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|library_id=CNhs11033
|library_id=CNhs11033
|library_id_phase_based=2:CNhs11033
|library_id_phase_based=2:CNhs11033
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;470
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;470
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520embryo%2520E16.CNhs11033.470-26G5.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520embryo%2520E16.CNhs11033.470-26G5.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520embryo%2520E16.CNhs11033.470-26G5.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/testis%252c%2520embryo%2520E16.CNhs11033.470-26G5.mm10.nobarcode.ctss.bed.gz

Revision as of 22:33, 18 May 2017


Name:testis, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs11033
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuetestis
dev stage16 days embryo
sexmale
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  SAMD00005676
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11033 CAGE DRX009104 DRR009978
Accession ID Mm9

Library idBAMCTSS
CNhs11033 DRZ001403 DRZ002786
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

CNhs11033

00
10
100
1000
10000
1001-2.109203e-4
10020.645
10030.0233
10040
1005-0.0389
10060.0538
10070.16
10080
10090.18
1010.0674
10100
10110.0703
10120
1013-0.156
10140.143
10150.152
10160.335
10170
10180.0772
10190
1020
10200
1021-0.0487
10220.0723
10230
1024-0.0624
10250
10260.0477
10270
10280
1029-0.0196
1030.248
10300
10310.437
10327.252914e-4
10330
10340
10350
10360.0663
10370
1038-0.0304
1039-0.0195
1040
10400.105
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: CNhs11033

Jaspar motifP-value
MA0002.20.00447
MA0003.10.812
MA0004.10.329
MA0006.10.123
MA0007.10.421
MA0009.10.749
MA0014.10.76
MA0017.10.00218
MA0018.20.708
MA0019.10.379
MA0024.18.08751e-6
MA0025.10.857
MA0027.10.664
MA0028.10.146
MA0029.10.799
MA0030.10.135
MA0031.10.34
MA0035.20.846
MA0038.10.00902
MA0039.20.0346
MA0040.10.305
MA0041.10.424
MA0042.10.559
MA0043.10.154
MA0046.14.47548e-25
MA0047.20.0469
MA0048.10.197
MA0050.10.00181
MA0051.10.00497
MA0052.10.00689
MA0055.10.0182
MA0057.10.446
MA0058.10.108
MA0059.10.456
MA0060.12.18761e-18
MA0061.10.131
MA0062.20.284
MA0065.20.00787
MA0066.10.0617
MA0067.10.775
MA0068.10.15
MA0069.10.777
MA0070.10.154
MA0071.10.682
MA0072.10.413
MA0073.10.931
MA0074.10.633
MA0076.10.0313
MA0077.10.929
MA0078.10.132
MA0079.20.0947
MA0080.21.16179e-4
MA0081.10.633
MA0083.10.588
MA0084.10.979
MA0087.10.518
MA0088.10.995
MA0090.10.933
MA0091.10.307
MA0092.10.333
MA0093.10.216
MA0099.25.83726e-4
MA0100.10.334
MA0101.10.518
MA0102.20.76
MA0103.10.00125
MA0104.20.0566
MA0105.19.40138e-5
MA0106.10.345
MA0107.10.343
MA0108.20.0716
MA0111.10.368
MA0112.28.67024e-5
MA0113.10.338
MA0114.10.00297
MA0115.10.052
MA0116.10.0201
MA0117.10.206
MA0119.10.314
MA0122.10.965
MA0124.10.169
MA0125.10.929
MA0131.10.632
MA0135.10.625
MA0136.10.0213
MA0137.20.261
MA0138.20.006
MA0139.10.56
MA0140.10.839
MA0141.10.537
MA0142.10.00344
MA0143.10.828
MA0144.10.156
MA0145.10.0463
MA0146.10.346
MA0147.10.137
MA0148.10.00176
MA0149.10.0869
MA0150.10.00299
MA0152.10.235
MA0153.16.02754e-18
MA0154.10.00597
MA0155.10.709
MA0156.10.769
MA0157.10.264
MA0159.16.64849e-5
MA0160.10.968
MA0162.10.0387
MA0163.10.163
MA0164.10.339
MA0258.13.72e-4
MA0259.10.0828



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: CNhs11033

Novel motifP-value
10.108
100.229
1000.725
1010.569
1020.648
1030.291
1040.834
1050.395
1062.95835e-4
1070.00349
1080.722
1090.697
110.343
1100.792
1110.415
1120.431
1130.397
1140.035
1150.613
1160.478
1170.642
1180.909
1190.169
120.463
1200.463
1210.51
1220.716
1230.127
1240.119
1250.0584
1260.939
1270.261
1281.61625e-4
1290.142
130.471
1300.423
1310.829
1320.568
1330.962
1340.645
1350.491
1360.0657
1370.852
1380.538
1390.0532
140.171
1400.5
1410.125
1420.888
1430.109
1440.133
1450.627
1460.429
1470.763
1480.0513
1490.326
150.111
1500.858
1510.0713
1520.266
1530.315
1540.799
1550.71
1565.53283e-4
1570.293
1580.215
1590.0388
1600.79
1610.659
1620.609
1630.128
1640.937
1650.0354
1660.846
1670.268
1680.215
1690.453
170.0895
180.185
190.975
20.556
200.731
210.674
220.803
230.134
240.983
250.42
260.39
270.313
280.339
290.957
30.199
300.93
310.148
320.467
330.726
340.957
350.0477
360.204
370.127
380.663
390.801
40.637
400.722
410.139
420.466
430.183
440.276
450.496
460.132
470.47
480.358
490.104
50.0561
500.913
510.784
520.0999
530.912
540.428
550.236
560.196
570.561
580.292
590.174
60.815
600.0345
610.967
620.0849
630.179
640.734
650.218
660.286
670.8
681.1007e-4
690.461
70.401
700.0139
710.114
720.765
730.302
740.654
750.275
760.787
770.316
780.341
790.533
80.0957
800.118
810.237
820.504
830.426
840.302
850.00602
860.09
870.411
880.857
890.0434
90.737
900.179
910.45
920.117
930.667
940.24
950.933
960.235
970.639
980.118
990.975



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: CNhs11033


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)
0000473 (testis)
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)
0003135 (male reproductive organ)
0003133 (reproductive organ)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0003101 (male organism)
0000079 (male reproductive 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)
0000299 (mouse embryonic day 16 sample)
0011364 (mouse testis- embryo E16 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:0009117 (indifferent gonad)
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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