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FF:389-23F5

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Name:testis, embryo E13
Species:Mouse (Mus musculus)
Library ID:CNhs11031
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissuetestis
dev stage13 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  SAMD00005814
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11031 CAGE DRX009102 DRR009976
Accession ID Mm9

Library idBAMCTSS
CNhs11031 DRZ001401 DRZ002784
Accession ID Mm10

Library idBAMCTSS
CNhs11031 DRZ012751 DRZ014134
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

CNhs11031

00
10
100
1000
10000
1001-0.0366
10020.276
1003-0.122
10040
1005-0.0389
1006-0.104
10070.133
10080
1009-0.0572
1010.136
10100
1011-0.0261
10120
1013-0.188
10140.114
10150.231
10160.262
10170
10180
10190
1020
10200
10210
1022-0.0271
10230
1024-0.0899
10250
10260
10270
10280
1029-0.0543
1030.0354
10300
10310.244
1032-0.121
10330
10340
10350.0605
1036-0.0157
10370
10380.0143
1039-0.0649
1040
10400.0401
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: CNhs11031

Jaspar motifP-value
MA0002.20.0017
MA0003.10.953
MA0004.10.497
MA0006.10.39
MA0007.10.453
MA0009.10.876
MA0014.10.727
MA0017.10.00776
MA0018.20.725
MA0019.10.353
MA0024.17.40215e-7
MA0025.10.582
MA0027.10.239
MA0028.10.0067
MA0029.10.867
MA0030.10.183
MA0031.10.13
MA0035.20.69
MA0038.10.0557
MA0039.20.528
MA0040.10.339
MA0041.10.358
MA0042.10.516
MA0043.10.354
MA0046.15.99726e-25
MA0047.20.0562
MA0048.10.0237
MA0050.18.17823e-4
MA0051.10.00184
MA0052.12.60087e-4
MA0055.10.009
MA0057.10.185
MA0058.10.294
MA0059.10.464
MA0060.15.09244e-13
MA0061.10.104
MA0062.20.0173
MA0065.20.0101
MA0066.10.0481
MA0067.10.69
MA0068.10.0279
MA0069.10.607
MA0070.10.582
MA0071.10.846
MA0072.10.366
MA0073.10.87
MA0074.10.918
MA0076.10.00488
MA0077.10.303
MA0078.10.661
MA0079.20.253
MA0080.21.02789e-5
MA0081.10.99
MA0083.10.223
MA0084.10.898
MA0087.10.584
MA0088.10.999
MA0090.10.79
MA0091.10.718
MA0092.10.38
MA0093.10.434
MA0099.21.03301e-4
MA0100.10.335
MA0101.10.791
MA0102.20.426
MA0103.10.00125
MA0104.20.188
MA0105.12.14407e-4
MA0106.10.339
MA0107.10.341
MA0108.26.38784e-4
MA0111.10.202
MA0112.22.20059e-4
MA0113.10.982
MA0114.10.007
MA0115.10.343
MA0116.10.019
MA0117.10.164
MA0119.10.32
MA0122.10.92
MA0124.10.072
MA0125.10.341
MA0131.10.217
MA0135.10.832
MA0136.10.105
MA0137.20.467
MA0138.24.30425e-4
MA0139.10.356
MA0140.10.576
MA0141.10.229
MA0142.10.242
MA0143.10.0894
MA0144.10.322
MA0145.10.00674
MA0146.10.407
MA0147.10.23
MA0148.10.00632
MA0149.10.099
MA0150.10.00933
MA0152.10.578
MA0153.12.64433e-15
MA0154.10.0109
MA0155.10.629
MA0156.10.908
MA0157.10.147
MA0159.10.00204
MA0160.10.685
MA0162.10.132
MA0163.10.0792
MA0164.10.799
MA0258.10.00126
MA0259.10.24



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: CNhs11031

Novel motifP-value
10.107
100.331
1000.705
1010.404
1020.637
1030.181
1040.841
1050.159
1060.00395
1070.048
1080.675
1090.399
110.28
1100.649
1110.336
1120.396
1130.436
1140.0973
1150.579
1160.426
1170.943
1180.68
1190.217
120.642
1200.529
1210.403
1220.655
1230.168
1240.253
1250.0327
1260.805
1270.118
1280.00317
1290.0274
130.945
1300.377
1310.541
1320.157
1330.823
1340.454
1350.976
1360.101
1370.632
1380.871
1390.0446
140.145
1400.371
1410.0447
1420.934
1430.077
1440.124
1450.918
1460.561
1470.508
1480.141
1490.165
150.146
1500.832
1510.0613
1520.343
1530.526
1540.871
1550.599
1562.03758e-4
1570.608
1580.394
1590.027
1600.902
1610.759
1620.623
1630.0915
1640.905
1650.15
1660.891
1670.437
1680.201
1690.286
170.0964
180.171
190.756
20.515
200.378
210.806
220.674
230.0452
240.896
250.37
260.735
270.238
280.388
290.873
30.319
300.678
310.136
320.154
330.816
340.833
350.0972
360.206
370.223
380.629
390.866
40.681
400.494
410.152
420.625
430.209
440.275
450.462
460.17
470.357
480.367
490.128
50.114
500.987
510.754
520.219
530.65
540.389
550.689
560.241
570.649
580.251
590.154
60.827
600.0742
610.512
620.0922
630.164
640.708
650.167
660.582
670.679
682.93841e-4
690.808
70.442
700.00356
710.254
720.545
730.411
740.494
750.529
760.452
770.309
780.528
790.713
80.258
800.151
810.219
820.528
830.499
840.154
850.0106
860.315
870.523
880.427
890.0727
90.844
900.126
910.316
920.105
930.561
940.322
950.757
960.285
970.831
980.0811
990.818



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: CNhs11031


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)
0000293 (mouse embryonic day 13 sample)
0011332 (mouse testis- 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: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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