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|library_id=CNhs11186
|library_id=CNhs11186
|library_id_phase_based=2:CNhs11186
|library_id_phase_based=2:CNhs11186
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;820
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;820
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N20.CNhs11186.820-7A2.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N20.CNhs11186.820-7A2.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N20.CNhs11186.820-7A2.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/thymus%252c%2520neonate%2520N20.CNhs11186.820-7A2.mm10.nobarcode.ctss.bed.gz

Revision as of 22:37, 18 May 2017


Name:thymus, neonate N20
Species:Mouse (Mus musculus)
Library ID:CNhs11186
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuethymus
dev stage20 days neonate
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  SAMD00004712
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11186 CAGE DRX009123 DRR009997
Accession ID Mm9

Library idBAMCTSS
CNhs11186 DRZ001422 DRZ002805
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

CNhs11186

00
10
100
1000
1000-0.0355
10010.0981
1002-0.0537
1003-0.0838
10040
10050.143
1006-0.14
10070.0617
10080.111
1009-0.0886
1010.0894
10100
10110.0404
10120.536
1013-0.157
1014-0.0874
10150.0156
1016-0.483
10170
10180.0773
10190
1020.0773
10200
10210.0286
1022-0.27
10230
1024-0.135
1025-0.0611
10260
10270
10280
10290.356
103-0.0788
10300.0404
1031-0.738
1032-0.469
10330.0449
10340
10350
10360.0906
10370
1038-0.257
1039-0.177
1040
1040-0.0865
10410.0404



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: CNhs11186

Jaspar motifP-value
MA0002.24.92799e-4
MA0003.10.428
MA0004.10.392
MA0006.10.794
MA0007.10.519
MA0009.10.454
MA0014.10.233
MA0017.10.921
MA0018.20.0523
MA0019.10.642
MA0024.10.00468
MA0025.10.0102
MA0027.10.645
MA0028.11.60227e-4
MA0029.10.143
MA0030.10.701
MA0031.10.273
MA0035.20.37
MA0038.10.626
MA0039.20.22
MA0040.10.997
MA0041.10.241
MA0042.10.944
MA0043.10.083
MA0046.12.59624e-14
MA0047.20.702
MA0048.10.886
MA0050.18.11051e-8
MA0051.13.05998e-6
MA0052.16.21576e-4
MA0055.10.405
MA0057.10.73
MA0058.10.664
MA0059.10.0588
MA0060.10.695
MA0061.11.17116e-5
MA0062.21.19128e-14
MA0065.20.45
MA0066.10.00798
MA0067.10.507
MA0068.10.961
MA0069.10.834
MA0070.10.423
MA0071.10.456
MA0072.14.61998e-5
MA0073.10.772
MA0074.10.882
MA0076.11.47848e-5
MA0077.10.168
MA0078.10.74
MA0079.20.0323
MA0080.21.16205e-13
MA0081.10.0263
MA0083.10.066
MA0084.10.347
MA0087.10.374
MA0088.10.487
MA0090.10.0355
MA0091.10.0571
MA0092.10.963
MA0093.10.464
MA0099.20.218
MA0100.10.024
MA0101.11.06221e-4
MA0102.20.833
MA0103.19.83106e-5
MA0104.20.213
MA0105.19.89957e-9
MA0106.10.666
MA0107.16.34631e-5
MA0108.20.0112
MA0111.10.283
MA0112.20.0074
MA0113.10.697
MA0114.10.442
MA0115.10.659
MA0116.10.00437
MA0117.10.81
MA0119.10.968
MA0122.10.845
MA0124.10.414
MA0125.10.228
MA0131.10.267
MA0135.10.167
MA0136.11.45624e-21
MA0137.20.103
MA0138.26.43836e-5
MA0139.10.2
MA0140.10.511
MA0141.10.54
MA0142.10.436
MA0143.10.326
MA0144.10.497
MA0145.10.459
MA0146.10.428
MA0147.10.109
MA0148.10.53
MA0149.10.0582
MA0150.10.593
MA0152.10.914
MA0153.14.33631e-9
MA0154.10.0616
MA0155.10.976
MA0156.13.11567e-23
MA0157.10.484
MA0159.10.102
MA0160.10.511
MA0162.10.532
MA0163.10.00334
MA0164.10.665
MA0258.10.0245
MA0259.10.831



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: CNhs11186

Novel motifP-value
10.167
100.012
1000.827
1010.663
1020.56
1030.181
1040.8
1050.754
1060.601
1070.958
1080.303
1090.371
110.139
1100.0612
1110.767
1120.131
1130.255
1140.52
1150.517
1160.794
1172.96113e-4
1180.15
1190.255
120.591
1200.24
1210.448
1220.914
1230.617
1240.813
1250.104
1260.555
1270.683
1280.367
1290.187
130.0319
1300.465
1310.516
1320.82
1330.761
1340.601
1350.537
1360.372
1370.279
1380.734
1390.214
140.84
1400.931
1410.784
1420.672
1430.271
1440.147
1450.0845
1460.833
1470.406
1480.265
1490.885
150.0884
1500.298
1510.127
1520.107
1530.186
1540.0985
1550.111
1560.635
1570.824
1580.0566
1590.0137
1600.934
1610.313
1620.566
1630.98
1640.15
1650.222
1660.386
1670.109
1680.248
1690.302
170.492
180.683
190.65
20.106
200.297
210.517
220.979
230.883
240.253
250.22
260.0371
270.41
280.145
290.0592
30.118
300.194
310.714
320.183
330.557
340.955
350.0443
360.204
370.232
380.325
390.819
40.95
400.662
410.989
420.0287
430.381
440.697
450.841
460.105
470.372
480.257
490.128
50.193
500.876
510.828
520.284
530.938
540.396
550.347
560.654
570.216
580.193
590.799
60.278
600.824
610.0435
620.0648
630.445
640.815
650.497
660.513
670.754
680.646
690.535
70.147
700.238
710.0348
720.495
730.434
740.846
750.0197
760.055
770.288
780.12
790.744
80.327
800.0937
810.947
820.757
830.939
840.246
850.989
860.177
870.13
880.282
890.612
90.302
900.0283
910.96
920.851
930.94
940.236
950.49
960.0169
970.505
980.546
990.397



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: CNhs11186


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000308 (mouse neonate N20 sample)
0011426 (mouse thymus- 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: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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