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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008970
|DRA_sample_Accession=CAGE@SAMD00005755
|accession_numbers=CAGE;DRX009107;DRR009981;DRZ001406;DRZ002789
|accession_numbers=CAGE;DRX009107;DRR009981;DRZ001406;DRZ002789
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000473,UBERON:0000991,UBERON:0000479,UBERON:0005156,UBERON:0000466,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003135,UBERON:0003133,UBERON:0002323,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0003101,UBERON:0000079
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000473,UBERON:0000991,UBERON:0000479,UBERON:0005156,UBERON:0000466,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003135,UBERON:0003133,UBERON:0002323,UBERON:0000464,UBERON:0004458,UBERON:0010317,UBERON:0003101,UBERON:0000079

Revision as of 21:30, 31 July 2014


Name:testis, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11189
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuetestis
dev stage0 day neonate
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005755
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11189 CAGE DRX009107 DRR009981
Accession ID Mm9

Library idBAMCTSS
CNhs11189 DRZ001406 DRZ002789
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

CNhs11189

00
10
100
1000
10000
10010.0398
10020.695
10030.167
10040.0482
1005-0.0249
10060.0482
10070.121
10080
10090.147
1010.0758
10100
10110.0268
10120.0482
1013-0.16
10140.556
10150.102
10160.336
10170
10180
10190
1020
10200.00655
10210.0932
10220.0482
10230
1024-0.0064
10250.0482
10260.0188
10270.0482
10280
10290.226
1030.313
10300
10310.348
1032-0.0928
10330.0369
10340
10350.131
10360.0184
10370
10380.0745
1039-0.071
1040
10400.216
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: CNhs11189

Jaspar motifP-value
MA0002.20.00106
MA0003.10.811
MA0004.10.683
MA0006.10.264
MA0007.10.681
MA0009.10.565
MA0014.10.73
MA0017.14.30614e-4
MA0018.20.143
MA0019.10.56
MA0024.11.97254e-5
MA0025.10.769
MA0027.10.748
MA0028.10.736
MA0029.10.929
MA0030.10.435
MA0031.10.643
MA0035.20.437
MA0038.10.231
MA0039.20.854
MA0040.10.27
MA0041.10.243
MA0042.10.396
MA0043.10.955
MA0046.11.07324e-24
MA0047.20.0646
MA0048.10.0784
MA0050.10.232
MA0051.10.188
MA0052.13.61132e-4
MA0055.10.0947
MA0057.10.064
MA0058.10.603
MA0059.10.885
MA0060.10.00428
MA0061.10.265
MA0062.20.482
MA0065.20.00315
MA0066.10.067
MA0067.10.666
MA0068.10.144
MA0069.10.995
MA0070.10.963
MA0071.10.915
MA0072.10.283
MA0073.10.322
MA0074.10.464
MA0076.10.532
MA0077.10.677
MA0078.10.109
MA0079.20.353
MA0080.28.55654e-6
MA0081.10.243
MA0083.10.762
MA0084.10.738
MA0087.10.36
MA0088.10.142
MA0090.10.573
MA0091.10.912
MA0092.10.403
MA0093.10.626
MA0099.23.40157e-4
MA0100.10.776
MA0101.10.571
MA0102.20.826
MA0103.12.21859e-4
MA0104.20.467
MA0105.19.61683e-4
MA0106.10.811
MA0107.10.525
MA0108.22.32371e-4
MA0111.10.303
MA0112.20.00255
MA0113.10.763
MA0114.12.66168e-4
MA0115.10.0731
MA0116.10.0383
MA0117.10.251
MA0119.10.438
MA0122.10.432
MA0124.10.148
MA0125.10.331
MA0131.10.456
MA0135.10.214
MA0136.16.87064e-5
MA0137.20.202
MA0138.20.00182
MA0139.10.234
MA0140.10.566
MA0141.10.175
MA0142.10.0282
MA0143.10.983
MA0144.10.191
MA0145.10.03
MA0146.10.825
MA0147.10.518
MA0148.10.0174
MA0149.10.195
MA0150.16.74283e-4
MA0152.10.0149
MA0153.17.25968e-14
MA0154.10.0248
MA0155.10.586
MA0156.10.0575
MA0157.10.838
MA0159.11.8363e-5
MA0160.10.997
MA0162.10.0412
MA0163.10.572
MA0164.10.522
MA0258.10.00259
MA0259.10.332



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: CNhs11189

Novel motifP-value
10.151
100.444
1000.602
1010.618
1020.789
1030.937
1040.995
1050.286
1060.0184
1070.143
1080.685
1090.419
110.211
1100.857
1110.311
1120.604
1130.406
1140.0914
1150.512
1160.218
1170.915
1180.723
1190.0879
120.189
1200.325
1210.601
1220.863
1230.152
1240.457
1250.135
1260.608
1270.119
1280.00531
1290.291
130.667
1300.493
1310.34
1320.549
1330.429
1340.835
1350.615
1360.294
1370.808
1380.466
1390.238
140.199
1400.695
1410.304
1420.209
1430.028
1440.0223
1450.837
1460.369
1470.639
1480.228
1490.494
150.0879
1500.897
1510.0423
1520.417
1530.639
1540.981
1550.252
1560.902
1570.597
1580.417
1590.478
1600.752
1610.835
1620.523
1630.0472
1640.801
1650.0531
1660.605
1670.974
1680.271
1690.556
170.167
180.212
190.738
20.547
200.8
210.383
220.727
230.125
240.73
250.226
260.814
270.326
280.287
290.858
30.316
300.64
310.293
320.418
330.749
340.793
350.117
360.377
370.133
380.609
390.847
40.773
400.481
410.0183
420.585
430.32
440.109
450.35
460.225
470.274
480.188
490.166
50.0973
500.896
510.798
520.277
530.712
540.371
550.197
560.284
570.766
580.262
590.163
60.577
600.109
610.796
620.0613
630.241
640.553
650.162
660.903
670.617
689.4639e-5
690.487
70.431
700.00823
710.213
720.484
730.34
740.669
750.254
760.383
770.326
780.403
790.892
80.143
800.0398
810.396
820.656
830.826
840.435
850.00877
860.122
870.106
880.985
890.0335
90.835
900.127
910.535
920.264
930.798
940.411
950.672
960.204
970.507
980.111
990.929



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: CNhs11189


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)
0000473 (testis)
0000991 (gonad)
0000479 (tissue)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003135 (male reproductive organ)
0003133 (reproductive organ)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0003101 (male organism)
0000079 (male reproductive system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011509 (mouse testis- neonate N00 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:0009117 (indifferent gonad)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0005564 (gonad primordium)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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