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|top_motifs=IKZF1:2.48739228108;AR:2.37453139279;TEAD1:1.92753648701;SRF:1.74074277536;UFEwm:1.69637223223;STAT2,4,6:1.67196886835;HOXA9_MEIS1:1.50356571786;NR3C1:1.46964475295;HAND1,2:1.45984579135;ZNF238:1.36354704323;TFCP2:1.35405711912;ESR1:1.33690144012;NKX3-1:1.31794586009;TLX1..3_NFIC{dimer}:1.30907943257;MTE{core}:1.29051576027;FOSL2:1.28463814836;EVI1:1.27578612143;GLI1..3:1.2610157005;ZNF423:1.23395625893;TP53:1.22518349295;NFATC1..3:1.17530934161;NFE2L2:1.14985932523;MAFB:1.14524383691;NFE2L1:1.13895874061;GTF2A1,2:1.11382569525;FOXP3:1.05308227869;GZF1:1.05194866605;NFE2:1.03735424106;ATF4:1.02107662944;BACH2:1.01681825049;HMGA1,2:0.977227159575;HIF1A:0.969183909391;IKZF2:0.968251273717;NKX2-2,8:0.944701089225;EBF1:0.942181783321;TAL1_TCF{3,4,12}:0.886729658252;HOX{A5,B5}:0.882415554069;TFAP4:0.859750880596;TFAP2{A,C}:0.814779722277;RXRA_VDR{dimer}:0.791486577299;CDC5L:0.762645898876;SMAD1..7,9:0.731889983474;MAZ:0.731226557486;IRF7:0.727499059529;FOS_FOS{B,L1}_JUN{B,D}:0.716147527541;GATA4:0.710102897317;HBP1_HMGB_SSRP1_UBTF:0.702930638847;MEF2{A,B,C,D}:0.700852456447;HES1:0.672187240474;PAX8:0.669081185119;GFI1B:0.614181043596;T:0.592296314632;GCM1,2:0.578382282151;NR1H4:0.576355674137;PDX1:0.576022376657;PAX5:0.570645656489;MYBL2:0.569631783969;FOXL1:0.560105520395;DMAP1_NCOR{1,2}_SMARC:0.558622577176;ZNF148:0.546143027116;HLF:0.532642364645;NFIL3:0.531724248139;ALX4:0.49950190458;DBP:0.492037629938;CEBPA,B_DDIT3:0.489906518192;XCPE1{core}:0.487528093469;GTF2I:0.480747755942;SREBF1,2:0.47977744664;ZBTB6:0.472724382445;ATF6:0.441696385645;MTF1:0.434902965792;SP1:0.428962699961;NFKB1_REL_RELA:0.346384492577;NKX2-1,4:0.343364659635;RXR{A,B,G}:0.339057483329;TOPORS:0.331455126774;RXR{A,B,G}_{NR1H2,PPAR}dimers:0.272681773968;PAX2:0.267765402326;PAX4:0.252877450056;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:0.240007136293;EP300:0.236827630511;IRF1,2:0.227201660748;HIC1:0.189475647528;PATZ1:0.18797955535;TGIF1:0.173697018123;TBX4,5:0.153693590853;FOX{D1,D2}:0.151867123614;TBP:0.14524743103;SOX5:0.129733698781;ELK1,4_GABP{A,B1}:0.121216791509;NHLH1,2:0.0983269887853;ELF1,2,4:0.0674659670245;RREB1:0.0670519014831;SOX17:0.0289732756628