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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008983
|DRA_sample_Accession=CAGE@SAMD00005698
|accession_numbers=CAGE;DRX009120;DRR009994;DRZ001419;DRZ002802
|accession_numbers=CAGE;DRX009120;DRR009994;DRZ001419;DRZ002802
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002370,UBERON:0000479,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0004177,UBERON:0005057,UBERON:0002530,UBERON:0005058,UBERON:0010317,UBERON:0000153,UBERON:0002390,UBERON:0000949,UBERON:0002193,UBERON:0002405,UBERON:0009113
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002370,UBERON:0000479,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0004177,UBERON:0005057,UBERON:0002530,UBERON:0005058,UBERON:0010317,UBERON:0000153,UBERON:0002390,UBERON:0000949,UBERON:0002193,UBERON:0002405,UBERON:0009113

Revision as of 21:59, 31 July 2014


Name:thymus, neonate N06
Species:Mouse (Mus musculus)
Library ID:CNhs11197
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuethymus
dev stage6 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  SAMD00005698
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11197 CAGE DRX009120 DRR009994
Accession ID Mm9

Library idBAMCTSS
CNhs11197 DRZ001419 DRZ002802
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs11197

00
10
100
1000
1000-0.0317
10010.0737
1002-0.0373
1003-0.0968
10040
10050.0104
1006-0.111
10070.0592
10080
1009-0.112
1010.165
10100
1011-0.00767
10120.418
1013-0.102
1014-0.0851
10150.082
1016-0.338
10170
10180.115
10190
1020.0418
10200
10210.0986
1022-0.124
10230
1024-0.0899
10250
10260
10270
10280
10290.46
103-0.0319
10300.0418
1031-0.547
1032-0.465
10330.0472
10340
10350
10360.206
10370
1038-0.372
1039-0.177
1040
1040-0.121
10410.0418



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: CNhs11197

Jaspar motifP-value
MA0002.24.95602e-4
MA0003.10.379
MA0004.10.342
MA0006.10.92
MA0007.10.513
MA0009.10.269
MA0014.10.247
MA0017.10.619
MA0018.20.0691
MA0019.10.34
MA0024.12.37613e-5
MA0025.10.0137
MA0027.10.745
MA0028.11.22031e-6
MA0029.10.053
MA0030.10.741
MA0031.10.254
MA0035.20.37
MA0038.10.979
MA0039.20.316
MA0040.10.91
MA0041.10.32
MA0042.10.922
MA0043.10.228
MA0046.11.35651e-17
MA0047.20.481
MA0048.10.645
MA0050.12.97991e-6
MA0051.13.75859e-5
MA0052.10.00682
MA0055.10.909
MA0057.10.613
MA0058.10.496
MA0059.10.0179
MA0060.10.00416
MA0061.19.76286e-5
MA0062.22.59171e-17
MA0065.20.416
MA0066.10.0175
MA0067.10.578
MA0068.10.87
MA0069.10.896
MA0070.10.414
MA0071.10.423
MA0072.18.69775e-7
MA0073.10.783
MA0074.10.931
MA0076.13.92694e-9
MA0077.10.179
MA0078.10.549
MA0079.20.0372
MA0080.23.18617e-13
MA0081.10.024
MA0083.10.152
MA0084.10.536
MA0087.10.411
MA0088.10.177
MA0090.10.0677
MA0091.10.0482
MA0092.10.896
MA0093.10.382
MA0099.20.181
MA0100.10.00868
MA0101.12.49555e-4
MA0102.20.557
MA0103.11.5078e-4
MA0104.20.13
MA0105.11.10858e-7
MA0106.10.697
MA0107.13.34361e-4
MA0108.20.0286
MA0111.10.309
MA0112.20.0155
MA0113.10.734
MA0114.10.32
MA0115.10.419
MA0116.10.00253
MA0117.10.731
MA0119.10.897
MA0122.11
MA0124.10.264
MA0125.10.583
MA0131.10.061
MA0135.10.268
MA0136.11.43845e-22
MA0137.20.0293
MA0138.25.3102e-5
MA0139.10.175
MA0140.10.566
MA0141.10.321
MA0142.10.873
MA0143.10.235
MA0144.10.337
MA0145.10.391
MA0146.10.531
MA0147.10.0607
MA0148.10.573
MA0149.10.0459
MA0150.10.327
MA0152.10.908
MA0153.11.32055e-8
MA0154.10.0923
MA0155.10.801
MA0156.11.04672e-27
MA0157.10.365
MA0159.10.0891
MA0160.10.266
MA0162.10.39
MA0163.19.71296e-4
MA0164.10.886
MA0258.10.0794
MA0259.10.548



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: CNhs11197

Novel motifP-value
10.176
100.0128
1000.681
1010.881
1020.521
1030.205
1040.843
1050.862
1060.82
1070.758
1080.266
1090.22
110.128
1100.0425
1110.786
1120.275
1130.463
1140.858
1150.485
1160.761
1176.22329e-4
1180.344
1190.291
120.647
1200.218
1210.301
1220.573
1230.611
1240.825
1250.105
1260.63
1270.734
1280.74
1290.222
130.00812
1300.212
1310.585
1320.538
1330.803
1340.54
1350.272
1360.479
1370.307
1380.582
1390.58
140.708
1400.812
1410.972
1420.575
1430.251
1440.142
1450.16
1460.732
1470.26
1480.402
1490.659
150.167
1500.39
1510.265
1520.087
1530.174
1540.107
1550.102
1560.0329
1570.724
1580.0941
1590.0217
1600.811
1610.605
1620.551
1630.862
1640.145
1650.199
1660.429
1670.132
1680.301
1690.253
170.616
180.909
190.654
20.0852
200.298
210.388
220.836
230.73
240.098
250.22
260.0401
270.479
280.226
290.0531
30.147
300.12
310.495
320.0961
330.304
340.991
350.101
360.174
370.164
380.239
390.926
40.871
400.588
410.96
420.0207
430.538
440.881
450.7
460.0982
470.309
480.157
490.215
50.318
500.85
510.935
520.146
530.962
540.236
550.381
560.926
570.26
580.259
590.743
60.216
600.839
610.0592
620.117
630.678
640.77
650.586
660.567
670.921
680.271
690.438
70.104
700.523
710.0258
720.517
730.495
740.851
750.0353
760.0847
770.266
780.0969
790.687
80.521
800.102
810.998
820.793
830.795
840.138
850.496
860.226
870.139
880.322
890.421
90.247
900.0515
910.676
920.669
930.93
940.311
950.247
960.0368
970.529
980.677
990.482



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: CNhs11197


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)
0000312 (mouse neonate N6 sample)
0011401 (mouse thymus- neonate N06 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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