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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;372
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;372
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;372
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;372
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520embryo%2520E13.CNhs10512.372-23H2.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520embryo%2520E13.CNhs10512.372-23H2.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520embryo%2520E13.CNhs10512.372-23H2.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/whole%2520body%252c%2520embryo%2520E13.CNhs10512.372-23H2.mm10.nobarcode.ctss.bed.gz

Revision as of 18:35, 4 August 2017


Name:whole body, embryo E13
Species:Mouse (Mus musculus)
Library ID:CNhs10512
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage13 days embryo
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00006017
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10512 CAGE DRX009144 DRR010018
Accession ID Mm9

Library idBAMCTSS
CNhs10512 DRZ001443 DRZ002826
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs10512

00
10.114
100
1000.18
1000-0.00125
1001-0.0749
10020.0979
10030.0046
10040.154
1005-0.0402
10060.0468
10070.0839
10080
1009-0.0105
1010.101
10100
10110.0424
10120
1013-0.169
10140.338
10150.27
10160.193
10170
10180.0685
10190
1020
10200
1021-7.232784e-4
1022-0.0188
10230
1024-0.066
10250.18
10260.039
10270.268
10280
1029-0.0553
1030.104
10300
10310.317
1032-0.177
10330.104
10340
10350
10360.197
10370
1038-0.0722
1039-0.123
1040
1040-0.00904
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



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: CNhs10512

Jaspar motifP-value
MA0002.29.71032e-5
MA0003.10.276
MA0004.10.651
MA0006.10.267
MA0007.10.141
MA0009.10.182
MA0014.10.188
MA0017.11.45862e-5
MA0018.20.496
MA0019.10.866
MA0024.14.24535e-4
MA0025.10.01
MA0027.10.0335
MA0028.10.534
MA0029.10.944
MA0030.10.135
MA0031.10.00862
MA0035.20.327
MA0038.10.00734
MA0039.20.14
MA0040.10.343
MA0041.10.515
MA0042.10.567
MA0043.10.389
MA0046.10.0135
MA0047.20.00531
MA0048.10.573
MA0050.16.33008e-6
MA0051.14.16219e-5
MA0052.10.845
MA0055.10.686
MA0057.10.0745
MA0058.10.758
MA0059.10.435
MA0060.12.05506e-16
MA0061.10.101
MA0062.20.052
MA0065.21.99506e-6
MA0066.10.0697
MA0067.10.488
MA0068.10.0731
MA0069.10.635
MA0070.10.114
MA0071.10.0334
MA0072.10.0146
MA0073.10.929
MA0074.10.281
MA0076.10.832
MA0077.10.0867
MA0078.10.896
MA0079.20.542
MA0080.21.45991e-10
MA0081.10.226
MA0083.10.331
MA0084.10.825
MA0087.10.323
MA0088.10.263
MA0090.10.533
MA0091.10.915
MA0092.10.466
MA0093.10.743
MA0099.22.86669e-5
MA0100.10.694
MA0101.10.145
MA0102.20.533
MA0103.10.0013
MA0104.20.821
MA0105.10.121
MA0106.10.0431
MA0107.10.108
MA0108.22.16709e-4
MA0111.10.424
MA0112.22.13946e-6
MA0113.10.245
MA0114.16.07343e-5
MA0115.10.0048
MA0116.10.0397
MA0117.10.424
MA0119.10.0992
MA0122.10.74
MA0124.10.94
MA0125.10.00591
MA0131.10.57
MA0135.10.214
MA0136.17.29847e-10
MA0137.20.0275
MA0138.20.435
MA0139.10.0895
MA0140.10.00415
MA0141.19.61289e-5
MA0142.10.186
MA0143.10.0249
MA0144.10.0551
MA0145.10.0316
MA0146.10.0229
MA0147.10.988
MA0148.10.00299
MA0149.18.17113e-4
MA0150.10.00659
MA0152.10.915
MA0153.10.0174
MA0154.10.00365
MA0155.10.768
MA0156.16.41909e-5
MA0157.10.0107
MA0159.13.26423e-4
MA0160.10.00126
MA0162.10.435
MA0163.10.00234
MA0164.10.952
MA0258.11.14377e-4
MA0259.10.909



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: CNhs10512

Novel motifP-value
10.0575
100.0793
1000.952
1010.766
1020.44
1030.0294
1040.662
1050.484
1060.0168
1070.119
1080.887
1090.0324
110.0645
1100.105
1110.0052
1120.00662
1130.901
1140.0101
1150.41
1160.47
1170.0194
1180.539
1190.107
120.846
1200.885
1210.677
1220.817
1230.987
1240.667
1250.0933
1260.116
1270.065
1280.0674
1290.236
130.00961
1300.196
1310.748
1320.285
1330.434
1340.966
1350.668
1360.0951
1370.562
1380.838
1390.0269
140.572
1400.0152
1410.0535
1420.623
1430.216
1440.652
1450.0881
1460.72
1470.617
1480.227
1490.341
150.0496
1500.284
1510.23
1520.0399
1530.162
1540.566
1550.179
1568.55989e-6
1570.847
1580.0885
1590.0966
1600.538
1610.29
1620.827
1630.299
1640.0269
1650.155
1660.39
1670.744
1680.608
1690.00257
170.0444
180.467
190.175
20.914
200.45
210.671
220.173
230.264
240.177
250.412
260.0147
270.563
280.337
290.0982
30.0957
300.843
310.528
320.215
330.215
340.963
350.25
360.222
370.018
380.311
390.36
40.626
400.236
410.346
420.354
430.118
440.0398
450.55
460.121
470.13
480.0768
490.0991
50.151
500.898
510.599
520.411
530.985
540.639
550.382
560.403
570.488
580.214
590.0699
60.65
600.0429
610.22
620.0718
630.13
640.5
650.18
660.679
670.984
680.176
690.488
70.116
701.78847e-4
710.0508
720.384
730.0205
740.367
750.0146
760.552
770.12
780.0911
790.715
80.0866
800.386
810.558
820.0305
830.322
840.252
850.0166
860.232
870.514
880.434
890.209
90.614
900.084
910.464
920.0798
930.119
940.898
950.0231
960.408
970.556
980.395
990.745



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: CNhs10512


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)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000293 (mouse embryonic day 13 sample)
0011326 (mouse whole body- embryo E13 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
FF:0000294 (mouse embryonic day 11 sample)

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