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|library_id=CNhs11013
|library_id=CNhs11013
|library_id_phase_based=2:CNhs11013
|library_id_phase_based=2:CNhs11013
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;376
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;376
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520embryo%2520E13.CNhs11013.376-3I9.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520embryo%2520E13.CNhs11013.376-3I9.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520embryo%2520E13.CNhs11013.376-3I9.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520embryo%2520E13.CNhs11013.376-3I9.mm10.nobarcode.ctss.bed.gz

Revision as of 22:30, 18 May 2017


Name:heart, embryo E13
Species:Mouse (Mus musculus)
Library ID:CNhs11013
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueheart
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  SAMD00005990
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11013 CAGE DRX008973 DRR009847
Accession ID Mm9

Library idBAMCTSS
CNhs11013 DRZ001272 DRZ002655
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

CNhs11013

00
10
100.134
1000
10000.0719
10010.205
10020.523
1003-0.0681
10040
1005-0.0967
10060.164
10070.0238
10080
10090.13
1010.033
10100
1011-0.019
10120
1013-0.236
10140.54
10150.171
10160.089
10170
10180
10190
1020
10200
10210.0719
10220.301
10230
10240.0719
10250
10260
1027-0.048
10280
10290.171
1030.0719
10300
10310.324
10320.00398
10330.024
10340
10350.387
10360.0388
10370
10380.0124
10390.0898
1040
10400.0667
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: CNhs11013

Jaspar motifP-value
MA0002.20.00472
MA0003.10.693
MA0004.10.807
MA0006.10.924
MA0007.10.147
MA0009.10.926
MA0014.10.803
MA0017.10.00216
MA0018.20.893
MA0019.10.654
MA0024.19.06794e-5
MA0025.10.151
MA0027.10.0215
MA0028.10.158
MA0029.10.405
MA0030.10.011
MA0031.10.0183
MA0035.20.118
MA0038.10.99
MA0039.20.0214
MA0040.10.0252
MA0041.10.171
MA0042.10.228
MA0043.10.924
MA0046.12.72163e-21
MA0047.20.00336
MA0048.10.0134
MA0050.14.25139e-6
MA0051.10.0021
MA0052.15.87717e-21
MA0055.19.18486e-5
MA0057.10.653
MA0058.10.788
MA0059.10.266
MA0060.10.135
MA0061.10.197
MA0062.20.327
MA0065.20.081
MA0066.10.637
MA0067.10.59
MA0068.10.386
MA0069.10.274
MA0070.10.793
MA0071.10.909
MA0072.10.109
MA0073.10.984
MA0074.10.605
MA0076.10.868
MA0077.10.917
MA0078.10.228
MA0079.20.527
MA0080.20.00393
MA0081.10.795
MA0083.13.18368e-16
MA0084.10.78
MA0087.10.786
MA0088.10.336
MA0090.10.00285
MA0091.10.946
MA0092.10.907
MA0093.10.858
MA0099.29.25482e-7
MA0100.10.867
MA0101.10.238
MA0102.20.00318
MA0103.15.66736e-6
MA0104.20.669
MA0105.10.439
MA0106.10.883
MA0107.10.102
MA0108.20.613
MA0111.10.333
MA0112.20.57
MA0113.10.893
MA0114.13.0006e-5
MA0115.10.886
MA0116.10.402
MA0117.10.434
MA0119.10.187
MA0122.10.864
MA0124.10.512
MA0125.10.879
MA0131.10.409
MA0135.10.369
MA0136.10.00841
MA0137.20.0541
MA0138.20.0152
MA0139.10.337
MA0140.10.0411
MA0141.10.00914
MA0142.10.21
MA0143.10.715
MA0144.10.28
MA0145.10.174
MA0146.10.927
MA0147.10.643
MA0148.10.0117
MA0149.10.0973
MA0150.10.00486
MA0152.10.947
MA0153.12.9713e-13
MA0154.10.656
MA0155.10.174
MA0156.13.7647e-4
MA0157.10.0654
MA0159.10.0939
MA0160.10.366
MA0162.10.292
MA0163.10.0393
MA0164.10.569
MA0258.10.372
MA0259.10.263



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: CNhs11013

Novel motifP-value
10.573
100.825
1000.866
1010.949
1020.773
1030.201
1040.871
1050.942
1060.176
1070.571
1080.839
1090.762
110.388
1100.233
1110.728
1120.378
1130.348
1140.554
1150.892
1160.533
1170.157
1180.521
1190.176
120.42
1200.204
1210.655
1220.21
1230.0155
1240.564
1250.672
1260.915
1270.285
1280.0376
1290.369
130.00121
1300.322
1310.671
1320.582
1330.646
1340.682
1350.899
1360.0665
1370.713
1380.0819
1390.821
140.424
1400.9
1410.191
1420.645
1430.735
1440.0607
1450.2
1460.205
1470.842
1480.545
1490.631
150.203
1500.511
1510.122
1520.626
1530.438
1540.604
1550.424
1560.207
1570.975
1580.826
1590.274
1600.324
1610.902
1620.947
1630.42
1640.761
1650.19
1660.831
1670.861
1680.75
1690.0989
170.524
180.314
190.58
20.258
200.111
210.69
220.784
230.089
240.451
250.566
260.0232
270.147
280.339
290.312
30.782
300.0477
310.613
320.402
330.189
340.784
350.457
360.191
370.243
380.205
390.33
40.808
400.00386
410.897
420.597
430.534
440.563
450.045
460.878
470.697
480.639
490.58
50.774
500.478
510.875
520.489
530.576
540.626
550.262
560.734
570.413
580.624
590.338
60.193
600.445
610.308
620.423
630.825
640.599
650.151
660.747
670.867
680.42
690.235
70.836
700.0126
710.0184
720.101
730.433
740.653
750.534
760.548
770.453
780.876
790.171
80.94
800.0161
810.5
820.677
830.819
840.593
850.559
860.943
870.00133
880.267
890.32
90.957
900.943
910.214
920.401
930.261
940.36
950.27
960.419
970.131
980.0946
990.531



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: CNhs11013


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)
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)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000293 (mouse embryonic day 13 sample)
0011327 (mouse heart- 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
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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