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FF:456-26C5

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Name:thymus, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs11002
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissuethymus
dev stage16 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  SAMD00005771
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11002 CAGE DRX009115 DRR009989
Accession ID Mm9

Library idBAMCTSS
CNhs11002 DRZ001414 DRZ002797
Accession ID Mm10

Library idBAMCTSS
CNhs11002 DRZ012764 DRZ014147
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

CNhs11002

00
10
100
1000
1000-1.32877e-4
1001-9.4797e-4
10020.0539
1003-0.00528
10040
10050
1006-0.143
10070.09
10080
1009-0.0997
1010.223
10100
10110.00955
10120.182
1013-0.157
10140.13
10150.0739
1016-0.141
10170
10180.342
10190
1020
10200
10210.00436
1022-0.262
10230
1024-0.0865
10250
10260
10270
10280
10290.0698
1030
10300
1031-0.27
1032-0.335
10330
10340
10350.053
10360.317
10370
1038-0.276
1039-0.0919
1040
1040-0.0609
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: CNhs11002

Jaspar motifP-value
MA0002.20.00194
MA0003.10.678
MA0004.10.281
MA0006.10.759
MA0007.10.15
MA0009.10.654
MA0014.10.171
MA0017.10.175
MA0018.27.37814e-4
MA0019.10.479
MA0024.14.44543e-8
MA0025.16.83001e-4
MA0027.10.566
MA0028.11.17125e-5
MA0029.10.341
MA0030.10.0253
MA0031.10.132
MA0035.20.448
MA0038.10.923
MA0039.20.245
MA0040.10.607
MA0041.10.0653
MA0042.10.524
MA0043.10.0173
MA0046.15.36164e-22
MA0047.20.132
MA0048.10.228
MA0050.11.88685e-7
MA0051.13.94405e-6
MA0052.16.45087e-5
MA0055.10.225
MA0057.10.541
MA0058.10.409
MA0059.10.00158
MA0060.10.0477
MA0061.11.90658e-5
MA0062.25.7297e-13
MA0065.20.764
MA0066.10.0736
MA0067.10.476
MA0068.10.812
MA0069.10.996
MA0070.10.404
MA0071.10.563
MA0072.10.478
MA0073.10.794
MA0074.10.906
MA0076.11.93733e-6
MA0077.10.0607
MA0078.10.657
MA0079.20.0526
MA0080.21.34809e-11
MA0081.10.0144
MA0083.10.0153
MA0084.10.325
MA0087.10.286
MA0088.10.0466
MA0090.10.087
MA0091.10.0212
MA0092.10.888
MA0093.10.35
MA0099.20.203
MA0100.10.0477
MA0101.18.17379e-6
MA0102.20.199
MA0103.10.00168
MA0104.20.0199
MA0105.16.55772e-8
MA0106.10.384
MA0107.11.43107e-5
MA0108.20.00407
MA0111.10.637
MA0112.20.0139
MA0113.10.983
MA0114.10.121
MA0115.10.701
MA0116.10.00124
MA0117.10.568
MA0119.10.795
MA0122.10.992
MA0124.10.734
MA0125.10.69
MA0131.10.0759
MA0135.10.102
MA0136.11.81381e-17
MA0137.20.0184
MA0138.21.42568e-4
MA0139.10.067
MA0140.10.608
MA0141.10.358
MA0142.10.484
MA0143.10.285
MA0144.10.37
MA0145.10.324
MA0146.10.634
MA0147.10.00386
MA0148.10.22
MA0149.10.246
MA0150.10.531
MA0152.10.661
MA0153.14.3964e-8
MA0154.10.0555
MA0155.10.635
MA0156.12.52861e-20
MA0157.10.331
MA0159.10.0877
MA0160.10.273
MA0162.10.154
MA0163.12.4804e-5
MA0164.10.937
MA0258.10.123
MA0259.10.266



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: CNhs11002

Novel motifP-value
10.269
100.0108
1000.652
1010.807
1020.636
1030.157
1040.867
1050.91
1060.488
1070.729
1080.383
1090.125
110.0583
1100.039
1110.284
1120.148
1130.659
1140.663
1150.911
1160.493
1170.00289
1180.202
1190.437
120.375
1200.556
1210.626
1220.813
1230.349
1240.333
1250.0889
1260.75
1270.873
1280.674
1290.304
130.01
1300.203
1310.976
1320.493
1330.217
1340.55
1350.49
1360.888
1370.0314
1380.639
1390.827
140.287
1400.539
1410.933
1420.672
1430.098
1440.604
1450.0202
1460.985
1470.297
1480.725
1490.728
150.153
1500.246
1510.502
1520.246
1530.187
1540.202
1550.293
1560.00898
1570.414
1580.442
1590.185
1600.282
1610.218
1620.306
1630.668
1640.0387
1650.0852
1660.3
1670.115
1680.179
1690.213
170.709
180.523
190.958
20.265
200.217
210.11
220.987
230.437
240.116
250.421
260.00319
270.355
280.951
290.0253
30.127
300.157
310.374
320.126
330.584
340.861
350.332
360.245
370.258
380.23
390.999
40.992
400.398
410.835
420.0304
430.503
440.487
450.85
460.06
470.349
480.134
490.313
50.575
500.54
510.927
520.307
530.776
540.324
550.806
560.935
570.166
580.195
590.523
60.266
600.935
610.0495
620.0927
630.546
640.434
650.399
660.8
670.938
680.313
690.835
70.124
700.138
710.0024
720.415
730.39
740.76
750.0434
760.0929
770.662
780.0922
790.928
80.106
800.105
810.826
820.703
830.768
840.0219
850.504
860.379
870.214
880.158
890.594
90.414
900.185
910.734
920.47
930.972
940.163
950.311
960.103
970.421
980.323
990.479



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: CNhs11002


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)
0002370 (thymus)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0004177 (hemopoietic organ)
0005057 (immune organ)
0002530 (gland)
0005058 (hemolymphoid system gland)
0010317 (germ layer / neural crest derived structure)
0000153 (anterior region of body)
0002390 (hematopoietic system)
0000949 (endocrine system)
0002193 (hemolymphoid system)
0002405 (immune system)
0009113 (thymic region)

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)
0011355 (mouse thymus- 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:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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