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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;178
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;178
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;178
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;178
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520adult.CNhs10496.178-9A3.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520adult.CNhs10496.178-9A3.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520adult.CNhs10496.178-9A3.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/intestine%252c%2520adult.CNhs10496.178-9A3.mm10.nobarcode.ctss.bed.gz

Revision as of 18:27, 4 August 2017


Name:intestine, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10496
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strain
    1. Klotho
tissueintestine
dev stageadult
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  SAMD00004890
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10496 CAGE DRX008989 DRR009863
Accession ID Mm9

Library idBAMCTSS
CNhs10496 DRZ001288 DRZ002671
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

CNhs10496

00
10
100
1000
10000.0155
1001-0.0353
1002-0.0179
1003-0.113
10040
10050.192
1006-0.0408
1007-0.0218
10082.207
1009-0.19
101-0.047
10100
1011-0.298
10120
10130.282
1014-0.0851
1015-0.267
1016-0.495
10170
10180.494
10190
1020
10200
10210
1022-0.0115
10230
1024-0.288
10250.313
10260
1027-0.048
10280
10290.386
103-0.0659
10300
1031-0.418
10320.577
10330.00318
10340
10350
1036-0.176
10370
1038-0.0125
1039-0.139
1040
1040-0.325
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: CNhs10496

Jaspar motifP-value
MA0002.23.79891e-4
MA0003.10.176
MA0004.10.938
MA0006.10.0599
MA0007.10.402
MA0009.10.155
MA0014.10.466
MA0017.11.62093e-34
MA0018.20.138
MA0019.10.192
MA0024.10.0501
MA0025.10.648
MA0027.10.418
MA0028.10.37
MA0029.10.621
MA0030.10.704
MA0031.10.807
MA0035.23.75995e-6
MA0038.10.967
MA0039.20.00175
MA0040.10.152
MA0041.10.238
MA0042.10.326
MA0043.10.0166
MA0046.11.66693e-41
MA0047.20.0138
MA0048.10.56
MA0050.11.06481e-6
MA0051.12.43281e-6
MA0052.19.53432e-4
MA0055.10.997
MA0057.10.0541
MA0058.10.733
MA0059.10.982
MA0060.10.101
MA0061.10.512
MA0062.20.102
MA0065.24.49523e-18
MA0066.10.2
MA0067.10.35
MA0068.10.0296
MA0069.10.375
MA0070.10.0191
MA0071.10.146
MA0072.10.539
MA0073.10.922
MA0074.10.104
MA0076.10.758
MA0077.10.878
MA0078.10.932
MA0079.20.372
MA0080.26.00372e-5
MA0081.10.573
MA0083.10.593
MA0084.10.763
MA0087.10.867
MA0088.10.139
MA0090.10.721
MA0091.10.489
MA0092.10.601
MA0093.10.837
MA0099.24.11847e-5
MA0100.10.283
MA0101.10.899
MA0102.20.458
MA0103.16.53781e-6
MA0104.20.29
MA0105.10.374
MA0106.10.617
MA0107.10.96
MA0108.20.466
MA0111.10.887
MA0112.28.26733e-5
MA0113.10.524
MA0114.16.5817e-36
MA0115.11.24654e-19
MA0116.10.253
MA0117.10.761
MA0119.10.0318
MA0122.10.867
MA0124.10.413
MA0125.10.554
MA0131.10.56
MA0135.10.448
MA0136.12.51448e-6
MA0137.20.108
MA0138.20.468
MA0139.10.0605
MA0140.10.0102
MA0141.18.11301e-7
MA0142.10.326
MA0143.10.0879
MA0144.10.0295
MA0145.10.00481
MA0146.10.19
MA0147.10.354
MA0148.10.00282
MA0149.10.00783
MA0150.10.115
MA0152.10.0619
MA0153.11.28782e-41
MA0154.10.0422
MA0155.10.8
MA0156.14.04664e-4
MA0157.10.679
MA0159.16.31063e-4
MA0160.14.08454e-5
MA0162.10.283
MA0163.10.122
MA0164.10.887
MA0258.10.00781
MA0259.10.477



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: CNhs10496

Novel motifP-value
10.137
100.156
1000.946
1010.895
1020.781
1030.284
1040.77
1050.24
1060.0424
1070.0915
1080.638
1090.0432
110.193
1100.19
1110.0472
1120.0218
1130.581
1140.0658
1150.558
1160.147
1170.125
1180.554
1190.0675
120.832
1200.597
1210.518
1220.667
1230.353
1240.267
1250.362
1260.0634
1270.143
1280.12
1290.198
136.41804e-4
1300.579
1310.694
1320.314
1330.776
1340.92
1350.711
1360.113
1370.927
1380.777
1390.037
140.703
1400.689
1410.175
1420.846
1430.191
1440.335
1450.0897
1460.211
1470.892
1480.54
1490.681
150.109
1500.36
1510.487
1520.0694
1530.796
1540.87
1550.565
1560.045
1570.613
1580.672
1590.531
1600.545
1610.515
1620.879
1630.229
1640.174
1650.898
1660.895
1670.88
1680.598
1690.00965
170.0583
180.958
190.162
20.351
200.858
210.917
220.296
230.28
240.65
250.419
260.00389
270.722
280.489
290.193
30.169
300.364
310.744
320.12
330.151
340.747
350.522
360.606
370.0472
380.285
390.189
40.44
400.19
410.942
420.448
430.296
440.0664
450.303
460.25
470.276
480.198
490.229
50.418
500.504
510.618
520.121
530.973
540.529
550.776
560.511
570.886
580.316
590.107
60.512
600.044
610.306
620.233
630.116
640.619
650.187
660.89
670.276
680.151
690.956
70.0382
700.0211
710.0719
720.36
730.0827
740.991
750.0641
760.902
770.0887
780.0525
790.855
80.191
800.515
810.746
820.133
830.175
840.134
850.0446
860.158
870.138
880.436
890.4
90.693
900.0849
910.397
920.225
930.0878
940.879
950.162
960.867
970.782
980.541
990.0846



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: CNhs10496


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)
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)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011285 (mouse intestine- 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:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)

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