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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;17
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;17
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;17
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;17
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/medulla%2520oblongata%252c%2520adult.CNhs10477.17-12C2.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/medulla%2520oblongata%252c%2520adult.CNhs10477.17-12C2.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/medulla%2520oblongata%252c%2520adult.CNhs10477.17-12C2.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/medulla%2520oblongata%252c%2520adult.CNhs10477.17-12C2.mm10.nobarcode.ctss.bed.gz

Revision as of 18:27, 4 August 2017


Name:medulla oblongata, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10477
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuemedulla oblongata
dev stageadult
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  SAMD00005853
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10477 CAGE DRX009046 DRR009920
Accession ID Mm9

Library idBAMCTSS
CNhs10477 DRZ001345 DRZ002728
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

CNhs10477

00
10.728
100
1000
10000.0138
10010.0534
10020
10030.0884
10040
10050.0863
10060.61
1007-0.0594
10080
1009-0.0691
101-0.0826
10100
10110.423
10120.0647
10130.295
1014-0.0299
1015-0.135
1016-0.153
10170
10180
10190
1020
10200
10210
10220.0505
10230
10240.203
10250.0598
10260
10270.443
10280
1029-0.00378
103-0.0813
10300
1031-0.304
10320.457
1033-0.0105
10340
10350
1036-0.279
10370
1038-0.112
10390.181
1040
1040-0.151
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: CNhs10477

Jaspar motifP-value
MA0002.20.00138
MA0003.10.4
MA0004.10.412
MA0006.10.26
MA0007.10.287
MA0009.10.796
MA0014.10.941
MA0017.12.88822e-6
MA0018.20.00566
MA0019.10.65
MA0024.10.0398
MA0025.16.74289e-4
MA0027.10.199
MA0028.10.122
MA0029.10.684
MA0030.10.637
MA0031.10.496
MA0035.20.0216
MA0038.10.247
MA0039.20.0887
MA0040.10.671
MA0041.10.0358
MA0042.10.183
MA0043.10.0332
MA0046.11.98885e-10
MA0047.20.00105
MA0048.10.0189
MA0050.15.37196e-4
MA0051.10.0036
MA0052.10.419
MA0055.10.00491
MA0057.10.312
MA0058.10.498
MA0059.10.126
MA0060.10.629
MA0061.10.017
MA0062.20.0042
MA0065.21.86399e-6
MA0066.10.0225
MA0067.10.371
MA0068.10.998
MA0069.10.0438
MA0070.10.178
MA0071.10.19
MA0072.10.733
MA0073.10.85
MA0074.10.0998
MA0076.10.277
MA0077.10.24
MA0078.10.621
MA0079.20.216
MA0080.22.69538e-9
MA0081.10.269
MA0083.10.0224
MA0084.10.451
MA0087.10.081
MA0088.10.421
MA0090.10.0908
MA0091.10.15
MA0092.10.142
MA0093.10.487
MA0099.20.012
MA0100.10.136
MA0101.10.0103
MA0102.20.532
MA0103.10.123
MA0104.20.656
MA0105.10.00157
MA0106.10.0417
MA0107.10.0197
MA0108.21.26154e-4
MA0111.10.769
MA0112.20.00123
MA0113.10.395
MA0114.14.04951e-6
MA0115.12.31787e-5
MA0116.10.0599
MA0117.10.922
MA0119.10.181
MA0122.10.958
MA0124.10.437
MA0125.10.0176
MA0131.10.728
MA0135.10.123
MA0136.14.20794e-10
MA0137.20.546
MA0138.22.71959e-5
MA0139.10.703
MA0140.11.43397e-5
MA0141.10.025
MA0142.10.222
MA0143.10.695
MA0144.10.144
MA0145.10.25
MA0146.10.0495
MA0147.10.467
MA0148.10.00137
MA0149.10.169
MA0150.10.405
MA0152.10.24
MA0153.17.75729e-11
MA0154.10.0352
MA0155.10.423
MA0156.11.01848e-6
MA0157.10.299
MA0159.10.0051
MA0160.10.0342
MA0162.10.288
MA0163.16.03178e-4
MA0164.10.94
MA0258.10.0166
MA0259.10.698



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: CNhs10477

Novel motifP-value
10.259
100.0434
1000.254
1010.859
1020.996
1030.0897
1040.999
1050.644
1060.0355
1070.146
1080.54
1090.0262
110.138
1100.0339
1110.232
1120.0129
1130.451
1140.516
1150.915
1160.274
1170.00243
1180.197
1190.255
120.762
1200.891
1210.683
1220.746
1232.19989e-4
1240.0206
1250.123
1260.0246
1270.186
1280.0529
1290.356
131.87954e-7
1300.179
1310.571
1320.723
1330.678
1340.214
1350.0713
1360.294
1370.713
1380.695
1390.251
140.634
1400.101
1410.95
1420.572
1430.314
1440.982
1458.44091e-5
1460.498
1470.363
1480.935
1490.848
150.198
1500.0691
1510.94
1520.166
1530.845
1540.719
1550.416
1560.00972
1570.27
1580.297
1590.67
1600.237
1610.327
1620.773
1630.612
1640.0329
1650.544
1660.446
1670.922
1680.782
1690.00432
170.0895
180.927
190.185
20.589
200.0127
210.189
220.225
230.831
240.115
250.786
265.54404e-10
270.283
280.853
290.0272
30.098
300.799
310.715
320.65
330.201
340.908
350.952
360.168
370.0703
380.527
390.403
40.22
400.154
410.535
420.238
430.132
440.504
450.777
460.034
470.634
480.418
490.137
50.193
500.298
510.757
520.4
530.27
540.966
550.807
560.64
570.475
580.342
590.169
60.981
600.0461
610.0735
620.229
630.197
640.741
650.427
660.802
670.857
680.31
690.655
70.0184
700.1
710.00221
720.633
730.0748
740.805
750.0558
760.198
770.563
780.0022
790.213
80.0476
800.976
810.542
820.372
830.401
840.874
850.299
860.149
870.746
880.61
890.712
90.538
900.103
910.0778
920.387
930.129
940.585
950.107
960.515
970.92
980.702
990.61



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: CNhs10477


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)
0007023 (adult organism)
0000955 (brain)
0001896 (medulla oblongata)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0004733 (segmental subdivision of hindbrain)
0004732 (segmental subdivision of nervous system)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0002298 (brainstem)
0002028 (hindbrain)
0005290 (myelencephalon)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011284 (mouse medulla oblongata- adult 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:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)

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