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FF:839-18H3

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Name:testis, neonate N20
Species:Mouse (Mus musculus)
Library ID:CNhs11110
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissuetestis
dev stage20 days neonate
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  SAMD00004759
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11110 CAGE DRX009110 DRR009984
Accession ID Mm9

Library idBAMCTSS
CNhs11110 DRZ001409 DRZ002792
Accession ID Mm10

Library idBAMCTSS
CNhs11110 DRZ012759 DRZ014142
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

CNhs11110

00.505
10
100
1000
10000.047
10010.392
10022.087892e-4
10030.00324
10040
1005-0.304
1006-0.0253
10070.232
10080
10090.18
1010.13
10100
10110.854
10120.094
10130.00566
1014-0.0851
10150.472
1016-0.205
10170
10180
10190
1020
10200
10210
10220
10230
1024-0.14
10250
10260.968
10270.033
10280
10290.0236
1030.0275
10300
1031-0.456
1032-0.418
10330.0188
10340
10350.294
1036-0.129
10370
1038-0.15
1039-0.0783
1040
1040-0.469
10410.237



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: CNhs11110

Jaspar motifP-value
MA0002.20.032
MA0003.10.801
MA0004.10.268
MA0006.10.0883
MA0007.10.946
MA0009.10.37
MA0014.10.344
MA0017.10.139
MA0018.20.045
MA0019.10.226
MA0024.10.0692
MA0025.10.776
MA0027.10.768
MA0028.14.81754e-5
MA0029.10.184
MA0030.10.965
MA0031.10.798
MA0035.20.0759
MA0038.10.143
MA0039.20.282
MA0040.10.392
MA0041.10.948
MA0042.10.959
MA0043.10.0289
MA0046.14.39153e-15
MA0047.20.00849
MA0048.10.0542
MA0050.10.00881
MA0051.10.611
MA0052.11.63504e-4
MA0055.18.53065e-4
MA0057.10.398
MA0058.10.139
MA0059.10.0286
MA0060.11.266e-11
MA0061.10.0218
MA0062.21.72785e-7
MA0065.20.704
MA0066.10.0392
MA0067.10.578
MA0068.10.698
MA0069.10.282
MA0070.10.496
MA0071.10.774
MA0072.10.448
MA0073.10.831
MA0074.10.638
MA0076.11.23549e-6
MA0077.10.948
MA0078.10.661
MA0079.20.703
MA0080.21.03555e-4
MA0081.10.329
MA0083.10.0145
MA0084.10.568
MA0087.10.503
MA0088.10.0813
MA0090.10.216
MA0091.10.437
MA0092.10.0967
MA0093.10.225
MA0099.20.00316
MA0100.12.20814e-15
MA0101.10.467
MA0102.20.228
MA0103.10.401
MA0104.26.35214e-4
MA0105.17.89549e-4
MA0106.10.0483
MA0107.10.0823
MA0108.21.09506e-5
MA0111.10.887
MA0112.20.0197
MA0113.10.794
MA0114.10.107
MA0115.10.266
MA0116.10.0195
MA0117.10.846
MA0119.10.0829
MA0122.10.428
MA0124.10.903
MA0125.10.169
MA0131.10.0197
MA0135.10.0508
MA0136.10.719
MA0137.20.612
MA0138.20.0182
MA0139.10.231
MA0140.10.00608
MA0141.10.842
MA0142.10.00503
MA0143.10.456
MA0144.10.317
MA0145.10.0112
MA0146.10.0326
MA0147.10.00182
MA0148.15.50124e-4
MA0149.10.214
MA0150.10.134
MA0152.10.832
MA0153.18.6966e-7
MA0154.10.00484
MA0155.10.101
MA0156.10.0658
MA0157.10.339
MA0159.10.424
MA0160.10.485
MA0162.10.455
MA0163.10.516
MA0164.10.328
MA0258.10.08
MA0259.10.0079



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: CNhs11110

Novel motifP-value
10.799
100.219
1000.254
1010.389
1020.534
1030.554
1040.918
1050.0192
1065.31924e-5
1075.0949e-4
1080.2
1090.703
110.962
1100.607
1110.18
1120.809
1130.181
1140.925
1150.465
1160.633
1170.0199
1180.449
1190.253
120.836
1200.894
1210.0858
1220.208
1230.0488
1240.0812
1250.481
1260.443
1270.438
1281.91663e-4
1290.233
130.519
1300.78
1310.0787
1320.279
1330.251
1340.78
1350.0287
1360.00915
1370.868
1380.973
1390.967
140.122
1400.205
1410.0055
1420.244
1430.11
1440.399
1450.968
1460.668
1470.27
1480.0966
1490.0198
150.263
1500.735
1510.105
1520.135
1530.486
1540.994
1550.233
1560.0311
1570.421
1580.618
1590.273
1600.0938
1610.308
1620.329
1630.244
1640.589
1650.143
1660.73
1670.428
1680.0512
1690.364
170.259
180.408
190.439
20.0171
200.0213
210.515
220.44
230.12
240.119
250.567
260.665
270.0314
280.546
290.214
30.493
300.193
310.0798
320.374
330.64
340.504
350.912
360.363
370.492
380.507
390.501
40.953
400.414
410.998
420.581
430.205
440.323
450.244
460.332
470.833
480.828
490.355
50.252
500.709
510.387
520.0399
530.254
540.315
550.253
560.0875
570.657
580.851
590.0561
60.654
600.111
610.691
620.642
630.262
640.861
650.0987
660.012
670.137
680.758
690.866
70.967
700.895
710.524
720.711
730.776
740.866
750.815
760.0641
770.289
780.0282
790.221
80.776
800.372
810.199
820.346
830.842
840.358
850.302
860.86
870.119
880.282
890.223
90.768
900.7
910.0793
920.299
930.909
940.349
950.336
960.932
970.603
980.291
990.421



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: CNhs11110


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000308 (mouse neonate N20 sample)
0011433 (mouse testis- neonate N20 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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