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|top_motifs=MEF2{A,B,C,D}:3.8433385396;NR5A1,2:3.73516681214;ESRRA:2.54834010836;NR3C1:2.49485060006;AR:2.46375766186;RXR{A,B,G}:2.41779651105;SRF:2.08098250478;NKX2-1,4:2.01740646082;NFE2L2:1.73898538311;NFE2L1:1.73216012339;TGIF1:1.66582847762;MAFB:1.59657103562;TEAD1:1.58980579827;NFATC1..3:1.43754256328;ESR1:1.39312800729;MYBL2:1.37105347925;PAX2:1.33919884658;NR6A1:1.27547368133;IKZF1:1.27043771593;FOXO1,3,4:1.26782366793;HAND1,2:1.18831044435;ALX1:1.18564866073;HOX{A5,B5}:1.11325609394;HBP1_HMGB_SSRP1_UBTF:1.10780017792;NFIX:1.10295526572;GATA6:1.0794380573;EVI1:1.0666178253;RBPJ:1.06088639104;HMGA1,2:0.996289315784;TFAP2{A,C}:0.96070473527;TFAP4:0.915755796476;FOXL1:0.886504170024;GCM1,2:0.881116462938;NKX2-2,8:0.872841408622;TLX2:0.858665309847;GATA4:0.85149678431;EBF1:0.850095549438;FOSL2:0.833496557337;GLI1..3:0.794006303011;TFCP2:0.759332547827;IKZF2:0.723263245897;SOX5:0.676798425227;SMAD1..7,9:0.659574891616;HIF1A:0.654236027745;TLX1..3_NFIC{dimer}:0.634003589976;RORA:0.604251421893;PAX4:0.595397990671;GTF2A1,2:0.549992878209;SOX{8,9,10}:0.548600252551;TFAP2B:0.538113518242;UFEwm:0.520180521179;MAZ:0.501864805678;FOX{I1,J2}:0.490902172617;SP1:0.477730934849;NHLH1,2:0.469649181583;PRDM1:0.448848280105;POU3F1..4:0.431854613398;BPTF:0.418381912652;MTE{core}:0.408585701765;NFIL3:0.399870420696;CDC5L:0.393249718584;FOXP1:0.388990761135;ATF4:0.379164650304;PAX5:0.351700375748;KLF4:0.337271926654;ZNF238:0.333901446482;PATZ1:0.330577991268;YY1:0.293551179801;IRF1,2:0.289951588556;HIC1:0.286231550599;SPIB:0.282497882898;CDX1,2,4:0.282059151474;NKX3-2:0.279160447976;FOX{D1,D2}:0.268953838658;NR1H4:0.252223791362;EP300:0.226525147505;HES1:0.223091810426;FOXN1:0.20230791258;GFI1B:0.196549464367;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.194790925536;CREB1:0.171732239993;NKX3-1:0.137087678388;TOPORS:0.131005966211;T:0.125041947098;XCPE1{core}:0.0989028905318;MZF1:0.092049771917;ATF2:0.0772753307598;ELF1,2,4:0.0711675694061;ZFP161:0.0585375283127;STAT2,4,6:0.0453057583387;GTF2I:0.0404176742676;ETS1,2:0.0369989580424;BREu{core}:0.0229102573676;SREBF1,2:0.0178871170327;HOX{A4,D4}:0.0177904666357;MTF1:0.0159700941549;RREB1:-0.0161770839612;ARID5B:-0.059994