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|library_id=CNhs10523
|library_id=CNhs10523
|library_id_phase_based=2:CNhs10523
|library_id_phase_based=2:CNhs10523
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;462
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;462
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E16.CNhs10523.462-17F5.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E16.CNhs10523.462-17F5.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E16.CNhs10523.462-17F5.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/liver%252c%2520embryo%2520E16.CNhs10523.462-17F5.mm10.nobarcode.ctss.bed.gz

Revision as of 22:32, 18 May 2017


Name:liver, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs10523
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stage16 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  SAMD00005920
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10523 CAGE DRX009019 DRR009893
Accession ID Mm9

Library idBAMCTSS
CNhs10523 DRZ001318 DRZ002701
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

CNhs10523

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.0692
1003-0.102
10040
10050.216
1006-0.127
1007-0.0917
10080
1009-0.0888
1010.0662
10100
1011-0.108
10120
10130.0742
10140.078
1015-0.13
1016-0.251
10170
10180
10190
1020
10200
10210
1022-0.0266
10230
1024-0.0707
10250.293
10260
10270
10280
1029-0.0538
103-0.0528
10300
1031-0.156
1032-0.262
10330
10340.175
10350
10360.119
10370
1038-0.134
1039-0.00475
1040
1040-0.21
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: CNhs10523

Jaspar motifP-value
MA0002.20.0152
MA0003.10.328
MA0004.10.447
MA0006.10.297
MA0007.10.583
MA0009.10.133
MA0014.10.529
MA0017.17.03595e-14
MA0018.21.15666e-4
MA0019.10.4
MA0024.17.5671e-4
MA0025.10.473
MA0027.10.557
MA0028.10.133
MA0029.10.0218
MA0030.10.156
MA0031.10.21
MA0035.26.46673e-25
MA0038.10.564
MA0039.20.0166
MA0040.10.0486
MA0041.10.13
MA0042.10.755
MA0043.10.166
MA0046.16.28856e-54
MA0047.21.72892e-5
MA0048.10.0877
MA0050.10.84
MA0051.10.784
MA0052.11.11283e-4
MA0055.10.043
MA0057.10.422
MA0058.10.349
MA0059.10.105
MA0060.16.05646e-5
MA0061.10.204
MA0062.20.0247
MA0065.22.40325e-7
MA0066.10.0296
MA0067.10.251
MA0068.10.818
MA0069.10.0621
MA0070.10.614
MA0071.10.0607
MA0072.10.0125
MA0073.10.864
MA0074.10.459
MA0076.10.314
MA0077.10.249
MA0078.10.431
MA0079.20.253
MA0080.21.48882e-4
MA0081.10.516
MA0083.10.247
MA0084.10.0744
MA0087.10.0269
MA0088.10.0539
MA0090.10.624
MA0091.10.569
MA0092.10.243
MA0093.10.443
MA0099.20.959
MA0100.10.166
MA0101.10.417
MA0102.20.0505
MA0103.10.59
MA0104.20.502
MA0105.10.00348
MA0106.10.81
MA0107.10.827
MA0108.20.0905
MA0111.10.943
MA0112.20.00113
MA0113.10.299
MA0114.13.23703e-12
MA0115.17.10274e-7
MA0116.10.00283
MA0117.10.836
MA0119.10.0284
MA0122.10.357
MA0124.10.48
MA0125.10.706
MA0131.10.751
MA0135.10.71
MA0136.18.42845e-4
MA0137.20.799
MA0138.20.273
MA0139.10.18
MA0140.14.01466e-52
MA0141.10.0186
MA0142.10.19
MA0143.10.16
MA0144.10.831
MA0145.10.739
MA0146.10.0607
MA0147.10.459
MA0148.12.16433e-7
MA0149.10.0429
MA0150.10.00121
MA0152.10.618
MA0153.15.43147e-42
MA0154.10.0224
MA0155.10.995
MA0156.10.00582
MA0157.10.519
MA0159.10.0151
MA0160.10.0142
MA0162.10.398
MA0163.11.00197e-5
MA0164.10.472
MA0258.10.0685
MA0259.10.868



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: CNhs10523

Novel motifP-value
10.137
100.131
1000.457
1010.63
1020.394
1030.0259
1040.982
1050.627
1060.166
1070.289
1080.582
1090.0074
110.0732
1100.0743
1110.0243
1120.013
1130.864
1140.419
1150.968
1160.883
1170.00496
1180.0318
1190.0913
120.999
1200.837
1210.53
1220.901
1230.0486
1240.888
1250.759
1260.124
1270.515
1280.0739
1290.924
139.40702e-5
1300.354
1310.113
1320.237
1330.568
1340.433
1350.326
1360.156
1370.373
1380.553
1390.564
140.821
1400.263
1410.754
1420.0802
1430.678
1440.948
1450.0294
1460.385
1470.891
1480.515
1490.906
150.0425
1500.192
1510.439
1520.282
1530.954
1540.68
1550.516
1560.0694
1570.569
1580.493
1590.43
1600.147
1610.133
1620.746
1630.87
1640.00473
1650.299
1660.677
1670.313
1680.338
1690.00897
170.187
180.553
190.0959
20.757
200.168
210.916
220.265
230.999
240.282
250.501
263.35138e-4
270.54
280.271
290.0227
30.0167
300.864
310.777
320.237
330.138
340.841
350.732
360.0452
370.155
380.568
390.798
40.553
400.085
410.931
420.0639
430.0702
440.63
450.936
460.107
470.101
480.119
490.044
50.101
500.608
510.55
520.479
530.971
540.631
550.197
560.508
570.606
580.49
590.171
60.758
600.149
610.255
620.118
630.229
640.336
650.443
660.204
670.418
680.63
690.44
70.0389
700.381
710.0253
720.405
730.178
740.824
750.0468
760.673
770.778
780.00494
790.871
80.012
800.0722
810.818
820.576
830.404
840.811
850.29
860.267
870.0412
880.81
890.527
90.651
900.198
910.28
920.412
930.591
940.439
950.0468
960.0789
970.837
980.183
990.459



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: CNhs10523


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)
0002107 (liver)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
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)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary 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)
0000299 (mouse embryonic day 16 sample)
0011361 (mouse liver- embryo E16 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:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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