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|sample_category=developmental
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Revision as of 15:52, 26 December 2012


Name:heart, neonate N10
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueheart
dev stage10 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]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



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

CNhs11118

00
10
100.735
1000
10000.637
10010.707
10020.223
10030.175
10040
1005-0.0389
10060.538
10070.037
10080
10090.204
101-0.0447
10100
1011-0.0394
10120.066
1013-0.0781
10140.126
1015-0.0787
10160.0997
10170
10180
10190
1020
10200
1021-0.0487
10220.832
10230
10240.388
10250
10260
10270.066
10280
10290.377
1030.228
10300
10310.14
10320.134
1033-0.0752
10340
10350.666
1036-0.166
10370
10380.144
10390.339
1040
10400.117
10410.066



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



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: CNhs11118

Jaspar motifP-value
MA0002.20.115
MA0003.10.665
MA0004.10.0824
MA0006.10.203
MA0007.10.616
MA0009.10.607
MA0014.10.717
MA0017.10.834
MA0018.20.00703
MA0019.10.507
MA0024.10.0285
MA0025.10.385
MA0027.10.356
MA0028.10.0709
MA0029.10.942
MA0030.10.216
MA0031.10.255
MA0035.20.176
MA0038.10.777
MA0039.20.122
MA0040.10.16
MA0041.10.276
MA0042.10.489
MA0043.10.0221
MA0046.11.6527e-16
MA0047.20.21
MA0048.10.432
MA0050.10.14
MA0051.10.194
MA0052.11.16072e-27
MA0055.10.225
MA0057.10.632
MA0058.10.0463
MA0059.10.363
MA0060.18.40571e-11
MA0061.10.933
MA0062.24.63144e-6
MA0065.20.146
MA0066.10.388
MA0067.10.277
MA0068.10.363
MA0069.10.193
MA0070.10.65
MA0071.10.0512
MA0072.10.829
MA0073.10.966
MA0074.10.151
MA0076.10.0022
MA0077.10.674
MA0078.10.811
MA0079.20.209
MA0080.20.00175
MA0081.10.772
MA0083.15.76585e-10
MA0084.10.565
MA0087.10.816
MA0088.10.717
MA0090.10.00198
MA0091.10.438
MA0092.10.428
MA0093.10.0591
MA0099.20.00198
MA0100.10.0416
MA0101.10.429
MA0102.20.0134
MA0103.10.00117
MA0104.20.041
MA0105.10.168
MA0106.10.091
MA0107.10.729
MA0108.20.242
MA0111.10.973
MA0112.21.29909e-6
MA0113.10.725
MA0114.10.53
MA0115.10.449
MA0116.10.413
MA0117.10.97
MA0119.10.0655
MA0122.10.203
MA0124.10.841
MA0125.10.307
MA0131.10.449
MA0135.10.0266
MA0136.17.92015e-5
MA0137.20.0336
MA0138.20.387
MA0139.10.574
MA0140.10.162
MA0141.12.41132e-9
MA0142.10.243
MA0143.10.546
MA0144.10.701
MA0145.10.226
MA0146.10.215
MA0147.10.117
MA0148.10.498
MA0149.10.753
MA0150.10.861
MA0152.10.0574
MA0153.14.77662e-11
MA0154.10.0119
MA0155.10.243
MA0156.11.19203e-5
MA0157.10.699
MA0159.16.06737e-5
MA0160.12.47769e-4
MA0162.10.0688
MA0163.10.0474
MA0164.10.326
MA0258.10.0022
MA0259.10.641



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: CNhs11118

Novel motifP-value
10.0422
100.285
1000.558
1010.714
1020.938
1030.532
1040.852
1050.162
1060.114
1070.0833
1080.966
1090.286
110.315
1100.0881
1110.109
1120.996
1130.703
1140.239
1150.99
1160.818
1170.571
1180.602
1190.268
120.66
1200.308
1210.519
1220.466
1230.69
1240.713
1250.693
1260.385
1270.166
1280.612
1290.227
133.16967e-4
1300.442
1310.379
1320.89
1330.231
1340.616
1350.923
1360.029
1370.273
1380.074
1390.0908
140.328
1400.182
1410.836
1420.577
1430.641
1440.239
1450.274
1460.68
1470.696
1480.252
1490.0669
150.672
1500.252
1510.505
1520.276
1530.268
1540.298
1550.149
1566.31452e-13
1570.684
1580.09
1590.0199
1600.111
1610.98
1620.707
1630.46
1640.355
1650.0195
1660.335
1670.585
1680.489
1694.31902e-5
170.238
180.261
190.015
20.859
200.924
210.551
220.0897
230.879
240.7
250.853
260.019
270.602
280.765
290.942
30.185
300.19
310.496
320.687
330.612
340.309
350.751
360.224
370.0117
380.843
390.406
40.331
400.0856
410.807
420.762
430.136
440.95
450.836
460.411
470.475
480.374
490.104
50.108
500.725
510.536
520.434
530.985
540.652
550.311
560.538
570.182
580.413
590.0584
60.161
600.195
610.562
620.431
630.165
640.857
650.935
660.146
670.705
680.823
690.248
70.0684
700.872
710.0457
720.399
730.124
740.341
750.706
760.497
770.422
780.0562
790.886
80.416
800.0589
810.969
820.173
830.668
840.81
850.0256
860.861
877.75832e-6
880.54
890.0804
90.112
900.489
910.143
920.207
930.665
940.309
950.433
960.333
970.318
980.563
990.741



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: CNhs11118


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
0000468 (multi-cellular organism)
0007100 (primary circulatory organ)
0000948 (heart)
0000479 (tissue)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0010317 (germ layer / neural crest derived structure)
0004535 (cardiovascular system)
0001009 (circulatory system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000305 (mouse neonate N10 sample)
0011414 (mouse heart- neonate N10 sample)

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
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0004140 (primary heart field)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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