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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;1564
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1564
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;1564
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1564
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/gonad%252c%2520embryo%2520E13.CNhs11044.1564-45I6.mm10.nobarcode.bam  
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/gonad%252c%2520embryo%2520E13.CNhs11044.1564-45I6.mm10.nobarcode.bam  
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/gonad%252c%2520embryo%2520E13.CNhs11044.1564-45I6.mm10.nobarcode.ctss.bed.gz  
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/gonad%252c%2520embryo%2520E13.CNhs11044.1564-45I6.mm10.nobarcode.ctss.bed.gz  

Revision as of 18:26, 4 August 2017


Name:gonad, embryo E13
Species:Mouse (Mus musculus)
Library ID:CNhs11044
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuegonad
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  SAMD00004837
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11044 CAGE DRX008970 DRR009844
Accession ID Mm9

Library idBAMCTSS
CNhs11044 DRZ001269 DRZ002652
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

CNhs11044

00
10
100
1000
1000-0.0322
1001-0.0356
10020.586
1003-0.102
10040.112
1005-0.0389
1006-0.0465
10070.113
10080
1009-0.00536
1010.0975
10100
1011-0.0287
10120
1013-0.116
10140.358
10150.159
10160.339
10170
10180
10190
1020
10200
10210
10220.0638
10230
1024-0.011
10250
10260.0494
10270
10280
10290.117
1030.164
10300
10310.416
1032-0.0159
10330.0397
10340
10350.0788
10360.132
10370
10380.0817
1039-0.108
1040
10400.0559
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: CNhs11044

Jaspar motifP-value
MA0002.22.30203e-4
MA0003.10.561
MA0004.10.601
MA0006.10.293
MA0007.10.427
MA0009.10.775
MA0014.10.646
MA0017.10.00329
MA0018.20.163
MA0019.10.906
MA0024.13.76289e-6
MA0025.10.00118
MA0027.10.129
MA0028.10.173
MA0029.10.986
MA0030.10.036
MA0031.10.00374
MA0035.20.24
MA0038.10.153
MA0039.20.127
MA0040.10.377
MA0041.10.244
MA0042.10.461
MA0043.10.319
MA0046.13.95704e-7
MA0047.20.0178
MA0048.10.0135
MA0050.10.0142
MA0051.10.0038
MA0052.15.56738e-6
MA0055.10.00532
MA0057.10.128
MA0058.10.432
MA0059.10.221
MA0060.11.93354e-6
MA0061.10.121
MA0062.20.727
MA0065.22.71987e-4
MA0066.10.0493
MA0067.10.411
MA0068.10.00216
MA0069.10.541
MA0070.10.851
MA0071.10.283
MA0072.10.0369
MA0073.10.655
MA0074.10.871
MA0076.10.154
MA0077.10.982
MA0078.10.527
MA0079.20.945
MA0080.21.85304e-7
MA0081.10.345
MA0083.10.128
MA0084.10.615
MA0087.10.318
MA0088.10.597
MA0090.10.987
MA0091.10.578
MA0092.10.677
MA0093.10.584
MA0099.22.69456e-7
MA0100.10.781
MA0101.10.305
MA0102.20.0726
MA0103.10.00372
MA0104.20.241
MA0105.10.0409
MA0106.10.226
MA0107.10.164
MA0108.20.00213
MA0111.10.474
MA0112.25.7843e-4
MA0113.10.463
MA0114.10.00204
MA0115.10.0459
MA0116.10.0482
MA0117.10.0299
MA0119.10.206
MA0122.10.926
MA0124.10.283
MA0125.10.831
MA0131.10.21
MA0135.10.273
MA0136.13.40985e-4
MA0137.20.194
MA0138.21.82196e-4
MA0139.10.638
MA0140.10.623
MA0141.10.591
MA0142.10.558
MA0143.10.111
MA0144.10.145
MA0145.10.00767
MA0146.10.729
MA0147.10.242
MA0148.10.00783
MA0149.10.0488
MA0150.13.2078e-4
MA0152.10.211
MA0153.16.38008e-5
MA0154.10.0489
MA0155.10.971
MA0156.10.0867
MA0157.10.0704
MA0159.10.0052
MA0160.10.149
MA0162.10.401
MA0163.10.835
MA0164.10.964
MA0258.10.00208
MA0259.10.203



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: CNhs11044

Novel motifP-value
10.115
100.41
1000.726
1010.519
1020.844
1030.366
1040.843
1050.228
1060.012
1070.2
1080.496
1090.256
110.247
1100.932
1110.288
1120.428
1130.418
1140.0418
1150.437
1160.463
1170.374
1180.844
1190.205
120.516
1200.818
1210.273
1220.737
1230.106
1240.169
1250.415
1260.957
1270.0615
1280.00599
1290.0312
130.973
1300.224
1310.222
1320.569
1330.527
1340.595
1350.932
1360.697
1370.698
1380.488
1390.0502
140.177
1400.94
1410.176
1420.322
1430.102
1440.372
1450.967
1460.268
1470.835
1480.192
1490.258
150.118
1500.88
1510.0439
1520.114
1530.882
1540.512
1550.837
1562.80617e-4
1570.574
1580.334
1590.198
1600.747
1610.862
1620.997
1630.00882
1640.464
1650.102
1660.316
1670.652
1680.122
1690.0915
170.112
180.111
190.803
20.526
200.377
210.696
220.559
230.137
240.6
250.277
260.848
270.369
280.244
290.751
30.385
300.561
310.219
320.308
330.947
340.764
350.111
360.262
370.169
380.657
390.85
40.743
400.404
410.0598
420.767
430.224
440.0775
450.409
460.312
470.287
480.283
490.13
50.169
500.8
510.683
520.268
530.564
540.365
550.503
560.318
570.912
580.25
590.142
60.848
600.0888
610.581
620.0705
630.194
640.657
650.206
660.967
670.821
680.0836
690.872
70.363
700.00188
710.31
720.35
730.143
740.747
750.197
760.469
770.317
780.214
790.88
80.236
800.0706
810.315
820.217
830.346
840.0786
850.00599
860.32
870.259
880.805
890.0947
90.753
900.104
910.517
920.125
930.681
940.364
950.188
960.503
970.908
980.131
990.799



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: CNhs11044


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)
0000991 (gonad)
0000479 (tissue)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003133 (reproductive organ)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)

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)
0011282 (mouse gonad- 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:0005564 (gonad primordium)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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