;TFAP2B:0.0282913010075;STAT1,3:0.0261598704547;SPIB:0.0242593512981;SPZ1:0.00968912580863;HOX{A4,D4}:0.00649861582911;SPI1:0.00608073345042;ALX1:0.00498887108388;NR6A1:-0.0376417649887;HMX1:-0.0448890747014;ETS1,2:-0.0570144432892;POU2F1..3:-0.0577690664335;EGR1..3:-0.0637389602244;POU1F1:-0.0767207218606;NKX2-3_NKX2-5:-0.0785385694797;FOXM1:-0.0851990109353;JUN:-0.10530658506;RUNX1..3:-0.109229984398;GATA6:-0.141476685334;FOXN1:-0.186811838774;POU3F1..4:-0.194127266229;LHX3,4:-0.200566438559;TLX2:-0.234201017031;BPTF:-0.238162313266;MYFfamily:-0.246473617721;NKX3-2:-0.27184226524;STAT5{A,B}:-0.297924649597;ATF2:-0.301442837471;NR5A1,2:-0.313272681296;KLF4:-0.314526460712;CDX1,2,4:-0.319572054574;MED-1{core}:-0.323683520275;CREB1:-0.334112968096;ZIC1..3:-0.340041789056;PRDM1:-0.367226386131;REST:-0.391477272418;ATF5_CREB3:-0.451293422811;HNF4A_NR2F1,2:-0.460741072633;PAX1,9:-0.467738602576;RFX1:-0.485606625835;NKX6-1,2:-0.48728041245;CRX:-0.493770736733;MYB:-0.503669819684;FOXD3:-0.514155358143;ONECUT1,2:-0.526722243621;ZFP161:-0.527174038268;FOXO1,3,4:-0.537910509189;ARID5B:-0.54053566171;MZF1:-0.558030989464;HNF1A:-0.564765939642;ESRRA:-0.573572945145;RORA:-0.573810980567;ZNF384:-0.577661069888;VSX1,2:-0.618945873175;TEF:-0.634682672009;RFX2..5_RFXANK_RFXAP:-0.641639599752;PITX1..3:-0.691532646118;PPARG:-0.706862693307;HSF1,2:-0.708247805548;bHLH_family:-0.709030024989;NANOG{mouse}:-0.72470297343;AHR_ARNT_ARNT2:-0.738170852955;PAX6:-0.75293647993;FOXP1:-0.808300550488;FOX{F1,F2,J1}:-0.816610519378;LEF1_TCF7_TCF7L1,2:-0.886013332379;FOXA2:-0.91406928866;ADNP_IRX_SIX_ZHX:-0.94133364898;NRF1:-0.943436966931;SOX2:-0.99441991557;POU5F1:-1.00270773461;BREu{core}:-1.04580789325;SNAI1..3:-1.05640655846;AIRE:-1.06125802706;RBPJ:-1.06345152322;ZBTB16:-1.0651819178;OCT4_SOX2{dimer}:-1.07915242002;EN1,2:-1.08280188304;ZNF143:-1.18927154968;FOX{I1,J2}:-1.19828461191;GFI1:-1.2751624471;E2F1..5:-1.28265962568;NFIX:-1.3260832405;NANOG:-1.37151307033;TFDP1:-1.39984966099;PBX1:-1.40053767053;PRRX1,2:-1.43972128579;ZEB1:-1.44956849998;MYOD1:-1.49013508251;POU6F1:-1.57266024981;YY1:-1.60578070043;FOXQ1:-1.62354611704;LMO2:-1.68625440059;SOX{8,9,10}:-1.79068703098;NFY{A,B,C}:-1.8100198664;CUX2:-1.86198782318
}}
}}

