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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;11852
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11852
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;11852
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11852
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool1.CNhs13236.11852-124I7.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool1.CNhs13236.11852-124I7.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool1.CNhs13236.11852-124I7.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool1.CNhs13236.11852-124I7.mm10.nobarcode.ctss.bed.gz

Revision as of 17:14, 4 August 2017


Name:CD326++ enterocyte isolated from mice, treated with RANKL, day03, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs13236
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainBalb/c
tissueileum
dev stageadult
sexmale
ageNA
cell typeenterocyte
cell lineNA
companyNA
collaborationShinji Fukuda (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRANKL_Ephigh_a
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004708
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13236 CAGE DRX008764 DRR009636
Accession ID Mm9

Library idBAMCTSS
CNhs13236 DRZ001061 DRZ002446
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

CNhs13236

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.175
10040
10051.1
1006-0.19
10070.182
10081.638
1009-0.19
101-0.0436
10100
1011-0.337
10120
10130.266
1014-0.0874
1015-0.166
1016-0.465
10170
10180.4
10190
1020
10200
10210
1022-0.0704
10230
1024-0.14
10250
10260
1027-0.048
10280
1029-0.148
103-0.0887
10300
1031-1.067
10320.661
10330.102
10340
10350
10360.0598
10370
10380.081
10390.0257
1040
1040-0.603
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: CNhs13236

Jaspar motifP-value
MA0002.20.0696
MA0003.10.476
MA0004.10.371
MA0006.10.0724
MA0007.10.216
MA0009.10.121
MA0014.10.0335
MA0017.19.16996e-22
MA0018.28.37433e-5
MA0019.10.0842
MA0024.10.999
MA0025.10.173
MA0027.10.403
MA0028.15.86277e-4
MA0029.10.966
MA0030.10.224
MA0031.10.217
MA0035.28.46445e-6
MA0038.10.944
MA0039.21.06561e-5
MA0040.10.145
MA0041.10.181
MA0042.10.272
MA0043.10.00349
MA0046.11.20228e-54
MA0047.21.00082e-4
MA0048.10.121
MA0050.10.00466
MA0051.14.56543e-5
MA0052.10.765
MA0055.10.0254
MA0057.10.0557
MA0058.10.444
MA0059.10.855
MA0060.10.00361
MA0061.19.78695e-5
MA0062.21.74093e-9
MA0065.21.54978e-10
MA0066.10.468
MA0067.10.317
MA0068.10.219
MA0069.10.755
MA0070.10.362
MA0071.10.126
MA0072.10.787
MA0073.10.998
MA0074.10.478
MA0076.10.00483
MA0077.10.0813
MA0078.10.396
MA0079.20.1
MA0080.24.43844e-6
MA0081.10.431
MA0083.10.752
MA0084.10.197
MA0087.10.257
MA0088.10.545
MA0090.10.439
MA0091.10.393
MA0092.10.68
MA0093.10.406
MA0099.21.80478e-9
MA0100.10.626
MA0101.12.25768e-10
MA0102.20.98
MA0103.19.5557e-9
MA0104.20.75
MA0105.10.713
MA0106.10.586
MA0107.14.803e-9
MA0108.23.04079e-6
MA0111.10.261
MA0112.20.507
MA0113.10.567
MA0114.19.30992e-32
MA0115.11.39109e-11
MA0116.10.517
MA0117.10.228
MA0119.10.522
MA0122.10.677
MA0124.10.482
MA0125.10.758
MA0131.10.77
MA0135.10.0987
MA0136.12.87744e-11
MA0137.20.00646
MA0138.20.298
MA0139.10.592
MA0140.10.263
MA0141.12.47823e-4
MA0142.10.0696
MA0143.10.0454
MA0144.15.94089e-4
MA0145.10.0303
MA0146.10.0826
MA0147.10.891
MA0148.16.30158e-4
MA0149.10.0333
MA0150.10.0189
MA0152.10.192
MA0153.16.99264e-35
MA0154.10.66
MA0155.10.372
MA0156.12.9341e-7
MA0157.10.931
MA0159.10.00102
MA0160.11.01971e-4
MA0162.10.619
MA0163.10.342
MA0164.10.842
MA0258.10.701
MA0259.10.997



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: CNhs13236

Novel motifP-value
10.485
100.546
1000.82
1010.45
1020.882
1030.5
1040.992
1050.205
1060.00365
1070.132
1080.566
1090.0631
110.357
1100.729
1110.598
1120.0759
1130.0584
1140.965
1150.675
1160.357
1170.0189
1180.866
1190.289
120.691
1200.547
1210.142
1220.984
1230.0339
1240.0146
1250.512
1260.00707
1270.216
1280.185
1290.462
131.08586e-5
1300.629
1310.625
1320.784
1330.477
1340.954
1350.0616
1362.79329e-4
1370.739
1380.316
1390.524
140.89
1400.665
1410.804
1420.652
1430.0602
1440.0259
1450.226
1460.25
1470.814
1480.882
1490.431
150.353
1500.497
1510.437
1520.0052
1530.345
1540.558
1550.658
1560.0522
1570.348
1580.43
1590.884
1600.2
1610.798
1620.624
1630.143
1640.247
1650.289
1660.407
1670.942
1680.692
1690.225
170.0579
180.379
190.832
20.863
200.238
210.577
220.497
230.856
240.636
250.548
260.0271
270.751
280.403
290.106
30.59
300.327
310.558
320.916
330.252
340.849
350.773
360.894
370.0808
380.655
390.543
40.194
400.257
410.146
420.804
430.96
440.554
450.298
460.656
470.796
480.414
490.726
50.783
500.557
510.909
520.138
530.362
540.587
550.609
560.786
570.406
580.512
590.632
60.966
600.0317
610.326
620.47
630.257
640.927
650.547
660.514
670.394
680.331
690.473
70.088
700.135
710.684
720.347
730.00457
740.351
750.0246
760.941
770.0632
780.0413
790.645
80.765
800.886
810.463
820.765
830.944
840.0798
850.406
860.133
873.85332e-4
880.202
890.606
90.809
900.992
910.35
920.489
930.142
940.503
956.11299e-5
960.828
970.754
980.775
990.91



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: CNhs13236


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000075 (columnar/cuboidal epithelial cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002563 (intestinal epithelial cell)
0000255 (eukaryotic cell)
0000239 (brush border epithelial cell)
0000677 (gut absorptive cell)
0000212 (absorptive cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)
0000584 (enterocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000160 (intestine)
0000483 (epithelium)
0001242 (intestinal mucosa)
0000479 (tissue)
0001007 (digestive system)
0000344 (mucosa)
0000064 (organ part)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0005911 (endo-epithelium)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0001262 (wall of intestine)
0004786 (gastrointestinal system mucosa)
0000485 (simple columnar epithelium)
0003350 (epithelium of mucosa)
0003929 (gut epithelium)
0004808 (gastrointestinal system epithelium)
0001277 (intestinal epithelium)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000383 (3 days sample)
0000627 (RANK ligand treatment sample)
0011445 (CD326-positive+ enterocyte isolated from mice- treated with RANKL- day03)

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
CL:0000223 (endodermal cell)

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