270853;EGR1..3:-0.103407326439;PPARG:-0.115116755161;IRF7:-0.13601177842;CRX:-0.136322629951;TEF:-0.137328483234;FOXQ1:-0.161419813785;FOXD3:-0.162729266198;RXRA_VDR{dimer}:-0.167411457393;BACH2:-0.171575402764;TP53:-0.17662456817;ZNF148:-0.182317223819;PITX1..3:-0.187938761446;RFX2..5_RFXANK_RFXAP:-0.189104686931;GFI1:-0.18940437341;SPI1:-0.212988937016;ZBTB16:-0.247638155075;NFE2:-0.266755971118;PDX1:-0.269519704742;MYFfamily:-0.276033439863;NANOG:-0.27836726942;ATF5_CREB3:-0.294451630318;ZNF143:-0.302787231632;HLF:-0.305517063272;TAL1_TCF{3,4,12}:-0.3187245288;ATF6:-0.326144260358;NRF1:-0.329483751111;REST:-0.337423906372;HSF1,2:-0.377334007149;MED-1{core}:-0.400663113303;SOX2:-0.410097374435;DMAP1_NCOR{1,2}_SMARC:-0.413942457292;POU6F1:-0.418351052357;TBP:-0.418994886006;JUN:-0.427035171967;VSX1,2:-0.455580546676;CUX2:-0.467958451425;DBP:-0.474346215308;FOXA2:-0.477777751239;LMO2:-0.479896558235;NKX2-3_NKX2-5:-0.481269718307;ZBTB6:-0.500643893774;NFKB1_REL_RELA:-0.531094192488;NANOG{mouse}:-0.534586575709;TFDP1:-0.540643534847;bHLH_family:-0.542316097556;AHR_ARNT_ARNT2:-0.556704429089;SOX17:-0.567359098257;HNF4A_NR2F1,2:-0.569785919882;MYOD1:-0.584331269762;ALX4:-0.589778063008;EN1,2:-0.595582732169;CEBPA,B_DDIT3:-0.602640909785;MYB:-0.644113022451;FOXP3:-0.659162857818;FOS_FOS{B,L1}_JUN{B,D}:-0.665884464799;ELK1,4_GABP{A,B1}:-0.667368347848;RUNX1..3:-0.682589983661;HOXA9_MEIS1:-0.712181680703;RFX1:-0.746017973817;TBX4,5:-0.773916396707;NKX6-1,2:-0.791636822671;HNF1A:-0.810820816334;STAT5{A,B}:-0.831890490167;ZEB1:-0.837687835327;ZIC1..3:-0.852746330111;LHX3,4:-0.897207974644;PRRX1,2:-0.900366842593;AIRE:-0.912682569307;E2F1..5:-0.944722458939;STAT1,3:-0.972586567324;PBX1:-0.980008171565;ZNF384:-0.981382396124;FOX{F1,F2,J1}:-1.08635904889;SNAI1..3:-1.14135369152;POU1F1:-1.19611653017;POU2F1..3:-1.20959593928;ZNF423:-1.26657653168;GZF1:-1.35782354919;PAX6:-1.37406121244;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-1.38939560429;ADNP_IRX_SIX_ZHX:-1.39897103946;LEF1_TCF7_TCF7L1,2:-1.44869814514;OCT4_SOX2{dimer}:-1.48279277319;HMX1:-1.63045030464;NFY{A,B,C}:-1.63182971144;SPZ1:-1.75253618901;PAX1,9:-1.79556805322;ONECUT1,2:-1.84702020812;POU5F1:-1.87996012909;PAX8:-1.97306273065;FOXM1:-2.13727847658
}}
}}

