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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;1322
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1322
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;1322
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1322
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N01.CNhs11192.1322-23E9.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N01.CNhs11192.1322-23E9.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N01.CNhs11192.1322-23E9.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520neonate%2520N01.CNhs11192.1322-23E9.mm10.nobarcode.ctss.bed.gz

Revision as of 18:05, 4 August 2017


Name:intestine, neonate N01
Species:Mouse (Mus musculus)
Library ID:CNhs11192
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueintestine
dev stage1 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  SAMD00005547
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11192 CAGE DRX008997 DRR009871
Accession ID Mm9

Library idBAMCTSS
CNhs11192 DRZ001296 DRZ002679
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

CNhs11192

00
10
100
1000
10000.106
10010.0318
10020.3
1003-0.0445
10040
10050.174
1006-0.0532
1007-0.158
10080.174
10090.117
101-0.0476
10100
1011-0.108
10120
10130.273
10140.365
1015-0.173
1016-0.0993
10170
10180.298
10190
1020
10200
10210.0662
1022-0.00418
10230
10240.0338
10250.642
10260.0942
10270
10280
10290.146
1030.085
10300
10310.126
10320.307
10330
10340
10350
1036-0.0474
10370
10380.0371
1039-0.0257
1040.0662
1040-0.0865
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: CNhs11192

Jaspar motifP-value
MA0002.20.227
MA0003.10.166
MA0004.10.572
MA0006.10.0497
MA0007.10.883
MA0009.10.447
MA0014.10.573
MA0017.12.67145e-32
MA0018.26.04303e-4
MA0019.10.137
MA0024.10.00825
MA0025.10.142
MA0027.10.22
MA0028.10.263
MA0029.10.836
MA0030.10.422
MA0031.10.277
MA0035.21.52642e-6
MA0038.10.354
MA0039.24.89281e-4
MA0040.10.245
MA0041.10.261
MA0042.10.868
MA0043.10.00918
MA0046.12.08841e-71
MA0047.20.00384
MA0048.10.496
MA0050.10.00157
MA0051.10.0194
MA0052.16.51544e-5
MA0055.10.24
MA0057.10.115
MA0058.10.386
MA0059.10.994
MA0060.11.13221e-4
MA0061.10.717
MA0062.20.169
MA0065.22.40831e-14
MA0066.10.296
MA0067.10.28
MA0068.10.389
MA0069.10.0783
MA0070.10.118
MA0071.10.805
MA0072.10.485
MA0073.10.805
MA0074.10.0345
MA0076.10.134
MA0077.10.219
MA0078.10.174
MA0079.20.555
MA0080.20.125
MA0081.10.0701
MA0083.10.294
MA0084.10.659
MA0087.10.499
MA0088.10.965
MA0090.10.204
MA0091.10.708
MA0092.10.114
MA0093.10.557
MA0099.20.0025
MA0100.10.00871
MA0101.10.514
MA0102.20.979
MA0103.11.09265e-5
MA0104.20.175
MA0105.10.423
MA0106.10.936
MA0107.10.334
MA0108.20.0882
MA0111.10.383
MA0112.22.63798e-4
MA0113.10.929
MA0114.13.14273e-39
MA0115.11.52012e-10
MA0116.10.392
MA0117.10.698
MA0119.10.24
MA0122.10.72
MA0124.10.282
MA0125.10.66
MA0131.10.708
MA0135.10.00977
MA0136.10.407
MA0137.20.472
MA0138.20.61
MA0139.10.0183
MA0140.10.0402
MA0141.14.77283e-4
MA0142.10.0159
MA0143.10.141
MA0144.10.0312
MA0145.10.0132
MA0146.10.125
MA0147.10.102
MA0148.11.314e-4
MA0149.10.0526
MA0150.10.648
MA0152.10.328
MA0153.12.6911e-57
MA0154.10.0161
MA0155.10.0557
MA0156.10.318
MA0157.10.574
MA0159.10.0153
MA0160.10.00991
MA0162.10.232
MA0163.10.00395
MA0164.10.922
MA0258.10.0499
MA0259.10.155



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: CNhs11192

Novel motifP-value
10.373
100.276
1000.609
1010.898
1020.454
1030.227
1040.812
1050.717
1060.0148
1070.0287
1080.503
1090.0536
110.242
1100.494
1110.265
1120.0213
1130.392
1140.128
1150.696
1160.18
1170.541
1180.337
1190.211
120.768
1200.847
1210.989
1220.826
1230.258
1240.364
1250.721
1260.0783
1270.4
1280.066
1290.437
130.00149
1300.969
1310.127
1320.424
1330.932
1340.373
1350.963
1360.037
1370.925
1380.17
1390.0258
140.764
1400.411
1410.334
1420.882
1430.195
1440.732
1450.142
1460.161
1470.31
1480.09
1490.0781
150.209
1500.302
1510.686
1520.0301
1530.369
1540.985
1550.488
1560.00216
1570.621
1580.442
1590.761
1600.0882
1610.487
1620.287
1630.061
1640.124
1650.49
1660.72
1670.49
1680.357
1690.0297
170.0757
180.507
190.0427
20.0752
200.633
210.727
220.331
230.243
240.818
250.73
260.0135
270.54
280.892
290.581
30.264
300.251
310.568
320.0195
330.109
340.432
350.909
360.924
370.0407
380.383
390.162
40.392
400.254
410.894
420.93
430.256
440.316
450.206
460.43
470.465
480.407
490.424
50.819
500.34
510.788
520.0264
530.851
540.725
550.125
560.392
570.602
580.6
590.0926
60.74
600.023
610.338
620.695
630.29
640.567
650.185
660.376
670.243
680.232
690.807
70.0465
700.0546
710.0888
720.554
730.128
740.825
750.206
760.912
770.0249
780.0438
790.596
80.466
800.212
810.416
820.122
830.652
840.241
850.0612
860.381
870.287
880.796
890.163
90.712
900.595
910.626
920.167
930.928
940.229
950.107
960.736
970.553
980.866
990.0395



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: CNhs11192


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000304 (mouse neonate N0 sample)
0000734 (mouse neonate N1 sample)
0011504 (mouse intestine- neonate N01 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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