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Revision as of 15:49, 26 December 2012


Name:testis, embryo E17
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuetestis
dev stage17 days embryo
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]


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

CNhs11029

00
10
100
1000
10000
1001-0.0631
10020.466
10030.0355
10040.0528
1005-0.0571
1006-0.00934
10070.00174
10080
10090.118
1010.0493
10100
10110.0372
10120
1013-0.157
10140.24
10150.203
10160.234
10170
10180
10190
1020
10200.0528
10210
1022-0.0712
10230
1024-0.0371
10250.0528
10260.0528
10270
10280.0528
10290.0433
1030.276
10300
10310.386
10320.0656
10330
10340
10350.0528
1036-0.0276
10370
1038-0.0113
1039-0.067
1040
1040-0.0343
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: CNhs11029

Jaspar motifP-value
MA0002.20.0118
MA0003.10.619
MA0004.10.198
MA0006.10.116
MA0007.10.621
MA0009.10.393
MA0014.10.776
MA0017.10.00228
MA0018.20.802
MA0019.10.317
MA0024.13.34561e-6
MA0025.10.88
MA0027.10.505
MA0028.10.128
MA0029.10.847
MA0030.10.0155
MA0031.10.133
MA0035.20.948
MA0038.10.00273
MA0039.20.0346
MA0040.10.365
MA0041.10.355
MA0042.10.382
MA0043.10.473
MA0046.13.83305e-18
MA0047.20.032
MA0048.10.0388
MA0050.10.00889
MA0051.10.0144
MA0052.10.0143
MA0055.10.00255
MA0057.10.388
MA0058.10.0409
MA0059.10.118
MA0060.13.33786e-16
MA0061.10.158
MA0062.20.558
MA0065.20.0468
MA0066.10.0586
MA0067.10.996
MA0068.10.0288
MA0069.10.887
MA0070.10.175
MA0071.10.977
MA0072.10.25
MA0073.10.938
MA0074.10.809
MA0076.10.0616
MA0077.10.769
MA0078.10.0819
MA0079.20.189
MA0080.21.1574e-5
MA0081.10.366
MA0083.10.786
MA0084.10.919
MA0087.10.396
MA0088.10.837
MA0090.10.891
MA0091.10.462
MA0092.10.342
MA0093.10.112
MA0099.28.06631e-4
MA0100.10.558
MA0101.10.484
MA0102.20.792
MA0103.15.2849e-4
MA0104.20.00634
MA0105.10.00859
MA0106.10.904
MA0107.10.228
MA0108.20.3
MA0111.10.235
MA0112.20.00772
MA0113.10.439
MA0114.10.00277
MA0115.10.0612
MA0116.10.315
MA0117.10.161
MA0119.10.689
MA0122.10.867
MA0124.10.253
MA0125.10.799
MA0131.10.511
MA0135.10.887
MA0136.10.00443
MA0137.20.475
MA0138.20.00203
MA0139.10.82
MA0140.10.879
MA0141.10.0969
MA0142.10.0136
MA0143.10.746
MA0144.10.263
MA0145.10.0254
MA0146.10.492
MA0147.10.0165
MA0148.10.0023
MA0149.10.185
MA0150.10.00104
MA0152.10.187
MA0153.11.2141e-12
MA0154.10.0497
MA0155.10.94
MA0156.10.204
MA0157.10.106
MA0159.11.15939e-4
MA0160.10.689
MA0162.10.153
MA0163.10.819
MA0164.10.577
MA0258.10.00192
MA0259.10.0338



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: CNhs11029

Novel motifP-value
10.199
100.43
1000.51
1010.545
1020.789
1030.586
1040.899
1050.499
1064.20138e-4
1070.00813
1080.645
1090.978
110.393
1100.883
1110.394
1120.587
1130.258
1140.0501
1150.722
1160.725
1170.934
1180.914
1190.138
120.452
1200.521
1210.801
1220.831
1230.277
1240.131
1250.041
1260.992
1270.109
1281.89609e-4
1290.141
130.923
1300.372
1310.746
1320.772
1330.845
1340.457
1350.54
1360.0463
1370.844
1380.373
1390.163
140.0928
1400.339
1410.304
1420.84
1430.199
1440.0962
1450.929
1460.317
1470.806
1480.0911
1490.39
150.101
1500.953
1510.0568
1520.577
1530.285
1540.873
1550.684
1560.00471
1570.428
1580.124
1590.0223
1600.691
1610.619
1620.573
1630.0248
1640.989
1650.0615
1660.736
1670.284
1680.658
1690.916
170.153
180.182
190.596
20.454
200.664
210.477
220.781
230.107
240.892
250.391
260.821
270.277
280.248
290.45
30.229
300.851
310.176
320.539
330.293
340.896
350.0494
360.474
370.228
380.718
390.911
40.878
400.911
410.0952
420.566
430.244
440.443
450.354
460.137
470.534
480.443
490.134
50.0565
500.767
510.794
520.116
530.86
540.355
550.276
560.302
570.758
580.325
590.602
60.814
600.0327
610.876
620.135
630.248
640.863
650.338
660.297
670.484
688.8302e-4
690.573
70.449
700.0143
710.231
720.811
730.466
740.928
750.459
760.797
770.414
780.281
790.926
80.253
800.077
810.331
820.46
830.528
840.187
850.00554
860.0997
870.277
880.92
890.021
90.851
900.178
910.601
920.161
930.441
940.224
950.489
960.422
970.806
980.126
990.737



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: CNhs11029


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)
0000922 (embryo)
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)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000300 (mouse embryonic day 17 sample)
0011372 (mouse testis- embryo E17 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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