.617892190847;NKX3-1:-0.628115712192;ALX1:-0.654383271865;POU1F1:-0.654972659862;TFDP1:-0.662086788646;EGR1..3:-0.680464019373;AIRE:-0.688376699257;ZFP161:-0.700031696104;ZNF384:-0.711767415557;OCT4_SOX2{dimer}:-0.712650016017;CREB1:-0.727788758542;PAX2:-0.734367057038;VSX1,2:-0.74575256315;TEF:-0.764533152785;CDC5L:-0.76521802281;RFX2..5_RFXANK_RFXAP:-0.766407515955;IRF1,2:-0.808632696587;IRF7:-0.910475337591;NR3C1:-0.93897955144;NKX2-1,4:-0.963166771646;POU5F1:-1.04240715916;NFE2L1:-1.09798268535;DMAP1_NCOR{1,2}_SMARC:-1.1829217733;FOXN1:-1.20144344014;NKX2-2,8:-1.22379579743;FOX{I1,J2}:-1.22936970376;EVI1:-1.24411919118;PITX1..3:-1.24786146484;BPTF:-1.26419443068;ZBTB16:-1.27605830079;POU3F1..4:-1.32109625682;FOXQ1:-1.36443436709;SREBF1,2:-1.38739016806;FOXP1:-1.67797946995;PAX4:-1.68661482638;FOXP3:-2.02581563419;NKX6-1,2:-2.31747427855
}}
}}

Revision as of 15:20, 15 February 2012


Name:pancreas, 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
tissuepancreas
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

CNhs10599

00
10
100
1000
10000
1001-0.0623
10020.00941
1003-0.0516
10040
10050
1006-0.143
1007-0.101
10080
1009-0.0424
101-0.0455
10100.527
1011-0.0616
10120
10130.595
10140.19
1015-0.00264
1016-0.0672
10170
10180.0904
10190
1020
10200
10210
10220.27
10230
10240.062
10250.214
10260
10270
10280
1029-0.148
1030.123
10300
10310.311
10320.0518
10330.0943
10340.357
10350
10360.0187
10370
1038-0.0845
10390.0918
1040
10400.0478
10410



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: CNhs10599

Jaspar motifP-value
MA0002.20.151
MA0003.10.198
MA0004.10.126
MA0006.10.268
MA0007.10.22
MA0009.10.967
MA0014.10.892
MA0017.10.769
MA0018.20.0126
MA0019.10.616
MA0024.10.583
MA0025.10.982
MA0027.10.514
MA0028.10.674
MA0029.10.391
MA0030.10.533
MA0031.10.67
MA0035.23.80273e-4
MA0038.10.731
MA0039.20.0136
MA0040.10.99
MA0041.10.164
MA0042.10.432
MA0043.10.416
MA0046.11.66643e-31
MA0047.28.16045e-5
MA0048.10.426
MA0050.12.63761e-4
MA0051.13.59467e-4
MA0052.10.488
MA0055.10.998
MA0057.10.541
MA0058.10.165
MA0059.10.0234
MA0060.10.00106
MA0061.10.372
MA0062.20.378
MA0065.20.0159
MA0066.10.411
MA0067.10.0263
MA0068.10.378
MA0069.10.177
MA0070.10.155
MA0071.10.96
MA0072.10.906
MA0073.10.772
MA0074.10.0462
MA0076.10.54
MA0077.10.133
MA0078.10.247
MA0079.20.196
MA0080.20.325
MA0081.10.209
MA0083.10.653
MA0084.10.624
MA0087.10.407
MA0088.10.138
MA0090.10.132
MA0091.11.74144e-6
MA0092.10.379
MA0093.10.118
MA0099.20.818
MA0100.10.00787
MA0101.10.675
MA0102.20.0817
MA0103.17.02301e-6
MA0104.20.19
MA0105.10.238
MA0106.10.731
MA0107.10.894
MA0108.26.22838e-4
MA0111.10.647
MA0112.20.0266
MA0113.10.419
MA0114.10.462
MA0115.10.983
MA0116.10.2
MA0117.10.875
MA0119.10.0686
MA0122.10.921
MA0124.10.523
MA0125.10.265
MA0131.10.645
MA0135.10.0137
MA0136.10.118
MA0137.20.139
MA0138.20.819
MA0139.10.125
MA0140.10.00298
MA0141.10.0482
MA0142.10.355
MA0143.10.612
MA0144.10.0527
MA0145.10.0148
MA0146.10.122
MA0147.10.0472
MA0148.12.89131e-4
MA0149.10.424
MA0150.10.511
MA0152.10.403
MA0153.13.03906e-13
MA0154.10.0203
MA0155.10.0653
MA0156.10.476
MA0157.10.669
MA0159.10.239
MA0160.10.0806
MA0162.10.287
MA0163.10.0542
MA0164.10.0369
MA0258.10.0644
MA0259.10.422



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: CNhs10599

Novel motifP-value
10.554
100.669
1000.952
1010.969
1020.239
1030.995
1040.699
1050.803
1060.167
1070.944
1080.461
1098.62507e-4
110.181
1100.344
1110.503
1120.306
1130.357
1140.849
1150.777
1160.0166
1170.575
1180.418
1190.42
120.529
1200.978
1210.987
1220.285
1230.381
1240.184
1250.17
1260.0167
1270.402
1280.396
1290.642
130.018
1300.975
1310.262
1320.266
1330.868
1340.106
1350.61
1360.0546
1370.343
1380.0595
1390.835
140.8
1400.904
1410.412
1420.0875
1430.716
1440.303
1450.291
1460.0505
1470.0148
1480.412
1490.0775
150.259
1500.506
1510.992
1520.0279
1530.531
1540.158
1550.973
1560.0162
1570.839
1580.891
1590.58
1600.191
1610.151
1620.965
1630.933
1640.974
1650.895
1660.158
1670.0667
1680.113
1690.102
170.331
180.706
190.054
20.136
200.612
210.691
220.171
230.388
240.0105
250.965
260.00909
270.374
280.413
290.54
30.714
300.119
310.439
320.221
330.598
340.346
350.511
360.158
370.13
380.53
390.146
40.0822
400.0199
410.793
420.303
430.789
440.0988
450.33
460.369
470.37
480.406
490.836
50.517
500.109
510.844
520.325
530.309
540.967
550.684
560.17
570.176
580.425
590.00489
60.441
600.18
610.464
620.558
630.0721
640.39
650.0785
660.0613
670.66
680.165
690.978
70.161
700.76
710.0512
720.409
730.0391
740.447
750.417
760.254
770.015
780.333
790.14
80.319
800.504
810.741
820.468
830.75
840.573
850.333
860.549
870.00812
880.272
890.165
90.638
900.21
910.883
920.616
930.746
940.012
950.0398
960.545
970.0368
980.5
990.104



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: CNhs10599


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)
0000077 (mixed endoderm/mesoderm-derived structure)
0000160 (intestine)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001041 (foregut)
0001045 (midgut)
0001048 (primordium)
0001062 (anatomical entity)
0001264 (pancreas)
0001555 (digestive tract)
0002050 (embryonic structure)
0002075 (viscus)
0002100 (trunk)
0002108 (small intestine)
0002114 (duodenum)
0002323 (body cavity)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003104 (mesenchyme)
0003921 (pancreas primordium)
0003922 (pancreatic epithelial bud)
0003923 (dorsal pancreatic bud)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004458 (body cavity or lining)
0004921 (subdivision of digestive tract)
0005177 (trunk region element)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
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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