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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005973
|DRA_sample_Accession=CAGE@SAMD00005973
|accession_numbers=CAGE;DRX009106;DRR009980;DRZ001405;DRZ002788
|accession_numbers=CAGE;DRX009106;DRR009980;DRZ001405;DRZ002788;DRZ012755;DRZ014138
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,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:0000922,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_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=

Revision as of 22:38, 10 August 2017


Name:testis, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs11027
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuetestis
dev stage18 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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005973
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11027 CAGE DRX009106 DRR009980
Accession ID Mm9

Library idBAMCTSS
CNhs11027 DRZ001405 DRZ002788
Accession ID Mm10

Library idBAMCTSS
CNhs11027 DRZ012755 DRZ014138
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11027

00
10
100
1000
1000-0.00141
10010.0615
10020.813
10030.25
10040
10050
10060
10070.036
10080
10090.066
1010.0691
10100
10110.0186
10120.126
1013-0.139
10140.474
10150.137
10160.321
10170
10180
10190
1020
10200
10210
10220.0678
10230
1024-0.0221
10250.0173
10260
10270
10280
10290.225
1030.266
10300
10310.427
1032-0.0213
10330.0013
10340
10350.126
10360.0511
10370
10380
1039-0.0443
1040
10400.0421
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: CNhs11027

Jaspar motifP-value
MA0002.20.00167
MA0003.10.972
MA0004.10.472
MA0006.10.0949
MA0007.10.818
MA0009.10.527
MA0014.10.856
MA0017.14.87936e-4
MA0018.20.102
MA0019.10.403
MA0024.11.84804e-6
MA0025.10.425
MA0027.10.956
MA0028.10.157
MA0029.10.794
MA0030.10.0272
MA0031.10.0334
MA0035.20.25
MA0038.10.0416
MA0039.20.19
MA0040.10.0623
MA0041.10.158
MA0042.10.378
MA0043.10.737
MA0046.13.78685e-24
MA0047.20.00787
MA0048.10.0108
MA0050.10.0796
MA0051.10.0329
MA0052.13.36375e-4
MA0055.10.00511
MA0057.10.22
MA0058.10.238
MA0059.10.162
MA0060.11.42891e-7
MA0061.10.33
MA0062.20.977
MA0065.20.00463
MA0066.10.0772
MA0067.10.587
MA0068.10.59
MA0069.10.78
MA0070.10.965
MA0071.10.788
MA0072.10.254
MA0073.10.229
MA0074.10.72
MA0076.10.131
MA0077.10.454
MA0078.10.0444
MA0079.20.487
MA0080.21.23917e-6
MA0081.10.301
MA0083.10.181
MA0084.10.397
MA0087.10.248
MA0088.10.754
MA0090.10.647
MA0091.10.993
MA0092.10.574
MA0093.10.356
MA0099.23.10009e-6
MA0100.10.715
MA0101.10.47
MA0102.20.803
MA0103.12.80116e-4
MA0104.20.0329
MA0105.10.19
MA0106.10.521
MA0107.10.261
MA0108.21.59278e-4
MA0111.10.283
MA0112.20.0356
MA0113.10.419
MA0114.17.87553e-4
MA0115.10.103
MA0116.10.404
MA0117.10.13
MA0119.10.97
MA0122.10.623
MA0124.10.127
MA0125.10.469
MA0131.10.559
MA0135.10.104
MA0136.11.16699e-5
MA0137.20.246
MA0138.20.0178
MA0139.10.867
MA0140.10.779
MA0141.10.0175
MA0142.10.0134
MA0143.10.852
MA0144.10.16
MA0145.10.00995
MA0146.10.416
MA0147.10.0488
MA0148.10.00141
MA0149.10.264
MA0150.11.21479e-4
MA0152.10.0239
MA0153.14.0512e-16
MA0154.10.0783
MA0155.10.971
MA0156.10.0321
MA0157.10.0915
MA0159.12.27186e-5
MA0160.10.729
MA0162.10.0816
MA0163.10.327
MA0164.10.731
MA0258.10.0018
MA0259.10.0341



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: CNhs11027

Novel motifP-value
10.275
100.922
1000.527
1010.71
1020.375
1030.641
1040.928
1050.226
1061.24604e-4
1070.0108
1080.714
1090.758
110.426
1100.595
1110.831
1120.941
1130.365
1140.0465
1150.503
1160.27
1170.525
1180.465
1190.22
120.427
1200.364
1210.946
1220.955
1230.235
1240.328
1250.261
1260.811
1270.412
1286.17341e-4
1290.19
130.77
1300.391
1310.59
1320.788
1330.537
1340.988
1350.178
1360.227
1370.879
1380.635
1390.201
140.127
1400.741
1410.0983
1420.145
1430.145
1440.0138
1450.726
1460.208
1470.612
1480.214
1490.457
150.127
1500.979
1510.0576
1520.241
1530.773
1540.564
1550.644
1560.716
1570.534
1580.327
1590.663
1600.562
1610.657
1620.431
1630.0415
1640.597
1650.0427
1660.652
1670.929
1680.226
1690.843
170.167
180.201
190.68
20.238
200.6
210.425
220.891
230.111
240.998
250.41
260.791
270.248
280.408
290.192
30.434
300.594
310.214
320.734
330.744
340.879
350.103
360.45
370.328
380.676
390.937
40.622
400.576
410.0129
420.705
430.401
440.59
450.186
460.15
470.676
480.409
490.207
50.136
500.781
510.844
520.0934
530.703
540.338
550.199
560.313
570.767
580.385
590.187
60.924
600.0283
610.841
620.124
630.309
640.836
650.262
660.771
670.192
680.00212
690.256
70.618
700.0113
710.469
720.543
730.281
740.701
750.851
760.489
770.521
780.429
790.85
80.264
800.0161
810.422
820.874
830.771
840.252
850.0103
860.0934
870.137
880.7
890.0266
90.745
900.545
910.481
920.277
930.293
940.494
950.909
960.678
970.949
980.123
990.88



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: CNhs11027


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)
0000302 (mouse embryonic day 18 sample)
0011377 (mouse testis- embryo E18 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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