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FF:38-12B5

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Name:thymus, adult, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuethymus
dev stageadult
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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs10471

00
10
100
1000
1000-0.012
1001-0.0356
10020.00855
1003-0.0966
10040
10050
1006-0.143
10070.0224
10080
1009-0.0807
1010.0634
10100
10110.0117
10120.29
1013-0.0487
1014-0.0874
1015-0.066
1016-0.379
10170
10180.119
10190
1020
10200
10210
1022-0.102
10230
1024-0.0899
10250
10260
1027-0.048
10280
10290.107
103-0.0829
10300
1031-0.627
1032-0.389
10330.044
10340
10350
10360.0968
10370
1038-0.418
1039-0.21
1040
1040-0.121
10410.119



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 no result for this sample


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: CNhs10471

Jaspar motifP-value
MA0002.21.42537e-7
MA0003.10.982
MA0004.10.425
MA0006.10.478
MA0007.10.412
MA0009.10.337
MA0014.10.233
MA0017.10.797
MA0018.20.142
MA0019.10.629
MA0024.10.0422
MA0025.10.162
MA0027.10.396
MA0028.10.00114
MA0029.10.109
MA0030.10.998
MA0031.10.0366
MA0035.20.537
MA0038.10.617
MA0039.20.566
MA0040.10.396
MA0041.10.824
MA0042.10.491
MA0043.10.115
MA0046.11.58767e-15
MA0047.20.356
MA0048.10.135
MA0050.15.55893e-10
MA0051.13.62711e-8
MA0052.10.00247
MA0055.10.0428
MA0057.10.642
MA0058.10.652
MA0059.10.185
MA0060.10.723
MA0061.13.57043e-6
MA0062.28.66102e-16
MA0065.20.516
MA0066.10.00851
MA0067.10.418
MA0068.10.729
MA0069.10.594
MA0070.10.605
MA0071.10.535
MA0072.19.1781e-6
MA0073.10.847
MA0074.10.989
MA0076.19.33152e-5
MA0077.10.148
MA0078.10.944
MA0079.20.0546
MA0080.21.18603e-14
MA0081.10.0114
MA0083.10.369
MA0084.10.434
MA0087.10.163
MA0088.10.344
MA0090.10.0792
MA0091.10.0547
MA0092.10.986
MA0093.10.461
MA0099.20.235
MA0100.10.0334
MA0101.14.1492e-4
MA0102.20.633
MA0103.15.53107e-5
MA0104.20.382
MA0105.13.0784e-9
MA0106.10.971
MA0107.19.46151e-5
MA0108.20.0238
MA0111.10.17
MA0112.20.00705
MA0113.10.698
MA0114.10.349
MA0115.10.488
MA0116.10.00293
MA0117.10.996
MA0119.10.893
MA0122.10.699
MA0124.10.351
MA0125.10.368
MA0131.10.519
MA0135.10.809
MA0136.16.54962e-24
MA0137.20.108
MA0138.20.00112
MA0139.10.125
MA0140.10.491
MA0141.10.278
MA0142.10.0613
MA0143.10.42
MA0144.10.365
MA0145.10.859
MA0146.10.176
MA0147.10.262
MA0148.10.356
MA0149.10.0799
MA0150.10.889
MA0152.10.697
MA0153.17.65464e-10
MA0154.10.037
MA0155.10.911
MA0156.13.80457e-25
MA0157.10.129
MA0159.10.0845
MA0160.10.43
MA0162.10.33
MA0163.10.00309
MA0164.10.859
MA0258.10.0481
MA0259.10.801



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: CNhs10471

Novel motifP-value
10.27
100.0332
1000.976
1010.528
1020.554
1030.185
1040.692
1050.988
1060.538
1070.994
1080.454
1090.24
110.102
1100.102
1110.654
1120.13
1130.0839
1140.466
1150.608
1160.813
1170.00122
1180.184
1190.0891
120.468
1200.0898
1210.106
1220.852
1230.423
1240.371
1250.134
1260.951
1270.788
1280.277
1290.202
130.0553
1300.457
1310.93
1320.723
1330.935
1340.553
1350.343
1360.803
1370.332
1380.504
1390.374
140.882
1400.444
1410.633
1420.956
1430.0714
1440.162
1450.143
1460.531
1470.596
1480.317
1490.632
150.0659
1500.467
1510.031
1520.21
1530.188
1540.335
1550.0926
1560.209
1570.879
1580.124
1590.0191
1600.63
1610.263
1620.27
1630.661
1640.176
1650.0632
1660.325
1670.289
1680.357
1690.0483
170.485
180.75
190.817
20.404
200.947
210.593
220.725
230.551
240.0913
250.142
260.0717
270.136
280.129
290.213
30.181
300.335
310.924
320.155
330.506
340.83
350.0883
360.252
370.146
380.232
390.716
40.981
400.453
410.817
420.0385
430.336
440.693
450.666
460.116
470.218
480.156
490.221
50.178
500.849
510.895
520.48
530.823
540.491
550.14
560.546
570.501
580.19
590.769
60.171
600.669
610.131
620.0458
630.436
640.629
650.27
660.608
670.959
680.644
690.767
70.0733
700.133
710.055
720.435
730.336
740.966
750.029
760.291
770.515
780.0993
790.813
80.383
800.032
810.844
820.299
830.65
840.594
850.732
860.106
870.892
880.331
890.718
90.221
900.171
910.916
920.871
930.387
940.305
950.693
960.0645
970.656
980.372
990.545



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: CNhs10471


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000065 (respiratory tract)
0000072 (segment of respiratory tract)
0000077 (mixed endoderm/mesoderm-derived structure)
0000078 (mixed ectoderm/mesoderm/endoderm-derived structure)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0000974 (neck)
0001004 (respiratory system)
0001007 (digestive system)
0001041 (foregut)
0001042 (chordate pharynx)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0001557 (upper respiratory tract)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002342 (neural crest)
0002346 (neurectoderm)
0002368 (endocrine gland)
0002370 (thymus)
0002390 (hematopoietic system)
0002405 (immune system)
0002530 (gland)
0002532 (epiblast (generic))
0003075 (neural plate)
0003104 (mesenchyme)
0003295 (pharyngeal gland)
0003351 (pharyngeal epithelium)
0003408 (gland of gut)
0003929 (gut epithelium)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004177 (hemopoietic organ)
0004185 (endodermal part of digestive tract)
0004807 (respiratory system epithelium)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005058 (hemolymphoid system gland)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005428 (vagal neural crest)
0005562 (thymus primordium)
0005911 (endo-epithelium)
0006562 (pharynx)
0006598 (presumptive structure)
0007023 (adult organism)
0007026 (primitive gut)
0007284 (presumptive neural plate)
0007690 (early pharyngeal endoderm)
0009113 (thymic region)
0009142 (entire embryonic mesenchyme)
0009145 (pharyngeal region of foregut)

FF: FANTOM5
NA

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
NA

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