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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000061,UBERON:0000062,UBERON:0000119,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000948,UBERON:0001009,UBERON:0001048,UBERON:0001062,UBERON:0002050,UBERON:0002532,UBERON:0003081,UBERON:0003084,UBERON:0003914,UBERON:0004120,UBERON:0004140,UBERON:0004141,UBERON:0004291,UBERON:0004535,UBERON:0004872,UBERON:0005291,UBERON:0005423,UBERON:0005498,UBERON:0007005,UBERON:0007100
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0007100,UBERON:0000948,UBERON:0000483,UBERON:0000926,UBERON:0000479,UBERON:0000062,UBERON:0004111,UBERON:0004120,UBERON:0000025,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0003914,UBERON:0002050,UBERON:0005423,UBERON:0000477,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0003103,UBERON:0005291,UBERON:0001048,UBERON:0006598,UBERON:0002532,UBERON:0004535,UBERON:0005498,UBERON:0003081,UBERON:0001009,UBERON:0004140,UBERON:0009881,UBERON:0006603,UBERON:0004141,UBERON:0004872,UBERON:0003084,UBERON:0007005,UBERON:0004139,UBERON:0004291
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=

Revision as of 18:34, 8 June 2012


Name:heart, neonate N20
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 stage20 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

CNhs11127

00
10
100.904
1000
10000.833
10010.629
10020.0322
10030.184
10040
10050
10060.574
1007-0.0188
10080
10090.22
101-0.114
10100
10117.48101e-4
10120.0135
1013-0.0762
1014-0.0281
1015-0.176
10160.0569
10170
10180
10190
1020
10200
10210
10220.817
10230
10240.547
10250
10260
10270
10280.0593
1029-0.0396
1030.0386
10300
10310.0541
10320.242
1033-0.00724
10340
10350.577
1036-0.307
10370
10380.201
10390.655
1040
10400.136
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: CNhs11127

Jaspar motifP-value
MA0002.20.34
MA0003.10.324
MA0004.10.12
MA0006.10.183
MA0007.10.616
MA0009.10.565
MA0014.10.57
MA0017.10.978
MA0018.20.357
MA0019.10.286
MA0024.17.06249e-6
MA0025.10.28
MA0027.10.431
MA0028.10.0149
MA0029.10.87
MA0030.10.63
MA0031.10.841
MA0035.26.06957e-6
MA0038.10.133
MA0039.20.842
MA0040.10.754
MA0041.10.422
MA0042.10.401
MA0043.10.362
MA0046.14.28322e-16
MA0047.20.762
MA0048.10.587
MA0050.10.884
MA0051.10.396
MA0052.13.91204e-58
MA0055.10.463
MA0057.10.514
MA0058.10.0992
MA0059.10.13
MA0060.17.99355e-13
MA0061.10.552
MA0062.21.75611e-5
MA0065.20.0241
MA0066.10.815
MA0067.10.79
MA0068.10.305
MA0069.10.149
MA0070.10.713
MA0071.14.7318e-4
MA0072.10.403
MA0073.10.46
MA0074.10.175
MA0076.10.00205
MA0077.10.911
MA0078.10.736
MA0079.20.272
MA0080.20.00555
MA0081.10.978
MA0083.11.7e-14
MA0084.10.847
MA0087.10.299
MA0088.10.735
MA0090.12.85691e-5
MA0091.10.934
MA0092.10.315
MA0093.10.0958
MA0099.20.121
MA0100.10.0128
MA0101.10.472
MA0102.20.0429
MA0103.10.00274
MA0104.20.045
MA0105.10.582
MA0106.10.773
MA0107.10.703
MA0108.20.23
MA0111.10.943
MA0112.28.68989e-6
MA0113.10.214
MA0114.10.555
MA0115.10.2
MA0116.10.53
MA0117.10.45
MA0119.10.139
MA0122.10.0419
MA0124.10.775
MA0125.10.298
MA0131.10.322
MA0135.10.408
MA0136.13.68508e-4
MA0137.20.15
MA0138.20.0154
MA0139.10.624
MA0140.10.00161
MA0141.12.04288e-10
MA0142.10.0692
MA0143.10.279
MA0144.10.68
MA0145.10.0393
MA0146.10.0438
MA0147.10.0853
MA0148.10.982
MA0149.10.895
MA0150.10.0482
MA0152.10.385
MA0153.13.84587e-11
MA0154.10.0413
MA0155.10.277
MA0156.10.00405
MA0157.10.493
MA0159.12.07955e-6
MA0160.15.28826e-6
MA0162.10.149
MA0163.10.71
MA0164.10.13
MA0258.10.00111
MA0259.10.277



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: CNhs11127

Novel motifP-value
10.147
100.886
1000.721
1010.538
1020.847
1030.917
1040.644
1050.08
1060.216
1070.232
1080.943
1090.287
110.372
1100.262
1110.0878
1120.803
1130.806
1140.0674
1150.532
1160.672
1170.743
1180.698
1190.132
120.593
1200.154
1210.115
1220.624
1230.674
1240.466
1250.853
1260.476
1270.384
1280.555
1290.0707
130.00106
1300.617
1310.815
1320.741
1330.775
1340.596
1350.73
1360.918
1370.175
1380.0914
1390.0574
140.0804
1400.56
1410.63
1420.941
1430.41
1440.491
1450.474
1460.57
1470.587
1480.461
1497.67032e-4
150.238
1500.495
1510.177
1520.0594
1530.562
1540.752
1550.0243
1560.0261
1570.859
1580.144
1590.777
1600.288
1610.909
1620.787
1630.219
1640.406
1654.27339e-4
1660.226
1670.601
1680.0818
1697.45152e-5
170.167
180.181
190.0241
20.522
200.774
210.311
220.0223
230.423
240.978
250.679
260.133
270.9
280.806
290.371
30.422
300.587
310.579
320.957
330.646
340.229
350.886
360.224
370.00709
380.715
390.455
40.349
400.416
410.779
420.93
430.194
440.96
450.522
460.709
470.898
480.498
490.168
50.237
500.853
510.558
520.307
530.657
540.302
550.868
560.559
570.412
580.351
590.0339
60.0616
600.121
610.591
620.321
630.101
640.742
650.507
660.118
670.755
680.89
690.0154
70.0815
700.358
710.184
720.613
730.0437
740.613
750.811
760.897
770.387
780.0407
790.76
80.832
800.288
810.622
820.164
830.454
840.436
850.00271
860.713
870.425
880.631
890.0228
90.0741
900.881
910.419
920.199
930.356
940.789
950.276
960.473
970.919
980.293
990.933



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: CNhs11127


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)
0000922 (embryo)
0007100 (primary circulatory organ)
0000948 (heart)
0000483 (epithelium)
0000926 (mesoderm)
0000479 (tissue)
0000062 (organ)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0000025 (tube)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0003914 (epithelial tube)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0000477 (anatomical cluster)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0000119 (cell layer)
0003103 (compound organ)
0005291 (embryonic tissue)
0001048 (primordium)
0006598 (presumptive structure)
0002532 (epiblast (generic))
0004535 (cardiovascular system)
0005498 (primitive heart tube)
0003081 (lateral plate mesoderm)
0001009 (circulatory system)
0004140 (primary heart field)
0009881 (anterior lateral plate mesoderm)
0006603 (presumptive mesoderm)
0004141 (heart tube)
0004872 (splanchnic layer of lateral plate mesoderm)
0003084 (heart primordium)
0007005 (cardiac mesoderm)
0004139 (cardiogenic plate)
0004291 (heart rudiment)

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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