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|is_obsolete=
|is_obsolete=
|library_id=CNhs11204
|library_id=CNhs11204
|library_ids=CNhs11204
|name=testis, neonate N10
|name=testis, neonate N10
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 16:06, 25 October 2013


Name:testis, neonate N10
Species:Mouse (Mus musculus)
Library ID:CNhs11204
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuetestis
dev stage10 days 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  DRS008972
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11204 CAGE DRX009109 DRR009983
Accession ID Mm9

Library idBAMCTSS
CNhs11204 DRZ001408 DRZ002791
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

CNhs11204

00
10
100
1000
1000-0.0155
10010.0663
10020.0785
10030.00516
10040
1005-0.122
10060.0823
10070.134
10080
10090.185
1010.178
10100
1011-0.0642
10120.0433
1013-0.126
10140.0433
10150.0472
10160.112
10170
10180
10190
1020
10200
10210.0433
10220.0484
10230
1024-0.0899
10250
10260
10270
10280.0433
10290.0045
1030.147
10300
1031-0.0596
1032-0.121
10330.0769
10340
10350.152
1036-0.01
10370
1038-0.0592
1039-0.0153
1040
1040-0.0776
10410.0433



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: CNhs11204

Jaspar motifP-value
MA0002.23.4027e-4
MA0003.10.783
MA0004.10.163
MA0006.10.114
MA0007.10.941
MA0009.10.472
MA0014.10.384
MA0017.10.0239
MA0018.20.255
MA0019.10.27
MA0024.11.08537e-4
MA0025.10.793
MA0027.10.685
MA0028.10.00267
MA0029.10.648
MA0030.10.577
MA0031.10.57
MA0035.20.97
MA0038.10.0153
MA0039.20.0287
MA0040.10.67
MA0041.10.608
MA0042.10.743
MA0043.10.0235
MA0046.19.29886e-20
MA0047.20.0375
MA0048.10.225
MA0050.10.355
MA0051.10.993
MA0052.10.0135
MA0055.10.0325
MA0057.10.296
MA0058.10.0842
MA0059.10.294
MA0060.12.43626e-16
MA0061.10.0384
MA0062.28.04837e-5
MA0065.20.0451
MA0066.10.00932
MA0067.10.295
MA0068.10.677
MA0069.10.516
MA0070.10.181
MA0071.10.951
MA0072.10.599
MA0073.10.664
MA0074.10.389
MA0076.11.37694e-4
MA0077.10.893
MA0078.10.241
MA0079.20.138
MA0080.25.24999e-6
MA0081.10.44
MA0083.10.113
MA0084.10.608
MA0087.10.952
MA0088.10.849
MA0090.10.599
MA0091.10.0823
MA0092.10.118
MA0093.10.114
MA0099.28.11781e-4
MA0100.10.166
MA0101.10.512
MA0102.20.568
MA0103.10.0531
MA0104.20.0218
MA0105.11.02361e-6
MA0106.10.885
MA0107.10.209
MA0108.27.271e-4
MA0111.10.257
MA0112.28.78513e-5
MA0113.10.894
MA0114.10.0171
MA0115.10.407
MA0116.10.00135
MA0117.10.683
MA0119.10.0802
MA0122.10.576
MA0124.10.341
MA0125.10.978
MA0131.10.189
MA0135.10.94
MA0136.10.205
MA0137.20.769
MA0138.20.0118
MA0139.10.299
MA0140.10.133
MA0141.10.726
MA0142.10.00595
MA0143.10.117
MA0144.10.162
MA0145.10.0112
MA0146.10.531
MA0147.10.0294
MA0148.10.00909
MA0149.10.61
MA0150.10.0145
MA0152.10.302
MA0153.11.74566e-14
MA0154.10.00237
MA0155.10.319
MA0156.10.238
MA0157.10.0918
MA0159.10.00752
MA0160.10.909
MA0162.10.0513
MA0163.10.061
MA0164.10.641
MA0258.10.00216
MA0259.10.0192



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: CNhs11204

Novel motifP-value
10.178
100.679
1000.744
1010.257
1020.769
1030.343
1040.955
1050.202
1060.00106
1070.00567
1080.53
1090.689
110.271
1100.773
1110.53
1120.529
1130.511
1140.064
1150.603
1160.209
1170.568
1180.984
1190.108
120.568
1200.244
1210.433
1220.833
1230.08
1240.234
1250.144
1260.977
1270.313
1280.0012
1290.232
130.82
1300.704
1310.507
1320.121
1330.103
1340.615
1350.243
1360.0171
1370.592
1380.576
1390.0911
140.103
1400.283
1410.0672
1420.787
1430.0224
1440.499
1450.565
1460.479
1470.601
1480.0636
1490.237
150.153
1500.711
1510.131
1520.232
1530.214
1540.955
1550.758
1560.00441
1570.264
1580.643
1590.654
1600.265
1610.745
1620.366
1630.0663
1640.746
1650.0742
1660.713
1670.845
1680.0931
1690.0491
170.104
180.198
190.449
20.245
200.356
210.92
220.412
230.101
240.958
250.907
260.274
270.165
280.339
290.883
30.156
300.507
310.0991
320.146
330.951
340.525
350.189
360.267
370.16
380.637
390.672
40.899
400.839
410.091
420.325
430.143
440.141
450.446
460.109
470.359
480.509
490.18
50.0876
500.831
510.627
520.0848
530.448
540.485
550.483
560.181
570.397
580.309
590.0556
60.643
600.0606
610.649
620.199
630.173
640.583
650.114
660.317
670.959
680.0533
690.534
70.542
700.0683
710.171
720.556
730.55
740.369
750.457
760.627
770.261
780.288
790.436
80.185
800.368
810.288
820.354
830.967
840.378
850.0219
860.25
870.274
880.206
890.0622
90.628
900.727
910.0503
920.273
930.917
940.0715
950.729
960.432
970.666
980.0823
990.325



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: CNhs11204


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)
0000305 (mouse neonate N10 sample)
0011422 (mouse testis- 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: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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