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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005683
|DRA_sample_Accession=CAGE@SAMD00005683
|accession_numbers=CAGE;DRX008932;DRR009806;DRZ001231;DRZ002614
|accession_numbers=CAGE;DRX008932;DRR009806;DRZ001231;DRZ002614;DRZ012581;DRZ013964
|ancestors_in_anatomy_facet=UBERON:0000468,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: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 22:01, 10 August 2017


Name:adrenal gland, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11191
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueadrenal gland
dev stage0 day neonate
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  SAMD00005683
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11191 CAGE DRX008932 DRR009806
Accession ID Mm9

Library idBAMCTSS
CNhs11191 DRZ001231 DRZ002614
Accession ID Mm10

Library idBAMCTSS
CNhs11191 DRZ012581 DRZ013964
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

CNhs11191

00
10.0695
100
1000
10000.111
10010.167
10020.351
1003-0.0087
10040
10050
10060.166
10070.039
10080
10090.295
1010.0227
10100
10110.0399
10120.0917
10130.0601
10140.476
1015-0.102
10160.188
10170
10180
10190
1020
10200
10210.0228
10220.108
10230.0483
10240.111
10250.0306
10260.0483
10270
10280
10290.239
1030.293
10300.0483
10310.276
10320.0175
10330
10340.0917
10350.0483
1036-0.0289
10370
1038-0.0119
10390.129
1040
10400.226
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: CNhs11191

Jaspar motifP-value
MA0002.20.0202
MA0003.10.673
MA0004.10.0319
MA0006.10.668
MA0007.10.534
MA0009.10.0259
MA0014.10.986
MA0017.10.0159
MA0018.20.111
MA0019.10.551
MA0024.10.654
MA0025.10.286
MA0027.10.0963
MA0028.17.79166e-4
MA0029.10.00299
MA0030.10.435
MA0031.10.748
MA0035.20.438
MA0038.10.801
MA0039.20.0715
MA0040.10.114
MA0041.10.233
MA0042.10.691
MA0043.10.108
MA0046.15.42554e-4
MA0047.20.506
MA0048.10.593
MA0050.10.84
MA0051.10.275
MA0052.10.615
MA0055.10.093
MA0057.10.223
MA0058.10.0517
MA0059.10.00721
MA0060.18.81034e-4
MA0061.10.0769
MA0062.28.53495e-8
MA0065.20.208
MA0066.10.507
MA0067.10.58
MA0068.10.401
MA0069.10.408
MA0070.10.112
MA0071.10.139
MA0072.10.335
MA0073.10.877
MA0074.10.308
MA0076.10.00351
MA0077.10.64
MA0078.10.201
MA0079.20.112
MA0080.21.00844e-7
MA0081.10.0579
MA0083.10.526
MA0084.10.0436
MA0087.10.0515
MA0088.10.144
MA0090.10.564
MA0091.10.956
MA0092.10.876
MA0093.10.0598
MA0099.20.352
MA0100.10.0359
MA0101.10.0946
MA0102.20.949
MA0103.12.88637e-8
MA0104.20.00182
MA0105.10.00924
MA0106.10.996
MA0107.10.205
MA0108.20.208
MA0111.10.879
MA0112.20.303
MA0113.10.96
MA0114.10.0129
MA0115.10.0959
MA0116.10.0925
MA0117.10.804
MA0119.10.603
MA0122.10.283
MA0124.10.515
MA0125.10.291
MA0131.10.477
MA0135.10.363
MA0136.12.03581e-10
MA0137.20.0698
MA0138.20.0271
MA0139.10.191
MA0140.10.116
MA0141.10.0392
MA0142.10.66
MA0143.10.42
MA0144.10.265
MA0145.10.783
MA0146.10.69
MA0147.13.80861e-4
MA0148.10.97
MA0149.10.496
MA0150.10.647
MA0152.10.114
MA0153.11.22581e-5
MA0154.10.869
MA0155.10.712
MA0156.11.82343e-6
MA0157.10.985
MA0159.10.0105
MA0160.10.59
MA0162.10.356
MA0163.10.982
MA0164.10.579
MA0258.10.409
MA0259.10.102



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: CNhs11191

Novel motifP-value
10.026
100.0924
1000.757
1010.627
1020.85
1030.67
1040.427
1050.295
1060.751
1070.164
1080.289
1090.0685
110.189
1100.813
1110.0625
1120.969
1130.823
1140.824
1150.737
1160.121
1170.0184
1180.703
1190.669
120.315
1200.117
1210.239
1220.98
1230.42
1240.22
1250.149
1260.0496
1270.805
1280.137
1290.476
130.0845
1300.602
1310.374
1320.926
1330.0933
1340.78
1350.0642
1360.216
1370.416
1380.315
1390.919
140.624
1400.727
1410.783
1420.453
1430.493
1440.0453
1450.631
1460.951
1470.697
1480.204
1490.19
150.199
1500.777
1510.64
1520.314
1530.394
1540.974
1550.162
1560.285
1570.937
1580.506
1590.0972
1600.424
1610.306
1620.658
1630.254
1640.914
1650.217
1660.321
1670.711
1680.929
1690.21
170.902
180.888
190.199
20.187
200.216
210.67
220.537
230.421
240.427
250.12
260.148
270.775
280.318
290.143
30.456
300.95
310.923
320.643
330.299
340.757
350.17
360.0602
370.661
380.552
390.785
40.513
400.0878
410.00445
420.536
430.772
440.381
450.55
460.421
470.3
480.293
490.39
50.512
500.612
510.94
520.823
530.518
540.758
550.00263
560.903
570.704
580.329
590.25
60.862
600.365
610.309
620.164
630.45
640.627
650.217
660.226
670.977
680.281
690.462
70.0817
700.0348
710.0213
720.482
730.783
740.812
750.15
760.897
770.797
780.923
790.523
80.583
800.406
810.88
820.16
830.112
840.958
850.241
860.692
879.1921e-5
880.76
890.0891
90.889
900.3
910.309
920.778
930.276
940.436
950.43
960.914
970.579
980.305
990.539



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: CNhs11191


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0011505 (mouse adrenal gland - 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:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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