Revision as of 15:17, 15 February 2012


Name:Mouse Cardiac Myocytes, donor3
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueheart
dev stageNA
sexNA
ageNA
cell typecardiac muscle cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
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

CNhs12353

00
10
100
1000
10000.244
1001-0.0275
10020.673
10030.0916
10040
10050
10060.00843
1007-0.223
10080
10090.606
101-0.163
10100
1011-0.263
10120
10130.139
10140
1015-0.207
1016-0.0744
10170
10180
10190
1020
10200.664
10210.00778
1022-0.0475
10230
1024-0.14
10250
10260
10270
10280.181
1029-0.115
1030.308
10300
10310.577
10320.0656
10330
10340
10350
1036-0.21
10370
10380.13
1039-0.0678
1040
10400.574
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: CNhs12353

Jaspar motifP-value
MA0002.20.473
MA0003.10.153
MA0004.10.586
MA0006.10.122
MA0007.10.038
MA0009.10.336
MA0014.10.245
MA0017.10.0866
MA0018.20.0258
MA0019.10.824
MA0024.18.30271e-11
MA0025.10.53
MA0027.10.331
MA0028.10.279
MA0029.10.645
MA0030.10.249
MA0031.10.901
MA0035.20.682
MA0038.10.0202
MA0039.20.203
MA0040.10.187
MA0041.10.466
MA0042.10.65
MA0043.10.101
MA0046.13.17186e-10
MA0047.20.105
MA0048.10.356
MA0050.10.00302
MA0051.10.0873
MA0052.11.93886e-5
MA0055.10.31
MA0057.10.147
MA0058.10.981
MA0059.10.224
MA0060.16.4272e-17
MA0061.10.183
MA0062.20.0738
MA0065.20.399
MA0066.10.342
MA0067.10.969
MA0068.10.189
MA0069.10.137
MA0070.10.831
MA0071.10.584
MA0072.10.981
MA0073.10.249
MA0074.10.679
MA0076.10.0476
MA0077.10.197
MA0078.10.482
MA0079.22.38233e-4
MA0080.20.275
MA0081.10.52
MA0083.11.19174e-11
MA0084.10.888
MA0087.10.943
MA0088.10.919
MA0090.19.38538e-8
MA0091.10.131
MA0092.10.143
MA0093.10.567
MA0099.22.5111e-5
MA0100.10.461
MA0101.10.143
MA0102.20.743
MA0103.12.62458e-4
MA0104.20.0548
MA0105.10.314
MA0106.18.08924e-4
MA0107.10.106
MA0108.20.071
MA0111.10.941
MA0112.20.011
MA0113.10.0293
MA0114.10.0594
MA0115.10.1
MA0116.10.431
MA0117.10.31
MA0119.10.159
MA0122.10.6
MA0124.10.231
MA0125.10.00137
MA0131.10.145
MA0135.10.962
MA0136.10.0688
MA0137.20.145
MA0138.20.393
MA0139.10.524
MA0140.10.984
MA0141.10.739
MA0142.10.169
MA0143.10.681
MA0144.10.0109
MA0145.10.0193
MA0146.10.0251
MA0147.10.0472
MA0148.10.252
MA0149.10.697
MA0150.10.0311
MA0152.10.197
MA0153.11.6401e-8
MA0154.10.0204
MA0155.10.142
MA0156.10.417
MA0157.10.159
MA0159.10.127
MA0160.10.575
MA0162.10.0938
MA0163.10.0363
MA0164.10.825
MA0258.10.444
MA0259.10.195



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: CNhs12353

Novel motifP-value
10.957
100.673
1000.315
1010.838
1020.409
1030.551
1040.433
1050.333
1060.0102
1070.168
1080.584
1090.0109
110.195
1100.128
1110.24
1120.634
1130.874
1140.0706
1150.851
1160.0215
1170.734
1180.561
1190.364
120.714
1200.175
1210.637
1220.132
1230.699
1240.234
1250.2
1260.48
1270.179
1280.0339
1290.407
130.204
1300.989
1310.113
1320.737
1330.716
1340.844
1350.712
1360.116
1370.781
1380.882
1390.393
140.813
1400.367
1410.262
1420.499
1430.173
1440.241
1450.123
1460.669
1470.413
1480.653
1490.00707
150.184
1500.119
1510.822
1520.00978
1530.481
1540.809
1550.799
1560.796
1570.713
1580.435
1590.108
1600.221
1610.245
1620.731
1630.232
1640.159
1650.276
1660.343
1670.387
1680.619
1690.0185
170.0327
180.304
190.0315
20.175
200.706
210.403
220.0343
230.0774
240.0708
250.325
260.156
270.453
280.955
290.26
30.24
300.864
310.533
320.291
330.687
340.7
350.334
360.0726
370.0183
380.696
390.453
40.327
400.417
410.768
420.545
430.0396
440.188
450.414
460.812
470.465
480.637
490.428
50.989
500.106
511
520.122
530.843
540.807
550.955
560.574
570.506
580.571
590.00423
60.135
600.116
610.82
620.86
630.109
640.928
650.196
660.809
670.493
680.912
690.26
70.738
700.0182
710.255
720.627
730.00287
740.109
750.455
760.634
770.0248
780.0469
790.648
80.574
800.0817
810.17
820.193
830.767
840.133
850.0186
860.538
870.0952
880.84
890.205
90.42
900.299
910.925
920.0155
930.908
940.643
950.0607
960.0572
970.319
980.688
990.894



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: CNhs12353


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000056 (myoblast)
0000183 (contractile cell)
0000187 (muscle cell)
0000211 (electrically active cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000355 (multi-potent skeletal muscle stem cell)
0000393 (electrically responsive cell)
0000513 (cardiac muscle myoblast)
0000548 (animal cell)
0000680 (muscle precursor cell)
0000723 (somatic stem cell)
0000737 (striated muscle cell)
0000746 (cardiac muscle cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002494 (cardiocyte)

UBERON: Anatomy
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000948 (heart)
0001009 (circulatory system)
0001015 (musculature)
0001048 (primordium)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003081 (lateral plate mesoderm)
0003082 (myotome)
0003084 (heart primordium)
0003104 (mesenchyme)
0003914 (epithelial tube)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004290 (dermomyotome)
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)
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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