Revision as of 15:19, 15 February 2012


Name:heart, neonate N16, 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
tissueheart
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

CNhs11209

00
10
100.797
1000
10000.652
10010.751
10020.0945
10030.129
10040
10050
10060.575
10070.0114
10080
10090.242
101-0.104
10100
10110
10120.0945
1013-0.0701
10140
1015-0.133
10160.159
10170
10180
10190
1020
10200
10210
10220.95
10230
10240.586
10250
10260.0653
10270.00517
10280.0339
10290.0695
1030.0653
10300
10310.147
10320.0761
1033-0.00996
10340
10350.419
1036-0.383
10370
10380.297
10390.509
1040
10400.252
10410.0653



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: CNhs11209

Jaspar motifP-value
MA0002.20.0814
MA0003.10.437
MA0004.10.0221
MA0006.10.121
MA0007.10.861
MA0009.10.792
MA0014.10.587
MA0017.10.526
MA0018.20.231
MA0019.10.167
MA0024.11.72232e-5
MA0025.10.201
MA0027.10.813
MA0028.10.00237
MA0029.10.857
MA0030.10.88
MA0031.10.594
MA0035.22.47125e-5
MA0038.10.336
MA0039.20.929
MA0040.10.441
MA0041.10.596
MA0042.10.678
MA0043.10.569
MA0046.11.08999e-17
MA0047.20.839
MA0048.10.568
MA0050.10.497
MA0051.10.585
MA0052.11.97195e-60
MA0055.10.421
MA0057.10.855
MA0058.10.007
MA0059.10.00269
MA0060.11.89579e-10
MA0061.10.336
MA0062.23.68804e-7
MA0065.20.0901
MA0066.10.982
MA0067.10.592
MA0068.10.738
MA0069.10.305
MA0070.10.465
MA0071.10.00142
MA0072.10.603
MA0073.10.746
MA0074.10.136
MA0076.14.07035e-4
MA0077.10.446
MA0078.10.989
MA0079.20.0397
MA0080.20.00299
MA0081.10.725
MA0083.16.50686e-14
MA0084.10.74
MA0087.10.286
MA0088.10.212
MA0090.16.10271e-5
MA0091.10.882
MA0092.10.355
MA0093.10.0185
MA0099.20.0259
MA0100.10.0324
MA0101.10.509
MA0102.20.049
MA0103.11.87865e-4
MA0104.20.00333
MA0105.10.0998
MA0106.10.424
MA0107.10.83
MA0108.20.807
MA0111.10.982
MA0112.20.00101
MA0113.10.12
MA0114.10.184
MA0115.10.284
MA0116.10.0176
MA0117.10.805
MA0119.10.157
MA0122.10.0451
MA0124.10.638
MA0125.10.492
MA0131.10.387
MA0135.10.594
MA0136.17.78767e-5
MA0137.20.187
MA0138.20.0307
MA0139.10.61
MA0140.10.00475
MA0141.12.67834e-10
MA0142.10.0887
MA0143.10.424
MA0144.10.606
MA0145.10.0783
MA0146.10.0309
MA0147.10.00349
MA0148.10.851
MA0149.10.763
MA0150.10.177
MA0152.10.396
MA0153.16.04034e-12
MA0154.10.126
MA0155.10.339
MA0156.10.00201
MA0157.10.278
MA0159.13.02891e-5
MA0160.12.93141e-6
MA0162.10.247
MA0163.10.243
MA0164.10.124
MA0258.10.0089
MA0259.10.134



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: CNhs11209

Novel motifP-value
10.272
100.32
1000.781
1010.498
1020.91
1030.825
1040.662
1050.0688
1060.266
1070.128
1080.93
1090.654
110.695
1100.329
1110.129
1120.752
1130.973
1140.146
1150.883
1160.516
1170.345
1180.756
1190.259
120.649
1200.0701
1210.108
1220.556
1230.52
1240.33
1250.752
1260.555
1270.297
1280.818
1290.154
130.00252
1300.405
1310.924
1320.842
1330.513
1340.493
1350.95
1360.739
1370.191
1380.118
1390.242
140.105
1400.546
1410.876
1420.862
1430.332
1440.378
1450.586
1460.425
1470.659
1480.486
1490.00177
150.433
1500.535
1510.373
1520.0604
1530.779
1540.967
1550.0197
1560.269
1570.771
1580.0571
1590.0471
1600.321
1610.546
1620.715
1630.126
1640.721
1650.00264
1660.245
1670.742
1680.152
1695.20431e-4
170.306
180.0509
190.0297
20.263
200.733
210.174
220.0312
230.538
240.922
250.924
260.199
270.798
280.921
290.113
30.685
300.624
310.627
320.7
330.986
340.158
350.573
360.117
370.0288
380.763
390.462
40.414
400.104
410.699
420.699
430.246
440.58
450.354
460.987
470.706
480.711
490.242
50.274
500.81
510.653
520.27
530.557
540.4
550.69
560.79
570.71
580.546
590.0638
60.0507
600.14
610.839
620.682
630.131
640.967
650.827
660.12
670.436
680.553
690.079
70.131
700.856
710.455
720.323
730.0565
740.698
750.462
760.805
770.326
780.0427
790.503
80.745
800.31
810.943
820.328
830.547
840.159
850.00756
860.813
870.0548
880.482
890.0789
90.0878
900.679
910.395
920.302
930.505
940.927
950.283
960.785
970.947
980.524
990.803



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: CNhs11209


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
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000948 (heart)
0001009 (circulatory system)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003084 (heart primordium)
0003914 (epithelial tube)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
0007005 (cardiac mesoderm)
0007100 (primary circulatory organ)

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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