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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;482
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;482
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;482
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;482
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520embryo%2520E17.CNhs10582.482-18D3.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520embryo%2520E17.CNhs10582.482-18D3.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520embryo%2520E17.CNhs10582.482-18D3.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520embryo%2520E17.CNhs10582.482-18D3.mm10.nobarcode.ctss.bed.gz

Revision as of 18:45, 4 August 2017


Name:intestine, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs10582
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueintestine
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  SAMD00005044
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10582 CAGE DRX008994 DRR009868
Accession ID Mm9

Library idBAMCTSS
CNhs10582 DRZ001293 DRZ002676
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

CNhs10582

00
10
100
1000
10000.0501
10010
10020.243
1003-0.038
10040
10050.194
1006-0.0554
1007-0.0136
10080.0872
1009-0.00584
101-0.00728
10100
1011-0.0758
10120
10130.0458
10140.16
1015-0.0332
1016-0.0214
10170
10180
10190
1020
10200
10210
1022-0.0631
10230
1024-0.00267
10250.822
10260
10270
10280
10290.332
1030.0825
10300
10310.267
10320.115
10330
10340
10350
1036-0.00419
10370
10380.0039
1039-0.189
1040
1040-0.0454
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: CNhs10582

Jaspar motifP-value
MA0002.20.751
MA0003.10.234
MA0004.10.118
MA0006.10.0783
MA0007.10.386
MA0009.10.913
MA0014.10.895
MA0017.15.44395e-35
MA0018.24.04319e-4
MA0019.10.191
MA0024.10.837
MA0025.10.0371
MA0027.10.267
MA0028.10.258
MA0029.10.963
MA0030.10.738
MA0031.10.985
MA0035.21.3355e-7
MA0038.10.297
MA0039.29.50032e-4
MA0040.10.384
MA0041.10.987
MA0042.10.862
MA0043.10.0114
MA0046.11.20518e-94
MA0047.20.00308
MA0048.10.409
MA0050.10.818
MA0051.10.596
MA0052.17.09562e-4
MA0055.10.529
MA0057.10.293
MA0058.10.0107
MA0059.10.782
MA0060.10.00821
MA0061.10.776
MA0062.20.239
MA0065.21.21566e-8
MA0066.10.401
MA0067.10.219
MA0068.10.102
MA0069.10.0553
MA0070.10.354
MA0071.10.801
MA0072.10.614
MA0073.10.958
MA0074.10.0303
MA0076.10.152
MA0077.10.938
MA0078.10.395
MA0079.20.494
MA0080.20.0586
MA0081.10.0497
MA0083.10.0269
MA0084.10.768
MA0087.10.777
MA0088.10.365
MA0090.10.364
MA0091.10.342
MA0092.10.355
MA0093.10.0618
MA0099.20.517
MA0100.10.00519
MA0101.10.545
MA0102.20.287
MA0103.11.8157e-5
MA0104.20.496
MA0105.10.703
MA0106.10.581
MA0107.10.397
MA0108.20.155
MA0111.10.218
MA0112.20.00822
MA0113.10.927
MA0114.11.74528e-44
MA0115.19.13058e-8
MA0116.10.28
MA0117.10.215
MA0119.10.206
MA0122.10.704
MA0124.10.316
MA0125.10.504
MA0131.10.994
MA0135.10.0163
MA0136.10.252
MA0137.20.588
MA0138.20.754
MA0139.10.0153
MA0140.10.0242
MA0141.10.00417
MA0142.10.0471
MA0143.10.165
MA0144.10.0717
MA0145.10.0888
MA0146.10.153
MA0147.10.192
MA0148.13.47321e-4
MA0149.10.243
MA0150.10.191
MA0152.10.855
MA0153.14.47003e-60
MA0154.10.077
MA0155.10.042
MA0156.10.069
MA0157.10.667
MA0159.10.0553
MA0160.10.0298
MA0162.10.196
MA0163.10.0293
MA0164.10.565
MA0258.10.238
MA0259.10.391



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: CNhs10582

Novel motifP-value
10.714
100.457
1000.363
1010.906
1020.228
1030.643
1040.976
1050.381
1060.0748
1070.151
1080.93
1090.297
110.609
1100.434
1110.612
1120.0438
1130.186
1140.864
1150.906
1160.483
1170.913
1180.53
1190.897
120.543
1200.645
1210.702
1220.638
1230.0156
1240.162
1250.908
1260.0344
1270.908
1280.44
1290.933
134.97818e-5
1300.481
1310.344
1320.459
1330.53
1340.402
1350.311
1360.223
1370.815
1380.0538
1390.227
140.948
1400.255
1410.221
1420.295
1430.0769
1440.191
1450.208
1460.0564
1470.438
1480.0733
1490.101
150.761
1500.276
1510.972
1520.0685
1530.13
1540.257
1550.837
1560.914
1570.636
1580.828
1590.0636
1600.0505
1610.495
1620.629
1630.364
1640.586
1650.592
1660.621
1670.662
1680.229
1690.115
170.334
180.0511
190.0281
20.181
200.618
210.94
220.227
230.725
240.443
250.975
260.0253
270.587
280.579
290.621
30.657
300.273
310.988
320.307
330.299
340.31
350.436
360.849
370.23
380.63
390.244
40.306
400.0994
410.348
420.782
430.502
440.567
450.0778
460.702
470.807
480.687
490.811
50.662
500.351
510.874
520.0195
530.664
540.754
550.0547
560.497
570.122
580.729
590.362
60.962
600.0728
610.409
620.541
630.604
640.719
650.502
660.86
670.0663
680.584
690.582
70.0659
700.664
710.113
720.446
730.419
740.818
750.504
760.473
770.0201
780.113
790.562
80.734
800.377
810.629
820.795
830.356
840.498
850.382
860.472
870.895
880.553
890.209
90.722
900.785
910.333
920.612
930.618
940.0714
950.657
960.384
970.343
980.958
990.0718



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: CNhs10582


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)
0000160 (intestine)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal 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)
0000300 (mouse embryonic day 17 sample)
0011370 (mouse intestine- 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:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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