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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008985
|DRA_sample_Accession=CAGE@SAMD00005475
|accession_numbers=CAGE;DRX009122;DRR009996;DRZ001421;DRZ002804
|accession_numbers=CAGE;DRX009122;DRR009996;DRZ001421;DRZ002804
|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 22:00, 31 July 2014


Name:thymus, neonate N10
Species:Mouse (Mus musculus)
Library ID:CNhs11194
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuethymus
dev stage10 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  SAMD00005475
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11194 CAGE DRX009122 DRR009996
Accession ID Mm9

Library idBAMCTSS
CNhs11194 DRZ001421 DRZ002804
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

CNhs11194

00
10
100
1000
10000
10010.129
1002-0.0259
1003-0.112
10040
10050
1006-0.172
10070.0849
10080.0417
1009-0.12
1010.112
10100
10110.0798
10120.547
1013-0.163
1014-0.0874
10150.0751
1016-0.459
10170
10180
10190
1020.0417
10200
10210.177
1022-0.22
10230
1024-0.0529
1025-0.0611
10260
1027-0.048
10280
10290.527
103-0.0678
10300.0417
1031-0.684
1032-0.521
10330.0419
10340
10350
10360.142
10370
1038-0.36
1039-0.166
1040
1040-0.121
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: CNhs11194

Jaspar motifP-value
MA0002.20.0108
MA0003.10.255
MA0004.10.338
MA0006.10.989
MA0007.10.515
MA0009.10.458
MA0014.10.297
MA0017.10.903
MA0018.20.0318
MA0019.10.367
MA0024.13.83111e-4
MA0025.10.00824
MA0027.10.724
MA0028.11.77824e-5
MA0029.10.152
MA0030.10.648
MA0031.10.276
MA0035.20.424
MA0038.10.414
MA0039.20.17
MA0040.10.915
MA0041.10.246
MA0042.10.94
MA0043.10.0731
MA0046.11.08319e-14
MA0047.20.455
MA0048.10.556
MA0050.11.49803e-5
MA0051.14.46721e-5
MA0052.13.58696e-4
MA0055.10.945
MA0057.10.749
MA0058.10.514
MA0059.10.0153
MA0060.10.386
MA0061.13.50978e-4
MA0062.22.89415e-14
MA0065.20.367
MA0066.10.0091
MA0067.10.599
MA0068.10.965
MA0069.10.769
MA0070.10.436
MA0071.10.254
MA0072.17.94811e-6
MA0073.10.776
MA0074.10.974
MA0076.11.35018e-6
MA0077.10.187
MA0078.10.889
MA0079.20.0252
MA0080.21.08083e-12
MA0081.10.0458
MA0083.10.0269
MA0084.10.479
MA0087.10.403
MA0088.10.324
MA0090.10.0646
MA0091.10.0407
MA0092.10.842
MA0093.10.385
MA0099.20.136
MA0100.10.0174
MA0101.18.15918e-4
MA0102.20.462
MA0103.12.92081e-4
MA0104.20.126
MA0105.13.00991e-7
MA0106.10.653
MA0107.10.00144
MA0108.26.81634e-4
MA0111.10.248
MA0112.20.0106
MA0113.10.682
MA0114.10.627
MA0115.10.84
MA0116.10.00157
MA0117.10.778
MA0119.10.964
MA0122.10.906
MA0124.10.363
MA0125.10.442
MA0131.10.155
MA0135.10.128
MA0136.19.91674e-20
MA0137.20.0971
MA0138.22.5952e-5
MA0139.10.197
MA0140.10.768
MA0141.10.807
MA0142.10.655
MA0143.10.392
MA0144.10.515
MA0145.10.342
MA0146.10.526
MA0147.10.0579
MA0148.10.52
MA0149.10.0218
MA0150.10.504
MA0152.10.795
MA0153.12.05904e-8
MA0154.10.112
MA0155.10.975
MA0156.11.79994e-21
MA0157.10.43
MA0159.10.108
MA0160.10.495
MA0162.10.551
MA0163.10.0015
MA0164.10.788
MA0258.10.0428
MA0259.10.615



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: CNhs11194

Novel motifP-value
10.141
100.0104
1000.591
1010.808
1020.573
1030.123
1040.869
1050.72
1060.703
1070.978
1080.251
1090.27
110.115
1100.052
1110.656
1120.157
1130.46
1140.495
1150.452
1160.861
1175.36424e-4
1180.2
1190.189
120.622
1200.368
1210.483
1220.674
1230.617
1240.842
1250.0675
1260.533
1270.688
1280.527
1290.12
130.0146
1300.334
1310.431
1320.811
1330.874
1340.553
1350.352
1360.271
1370.49
1380.618
1390.28
140.796
1400.99
1410.86
1420.467
1430.33
1440.201
1450.093
1460.867
1470.413
1480.202
1490.628
150.114
1500.341
1510.256
1520.0568
1530.182
1540.0626
1550.0955
1560.00347
1570.747
1580.0529
1590.0178
1600.966
1610.277
1620.599
1630.951
1640.121
1650.451
1660.375
1670.123
1680.289
1690.462
170.527
180.699
190.747
20.0737
200.207
210.558
220.884
230.931
240.251
250.228
260.0287
270.629
280.201
290.03
30.116
300.102
310.606
320.211
330.389
340.963
350.0461
360.113
370.215
380.232
390.984
40.779
400.535
410.975
420.0336
430.352
440.839
450.666
460.107
470.336
480.2
490.107
50.307
500.801
510.904
520.191
530.81
540.304
550.465
560.818
570.16
580.235
590.628
60.223
600.914
610.067
620.102
630.567
640.69
650.478
660.544
670.765
680.467
690.518
70.141
700.293
710.0276
720.592
730.533
740.777
750.0205
760.0332
770.261
780.136
790.716
80.268
800.132
810.998
820.742
830.911
840.129
850.854
860.283
870.0359
880.304
890.514
90.361
900.0308
910.881
920.978
930.832
940.268
950.383
960.0104
970.516
980.471
990.477



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: CNhs11194


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)
0000305 (mouse neonate N10 sample)
0011413 (mouse thymus- neonate N10 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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