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|library_id=CNhs10581
|library_id=CNhs10581
|library_id_phase_based=2:CNhs10581
|library_id_phase_based=2:CNhs10581
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520embryo%2520E17.CNhs10581.478-18C1.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520embryo%2520E17.CNhs10581.478-18C1.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520embryo%2520E17.CNhs10581.478-18C1.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520embryo%2520E17.CNhs10581.478-18C1.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/thymus%252c%2520embryo%2520E17.CNhs10581.478-18C1.mm9.nobarcode.rdna.fa.gz
|name=thymus, embryo E17
|name=thymus, embryo E17
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 18:15, 17 May 2017


Name:thymus, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs10581
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuethymus
dev stage17 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  SAMD00004685
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10581 CAGE DRX009116 DRR009990
Accession ID Mm9

Library idBAMCTSS
CNhs10581 DRZ001415 DRZ002798
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

CNhs10581

00
10
100
1000
10000
10010.00829
10020.0389
1003-0.0479
10040
10050
1006-0.0762
10070.113
10080
1009-0.0964
1010.146
10100
10110.0288
10120.0715
1013-0.128
10140.0478
10150.116
1016-0.206
10170
10180.235
10190
1020
10200
10210.0842
1022-0.209
10230
1024-0.00664
10250
10260
1027-0.048
10280
10290.0719
1030
10300
1031-0.284
1032-0.345
10330.0577
10340
10350.0715
10360.276
10370
1038-0.15
1039-0.134
1040
1040-0.0425
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: CNhs10581

Jaspar motifP-value
MA0002.29.40968e-5
MA0003.10.695
MA0004.10.307
MA0006.10.935
MA0007.10.215
MA0009.10.721
MA0014.10.202
MA0017.10.0087
MA0018.20.0509
MA0019.10.43
MA0024.11.76865e-10
MA0025.10.00136
MA0027.10.806
MA0028.11.8151e-8
MA0029.10.0442
MA0030.10.519
MA0031.10.472
MA0035.20.401
MA0038.10.162
MA0039.20.576
MA0040.10.666
MA0041.10.979
MA0042.10.864
MA0043.10.377
MA0046.12.64938e-18
MA0047.20.906
MA0048.10.43
MA0050.11.08625e-7
MA0051.15.6976e-7
MA0052.10.00451
MA0055.10.408
MA0057.10.547
MA0058.10.45
MA0059.10.029
MA0060.11.21326e-10
MA0061.12.34278e-7
MA0062.23.4721e-20
MA0065.20.597
MA0066.10.217
MA0067.10.904
MA0068.10.936
MA0069.10.908
MA0070.10.955
MA0071.10.803
MA0072.12.17557e-4
MA0073.10.709
MA0074.10.783
MA0076.14.64894e-11
MA0077.10.429
MA0078.10.692
MA0079.20.0666
MA0080.21.51319e-13
MA0081.10.00254
MA0083.10.105
MA0084.10.98
MA0087.10.571
MA0088.10.0572
MA0090.10.124
MA0091.10.166
MA0092.10.843
MA0093.10.332
MA0099.20.111
MA0100.10.00454
MA0101.16.17705e-7
MA0102.20.386
MA0103.16.24812e-5
MA0104.20.0317
MA0105.15.61405e-8
MA0106.10.55
MA0107.13.06282e-7
MA0108.20.0668
MA0111.10.914
MA0112.20.382
MA0113.10.746
MA0114.10.00306
MA0115.10.149
MA0116.10.00855
MA0117.10.375
MA0119.10.56
MA0122.10.899
MA0124.10.232
MA0125.10.722
MA0131.10.00537
MA0135.10.833
MA0136.13.26113e-26
MA0137.20.00711
MA0138.22.88543e-5
MA0139.10.224
MA0140.10.391
MA0141.10.00925
MA0142.10.658
MA0143.10.147
MA0144.10.246
MA0145.10.275
MA0146.10.289
MA0147.10.0125
MA0148.10.668
MA0149.10.308
MA0150.10.157
MA0152.10.958
MA0153.11.4306e-8
MA0154.10.223
MA0155.10.638
MA0156.17.68435e-31
MA0157.10.612
MA0159.10.429
MA0160.10.0687
MA0162.10.232
MA0163.14.86292e-4
MA0164.10.849
MA0258.10.782
MA0259.10.348



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: CNhs10581

Novel motifP-value
10.93
100.0341
1000.9
1010.897
1020.499
1030.363
1040.693
1050.741
1060.815
1070.46
1080.37
1090.315
110.187
1100.0835
1110.878
1120.614
1130.303
1140.187
1150.535
1160.743
1170.00403
1180.197
1190.485
120.329
1200.336
1210.246
1220.795
1230.608
1240.556
1250.174
1260.958
1270.78
1280.907
1290.368
130.0113
1300.133
1310.862
1320.464
1330.591
1340.534
1350.417
1360.814
1370.269
1380.394
1390.542
140.44
1400.276
1410.539
1420.54
1430.124
1440.191
1450.121
1460.599
1470.146
1480.838
1490.672
150.252
1500.333
1510.483
1520.0893
1530.417
1540.434
1550.318
1560.605
1570.399
1580.38
1590.213
1600.949
1610.63
1620.159
1630.867
1640.226
1650.384
1660.211
1670.859
1680.42
1690.673
170.839
180.876
190.305
20.0535
200.254
210.254
220.749
230.286
240.0365
250.251
260.0241
270.42
280.859
290.14
30.559
300.232
310.153
320.0217
330.571
340.459
350.531
360.343
370.715
380.322
390.528
40.992
400.261
410.875
420.0193
430.89
440.966
450.896
460.191
470.695
480.353
490.73
50.92
500.49
510.886
520.115
530.656
540.0846
550.695
560.844
570.898
580.299
590.913
60.251
600.519
610.0794
620.219
630.879
640.849
650.791
660.668
670.593
680.0854
690.991
70.144
700.969
710.0257
720.402
730.719
740.809
750.0989
760.109
770.163
780.231
790.702
80.923
800.0256
810.588
820.466
830.914
840.103
850.0725
860.487
870.72
880.15
890.356
90.301
900.472
910.328
920.0774
930.998
940.434
950.479
960.386
970.508
980.575
990.257



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: CNhs10581


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)
0000300 (mouse embryonic day 17 sample)
0011366 (mouse thymus- embryo E17 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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