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|top_motifs=RXRA_VDR{dimer}:3.05846655425;EN1,2:2.96930629935;NR1H4:2.10827865579;MYOD1:1.88936971286;TAL1_TCF{3,4,12}:1.63609592969;FOXP1:1.61731386994;TOPORS:1.5934153472;ARID5B:1.47723302751;TLX2:1.47025978261;RBPJ:1.43370491597;PDX1:1.43252277064;FOXA2:1.39001566584;ZNF238:1.37750565479;SNAI1..3:1.36323733258;GCM1,2:1.2809132661;PAX1,9:1.13654925739;MYBL2:1.10158003007;PBX1:1.08610790967;LMO2:1.07882695493;TEF:1.07827736161;ALX4:1.02645306222;NR6A1:0.965940070339;ESR1:0.947347302377;ATF6:0.921420719657;HSF1,2:0.896116596613;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.870884859953;CDX1,2,4:0.869988974707;PAX6:0.799059812011;CEBPA,B_DDIT3:0.790842211343;XCPE1{core}:0.780847545261;HNF1A:0.778902818533;TBP:0.762096978207;TLX1..3_NFIC{dimer}:0.740787961733;TFAP4:0.713055767619;ALX1:0.688530122754;ONECUT1,2:0.683308358136;DBP:0.668502847905;STAT5{A,B}:0.651477677764;GATA6:0.647760556014;IKZF1:0.646308857812;ZEB1:0.598857488077;NKX3-2:0.571985552444;E2F1..5:0.468722300389;MAFB:0.464640243229;MEF2{A,B,C,D}:0.43902090448;GFI1:0.408879695701;FOXL1:0.407890567703;bHLH_family:0.402526091113;GZF1:0.400628566567;FOXM1:0.400491623392;NR5A1,2:0.378063464718;TEAD1:0.372355470219;PAX8:0.343749909514;HOX{A4,D4}:0.338255080833;HOXA9_MEIS1:0.299975378104;FOXD3:0.295009342841;T:0.283919347026;SP1:0.276332980083;TGIF1:0.263229766671;TFAP2B:0.255927792047;UFEwm:0.255228885284;GATA4:0.253220959081;ZNF148:0.246517233145;RXR{A,B,G}:0.246303178286;MAZ:0.24429406547;SMAD1..7,9:0.231568669098;CRX:0.220303528826;CDC5L:0.198630591886;ZIC1..3:0.191333644196;HMGA1,2:0.189196013769;STAT2,4,6:0.187627548441;IKZF2:0.183231790787;ZNF423:0.181495655868;FOXQ1:0.1697274067;GTF2I:0.168143685936;POU6F1:0.157357980315;SRF:0.148097815266;MTF1:0.129232071091;TFCP2:0.09548155111;HBP1_HMGB_SSRP1_UBTF:0.0684565042273;ELF1,2,4:0.0667571088339;STAT1,3:0.0647686616378;BPTF:0.0563288742244;SPZ1:0.0546057356399;NANOG{mouse}:0.0513396654173;DMAP1_NCOR{1,2}_SMARC:0.04355587101;HIC1:0.020022170805;FOX{D1,D2}:0.0197029970615;PAX4:0.0169186593127;ADNP_IRX_SIX_ZHX:0.00791452075586;PATZ1:0.00711762693158;SOX{8,9,10}:-0.0209745963724;NKX2-1,4:-0.0278332275663;IRF1,2:-0.0360033143452;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