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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;1377
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1377
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;1377
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1377
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520neonate%2520N25.CNhs11223.1377-27I3.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520neonate%2520N25.CNhs11223.1377-27I3.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520neonate%2520N25.CNhs11223.1377-27I3.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520neonate%2520N25.CNhs11223.1377-27I3.mm10.nobarcode.ctss.bed.gz

Revision as of 18:18, 4 August 2017


Name:adrenal gland, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11223
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueadrenal gland
dev stage25 days 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  SAMD00005199
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11223 CAGE DRX008933 DRR009807
Accession ID Mm9

Library idBAMCTSS
CNhs11223 DRZ001232 DRZ002615
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

CNhs11223

00
10
100
1000
10000.138
10010.161
10020.0514
1003-0.0159
10040
10050
10060.0845
1007-0.0437
10080
10090.269
101-0.0793
10100
1011-0.00857
10128.764537e-4
10130.141
1014-0.0874
1015-0.149
10160.00282
10170
10180
10190
1020
10200
10210.0514
10220.274
10230
10240.177
10250
10260
10270
10280
1029-0.0379
1030
10300
1031-0.0421
10320.0574
1033-0.0151
10340.0514
10350
1036-0.348
10370
1038-0.0542
10390.501
1040
1040-0.032
10410.63



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: CNhs11223

Jaspar motifP-value
MA0002.20.606
MA0003.10.312
MA0004.10.104
MA0006.10.122
MA0007.10.264
MA0009.10.366
MA0014.10.075
MA0017.10.00623
MA0018.20.545
MA0019.10.526
MA0024.10.0134
MA0025.10.00498
MA0027.10.102
MA0028.10.493
MA0029.10.0119
MA0030.10.506
MA0031.10.22
MA0035.20.864
MA0038.10.0575
MA0039.20.00485
MA0040.10.974
MA0041.10.271
MA0042.10.71
MA0043.10.419
MA0046.10.476
MA0047.20.723
MA0048.10.494
MA0050.10.00258
MA0051.10.00107
MA0052.10.408
MA0055.10.425
MA0057.10.935
MA0058.10.218
MA0059.10.0571
MA0060.10.212
MA0061.10.604
MA0062.20.883
MA0065.22.22947e-7
MA0066.10.578
MA0067.10.883
MA0068.10.498
MA0069.10.0598
MA0070.10.0252
MA0071.15.52998e-5
MA0072.10.00373
MA0073.10.769
MA0074.10.996
MA0076.10.348
MA0077.10.994
MA0078.10.142
MA0079.20.0414
MA0080.20.00585
MA0081.10.815
MA0083.10.727
MA0084.10.604
MA0087.10.849
MA0088.10.455
MA0090.10.865
MA0091.10.262
MA0092.10.968
MA0093.10.17
MA0099.20.197
MA0100.10.205
MA0101.10.85
MA0102.20.8
MA0103.11.62727e-5
MA0104.20.0523
MA0105.10.0245
MA0106.10.695
MA0107.10.918
MA0108.20.0676
MA0111.10.355
MA0112.20.0673
MA0113.10.812
MA0114.14.03915e-6
MA0115.10.732
MA0116.10.52
MA0117.10.818
MA0119.10.0256
MA0122.10.732
MA0124.10.785
MA0125.10.448
MA0131.10.613
MA0135.10.487
MA0136.10.0576
MA0137.20.704
MA0138.20.179
MA0139.10.992
MA0140.10.903
MA0141.11.12831e-8
MA0142.10.00911
MA0143.10.819
MA0144.10.804
MA0145.10.186
MA0146.10.00268
MA0147.10.0408
MA0148.10.503
MA0149.10.0935
MA0150.10.0123
MA0152.10.995
MA0153.10.131
MA0154.10.288
MA0155.10.891
MA0156.10.469
MA0157.10.625
MA0159.10.714
MA0160.11.30517e-7
MA0162.10.488
MA0163.10.596
MA0164.10.345
MA0258.10.0504
MA0259.10.0441



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: CNhs11223

Novel motifP-value
10.298
100.639
1000.18
1010.971
1020.786
1030.747
1040.809
1050.739
1060.255
1070.725
1080.0811
1090.243
110.152
1100.284
1110.399
1120.46
1130.951
1140.815
1150.119
1160.353
1170.463
1180.948
1190.613
120.683
1200.0117
1210.137
1220.96
1230.261
1240.383
1250.711
1260.23
1270.245
1280.169
1290.543
130.0957
1300.496
1310.18
1320.978
1330.787
1340.638
1350.144
1360.0161
1370.812
1380.194
1390.281
140.278
1400.0679
1410.926
1420.65
1430.614
1440.805
1450.839
1460.27
1470.786
1480.253
1490.0136
150.69
1500.387
1510.464
1520.00446
1530.803
1540.31
1550.917
1566.46565e-4
1570.43
1580.724
1590.907
1600.423
1610.669
1620.795
1630.828
1640.746
1650.996
1660.448
1670.0656
1680.847
1690.0257
170.153
180.961
190.251
20.24
200.303
210.956
220.0153
230.186
240.158
250.738
260.672
270.922
280.866
290.385
30.755
300.588
310.705
320.583
330.36
340.673
350.427
360.232
370.247
380.18
390.237
40.903
400.659
410.094
420.626
430.921
440.258
450.693
460.176
470.505
480.306
490.463
50.788
500.392
510.864
520.984
530.679
540.664
550.0073
560.667
570.621
580.318
590.728
60.986
600.784
610.815
620.148
630.22
640.397
650.784
660.863
670.257
680.9
690.393
70.853
700.356
710.0453
720.744
730.0031
740.952
750.944
760.263
770.402
780.389
790.623
80.639
800.28
810.538
820.0909
835.40063e-4
840.101
850.51
860.551
870.0153
880.432
890.637
90.49
900.51
910.00198
920.732
930.887
940.151
950.0026
960.94
970.328
980.334
990.447



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: CNhs11223


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)
0000309 (mouse neonate N25 sample)
0011466 (mouse adrenal gland - neonate N25 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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