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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004758
|DRA_sample_Accession=CAGE@SAMD00004758
|accession_numbers=CAGE;DRX008930;DRR009804;DRZ001229;DRZ002612
|accession_numbers=CAGE;DRX008930;DRR009804;DRZ001229;DRZ002612;DRZ012579;DRZ013962
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002369,UBERON:0002100,UBERON:0000479,UBERON:0010314,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0005172,UBERON:0002530,UBERON:0006858,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0000916
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002369,UBERON:0002100,UBERON:0000479,UBERON:0010314,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009569,UBERON:0002368,UBERON:0005177,UBERON:0005172,UBERON:0002530,UBERON:0006858,UBERON:0010317,UBERON:0005173,UBERON:0002417,UBERON:0000949,UBERON:0000916
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=

Revision as of 21:49, 10 August 2017


Name:adrenal gland, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs11043
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueadrenal gland
dev stage17 days embryo
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  SAMD00004758
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11043 CAGE DRX008930 DRR009804
Accession ID Mm9

Library idBAMCTSS
CNhs11043 DRZ001229 DRZ002612
Accession ID Mm10

Library idBAMCTSS
CNhs11043 DRZ012579 DRZ013962
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

CNhs11043

00
10
100
1000
10000.0901
10010
10020.261
1003-0.0704
10040
1005-0.0221
10060.0465
1007-0.0952
10080
10090.107
101-0.0277
10100
1011-0.0694
10120
1013-0.00155
10140.239
10150.0435
10160.0833
10170
10180
10190
1020
10200
10210
10220.0123
10230
10240.0259
10250.0676
10260
1027-0.0174
10280
1029-0.0181
1030.284
10300
10310.218
1032-0.0526
10330.0901
10340.00392
10350
10360.0455
10370
1038-0.0699
10390.127
1040
1040-0.0215
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: CNhs11043

Jaspar motifP-value
MA0002.20.461
MA0003.10.176
MA0004.10.00297
MA0006.10.317
MA0007.10.854
MA0009.10.0202
MA0014.10.598
MA0017.10.906
MA0018.20.332
MA0019.10.679
MA0024.10.0949
MA0025.10.797
MA0027.10.0261
MA0028.10.151
MA0029.11.40336e-4
MA0030.10.936
MA0031.10.815
MA0035.20.0202
MA0038.10.316
MA0039.20.203
MA0040.10.103
MA0041.10.184
MA0042.10.357
MA0043.10.15
MA0046.10.00274
MA0047.20.53
MA0048.10.0378
MA0050.10.00137
MA0051.11.13337e-5
MA0052.10.523
MA0055.10.348
MA0057.11
MA0058.10.121
MA0059.10.368
MA0060.10.284
MA0061.10.876
MA0062.20.0032
MA0065.20.0394
MA0066.10.968
MA0067.10.185
MA0068.10.238
MA0069.10.0817
MA0070.10.00166
MA0071.10.0575
MA0072.10.107
MA0073.10.767
MA0074.10.894
MA0076.10.138
MA0077.10.537
MA0078.10.933
MA0079.20.396
MA0080.22.09595e-5
MA0081.10.182
MA0083.10.0348
MA0084.10.0474
MA0087.10.0175
MA0088.10.397
MA0090.10.449
MA0091.10.22
MA0092.10.84
MA0093.10.0382
MA0099.20.067
MA0100.10.0467
MA0101.10.144
MA0102.20.163
MA0103.12.55865e-7
MA0104.20.157
MA0105.10.407
MA0106.10.926
MA0107.10.029
MA0108.20.00484
MA0111.10.733
MA0112.20.0428
MA0113.10.963
MA0114.10.165
MA0115.10.717
MA0116.10.202
MA0117.10.721
MA0119.10.00809
MA0122.10.512
MA0124.10.906
MA0125.10.154
MA0131.10.32
MA0135.10.596
MA0136.14.33673e-5
MA0137.20.29
MA0138.20.221
MA0139.10.681
MA0140.12.29917e-5
MA0141.11.97647e-4
MA0142.10.37
MA0143.10.1
MA0144.10.565
MA0145.10.214
MA0146.10.508
MA0147.10.149
MA0148.10.854
MA0149.10.575
MA0150.10.0839
MA0152.10.928
MA0153.10.0737
MA0154.10.0342
MA0155.10.319
MA0156.12.82498e-4
MA0157.10.328
MA0159.10.908
MA0160.10.0722
MA0162.10.296
MA0163.10.0332
MA0164.10.551
MA0258.10.263
MA0259.10.132



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: CNhs11043

Novel motifP-value
10.136
100.688
1000.882
1010.884
1020.914
1030.855
1040.918
1050.665
1060.565
1070.361
1080.176
1090.245
110.313
1100.0748
1110.0923
1120.713
1130.801
1140.236
1150.493
1160.523
1170.285
1180.849
1190.535
120.351
1200.143
1210.908
1220.413
1230.202
1240.31
1250.00928
1260.136
1270.947
1280.109
1290.727
130.409
1300.999
1310.357
1320.754
1330.298
1340.266
1350.231
1360.171
1370.653
1380.112
1390.9
140.728
1400.664
1410.916
1420.38
1430.551
1440.305
1450.791
1460.159
1470.87
1480.406
1490.108
150.359
1500.379
1510.923
1520.185
1530.663
1540.126
1550.616
1569.22466e-6
1570.0903
1580.0528
1590.0151
1600.201
1610.844
1620.785
1630.46
1640.555
1650.344
1660.148
1670.0902
1680.526
1690.0729
170.483
180.289
190.0197
20.134
200.157
210.818
220.0598
230.783
240.753
250.374
260.98
270.587
280.246
290.728
30.602
300.372
310.904
320.73
330.711
340.287
350.0806
360.723
370.437
380.9
390.706
40.951
400.274
410.00636
420.925
430.315
440.895
450.893
460.669
470.469
480.489
490.67
50.662
500.145
510.773
520.731
530.0651
540.752
550.0403
560.751
570.872
580.516
590.0602
60.914
600.225
610.398
620.701
630.495
640.338
650.992
660.745
670.853
680.428
690.0793
70.443
700.057
710.872
720.989
730.34
740.323
750.442
760.343
770.0518
780.173
790.924
80.545
800.326
810.96
820.203
830.123
840.431
850.683
860.707
870.201
880.496
890.311
90.926
900.743
910.339
920.421
930.328
940.766
950.244
960.581
970.683
980.708
990.168



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: CNhs11043


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)
0002369 (adrenal gland)
0002100 (trunk)
0000479 (tissue)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0005172 (abdomen element)
0002530 (gland)
0006858 (adrenal/interrenal gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0000916 (abdomen)

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)
0011520 (adrenal gland - 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:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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