.0462757965771;PRDM1:-0.0471460083508;FOSL2:-0.0619690300427;NFY{A,B,C}:-0.0667464632484;MTE{core}:-0.0709592911552;HNF4A_NR2F1,2:-0.0782635775057;ZBTB16:-0.082282523571;PITX1..3:-0.0887070214327;FOX{F1,F2,J1}:-0.0896641358263;ESRRA:-0.0930261080792;EVI1:-0.11513388352;LEF1_TCF7_TCF7L1,2:-0.123058683419;CUX2:-0.127303015972;ETS1,2:-0.131866052126;MYFfamily:-0.134938263858;YY1:-0.136337769367;POU1F1:-0.144590948815;SOX17:-0.146735596797;BREu{core}:-0.15396831582;HIF1A:-0.160718638952;NFIL3:-0.162996049697;GTF2A1,2:-0.166076916289;RREB1:-0.172699213144;CREB1:-0.188820107943;KLF4:-0.200007800223;NR3C1:-0.202791986638;NKX2-2,8:-0.20356376576;MED-1{core}:-0.224466793749;TFAP2{A,C}:-0.241855575849;NFATC1..3:-0.247135074528;SPIB:-0.255697747938;AIRE:-0.283997292603;SOX5:-0.284999021298;AR:-0.286756981067;GFI1B:-0.289748508313;HOX{A5,B5}:-0.29073887327;NKX6-1,2:-0.293406664551;RFX1:-0.300387235123;ZNF143:-0.314624580839;BACH2:-0.316626774742;NFIX:-0.317952591556;ELK1,4_GABP{A,B1}:-0.352364406045;NFKB1_REL_RELA:-0.364578741033;EGR1..3:-0.368184745647;POU5F1:-0.376183381258;MYB:-0.376275808638;GLI1..3:-0.397457497944;AHR_ARNT_ARNT2:-0.400404149214;NFE2L2:-0.411492360237;TFDP1:-0.416029320995;NKX2-3_NKX2-5:-0.422641295119;TP53:-0.432230854856;NRF1:-0.436424644459;EP300:-0.436459306515;NKX3-1:-0.441975489249;MZF1:-0.443939861689;NHLH1,2:-0.455075607729;EBF1:-0.467281976988;HAND1,2:-0.467976263024;ZFP161:-0.470108693425;PPARG:-0.482585142126;FOXO1,3,4:-0.530577391692;REST:-0.533562742339;SPI1:-0.534888760112;HLF:-0.537671130822;SOX2:-0.550507126993;HMX1:-0.576870443299;ATF2:-0.583157902065;ZNF384:-0.592460562923;LHX3,4:-0.608684710916;FOXN1:-0.609320016971;NFE2:-0.628240177533;IRF7:-0.634216633729;FOX{I1,J2}:-0.637219642855;RUNX1..3:-0.65228634796;HES1:-0.653946832551;FOS_FOS{B,L1}_JUN{B,D}:-0.669461052331;RFX2..5_RFXANK_RFXAP:-0.670987062078;NANOG:-0.676472476377;OCT4_SOX2{dimer}:-0.679169589086;PAX5:-0.705543517754;RORA:-0.71843003246;ZBTB6:-0.744409174766;ATF5_CREB3:-0.808692078916;POU2F1..3:-0.809019975326;JUN:-0.831001886601;PRRX1,2:-0.867283195656;PAX2:-1.01181246608;FOXP3:-1.04764228957;SREBF1,2:-1.08102021713;ATF4:-1.27190273383;POU3F1..4:-1.37780471286;VSX1,2:-1.44652030502;NFE2L1:-1.72597221427;TBX4,5:-1.80514581652
}}
}}

Revision as of 15:20, 15 February 2012


Name:pancreas, neonate N02, 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 stage2 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

CNhs11139

00
10
100
1000
10000.0291
10010.0694
10020.0189
10030.0454
10040
10050
10060.0355
10070.0329
10080
10090.0437
1010.0295
10100.385
1011-0.108
10120
10130.311
10140.234
1015-0.0254
10160.013
10170
10180.0243
10190
1020
10200
10210
10220.468
10230
10240.19
10250.0713
10260
10270
10280
10290.119
1030.324
10300
10310.159
10320.0502
10330
10340.532
10350.0134
10360.0888
10370
10380.0118
10390.0961
1040
10400.0456
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: CNhs11139

Jaspar motifP-value
MA0002.20.0245
MA0003.10.152
MA0004.10.709
MA0006.10.0577
MA0007.10.397
MA0009.10.318
MA0014.10.782
MA0017.10.504
MA0018.22.0309e-7
MA0019.10.487
MA0024.10.0677
MA0025.10.136
MA0027.10.876
MA0028.10.17
MA0029.10.657
MA0030.10.449
MA0031.10.711
MA0035.20.424
MA0038.10.467
MA0039.20.571
MA0040.10.5
MA0041.10.385
MA0042.10.678
MA0043.10.00119
MA0046.15.98311e-21
MA0047.20.00497
MA0048.10.955
MA0050.10.797
MA0051.10.255
MA0052.10.377
MA0055.10.445
MA0057.10.432
MA0058.10.981
MA0059.10.0636
MA0060.10.356
MA0061.10.609
MA0062.20.0102
MA0065.20.163
MA0066.10.449
MA0067.10.0206
MA0068.10.67
MA0069.10.163
MA0070.10.845
MA0071.10.9
MA0072.10.503
MA0073.10.939
MA0074.10.0957
MA0076.10.0475
MA0077.10.922
MA0078.10.967
MA0079.20.773
MA0080.20.013
MA0081.10.0833
MA0083.10.782
MA0084.10.201
MA0087.10.425
MA0088.10.371
MA0090.10.0206
MA0091.13.35585e-5
MA0092.10.171
MA0093.10.77
MA0099.20.00476
MA0100.10.00941
MA0101.10.892
MA0102.20.00617
MA0103.18.41783e-5
MA0104.20.867
MA0105.10.169
MA0106.10.763
MA0107.10.553
MA0108.20.25
MA0111.10.779
MA0112.20.00385
MA0113.10.627
MA0114.10.689
MA0115.10.697
MA0116.10.454
MA0117.10.582
MA0119.10.121
MA0122.10.931
MA0124.10.94
MA0125.10.259
MA0131.10.96
MA0135.10.755
MA0136.13.85569e-4
MA0137.20.359
MA0138.20.819
MA0139.10.19
MA0140.10.0717
MA0141.10.229
MA0142.10.701
MA0143.10.899
MA0144.10.296
MA0145.10.0518
MA0146.10.702
MA0147.10.354
MA0148.11.24068e-4
MA0149.10.631
MA0150.10.284
MA0152.10.58
MA0153.12.68902e-9
MA0154.10.00924
MA0155.10.00869
MA0156.10.00802
MA0157.10.441
MA0159.10.269
MA0160.10.754
MA0162.10.324
MA0163.15.9987e-4
MA0164.10.487
MA0258.10.0636
MA0259.10.852



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: CNhs11139

Novel motifP-value
10.164
100.217
1000.293
1010.493
1020.73
1030.231
1040.327
1050.973
1060.0091
1070.093
1080.757
1090.0813
110.417
1100.0559
1110.575
1120.401
1130.128
1140.385
1150.301
1160.258
1170.359
1180.514
1190.233
120.0624
1200.471
1210.0984
1220.9
1230.611
1240.344
1250.33
1260.0716
1270.385
1280.0298
1290.436
133.49131e-5
1300.42
1310.228
1320.46
1330.0884
1340.256
1350.905
1360.323
1370.0446
1380.00798
1390.601
140.569
1400.074
1410.0446
1420.545
1430.868
1440.626
1450.0737
1460.551
1470.16
1480.0777
1490.322
150.832
1500.318
1510.772
1520.028
1530.788
1540.98
1550.988
1560.00343
1570.0972
1580.711
1590.431
1600.0533
1610.832
1620.333
1630.898
1640.487
1650.636
1660.545
1670.543
1680.3
1690.00665
170.169
180.362
190.00851
20.511
200.604
210.5
220.197
230.719
240.186
250.722
267.0759e-4
270.683
280.28
290.929
30.385
300.867
310.353
320.0839
330.63
340.933
350.594
360.623
370.0577
380.539
390.0199
40.338
400.67
410.0694
420.35
430.303
440.771
450.945
460.135
470.711
480.833
490.456
50.87
500.211
510.577
520.12
530.85
540.903
550.435
560.351
570.854
580.576
590.0303
60.851
600.0737
610.227
620.887
630.141
640.7
650.23
660.32
670.454
680.475
690.512
70.0911
700.997
710.0134
720.704
730.142
740.368
750.695
760.414
770.0783
780.206
790.0256
80.0307
800.379
810.854
820.278
830.87
840.028
850.185
860.366
870.492
880.133
890.303
90.55
900.4
910.363
920.26
930.563
940.256
950.958
960.382
970.0558
980.667
990.112



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: CNhs11139


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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