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|library_id=CNhs13210
|library_id=CNhs13210
|library_id_phase_based=2:CNhs13210
|library_id_phase_based=2:CNhs13210
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;11853
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;11853
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool2.CNhs13210.11853-124I8.mm10.nobarcode.bam  
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool2.CNhs13210.11853-124I8.mm10.nobarcode.bam  
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool2.CNhs13210.11853-124I8.mm10.nobarcode.ctss.bed.gz  
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%252b%2520enterocyte%2520isolated%2520from%2520mice%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool2.CNhs13210.11853-124I8.mm10.nobarcode.ctss.bed.gz  

Revision as of 21:37, 18 May 2017


Name:CD326++ enterocyte isolated from mice, treated with RANKL, day03, pool2
Species:Mouse (Mus musculus)
Library ID:CNhs13210
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_b
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005805
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13210 CAGE DRX008789 DRR009661
Accession ID Mm9

Library idBAMCTSS
CNhs13210 DRZ001086 DRZ002471
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

CNhs13210

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.156
10040
10051.167
1006-0.344
10070.0296
10082.264
1009-0.19
101-0.0219
10100
1011-0.337
10120
10130.238
1014-0.0874
1015-0.206
1016-0.378
10170
10180.606
10190
1020
10200
10210.409
1022-0.0704
10230
1024-0.18
10250
10260
1027-0.048
10280
1029-0.0989
103-0.0861
10300
1031-1.026
10320.577
10330.0913
10340
10350
1036-0.0104
10370
10380.0677
1039-0.0327
1040
1040-0.564
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: CNhs13210

Jaspar motifP-value
MA0002.20.103
MA0003.10.287
MA0004.10.517
MA0006.10.0969
MA0007.10.323
MA0009.10.0895
MA0014.10.0378
MA0017.13.36802e-23
MA0018.20.02
MA0019.10.186
MA0024.10.754
MA0025.10.695
MA0027.10.49
MA0028.10.00977
MA0029.10.91
MA0030.10.653
MA0031.10.452
MA0035.21.17015e-5
MA0038.10.495
MA0039.25.8337e-6
MA0040.10.274
MA0041.10.192
MA0042.10.286
MA0043.10.129
MA0046.14.26875e-45
MA0047.20.00168
MA0048.10.141
MA0050.10.00262
MA0051.11.12068e-4
MA0052.10.181
MA0055.10.0496
MA0057.10.0624
MA0058.10.601
MA0059.10.409
MA0060.10.228
MA0061.17.7545e-5
MA0062.21.55812e-5
MA0065.23.52239e-12
MA0066.10.398
MA0067.10.583
MA0068.10.194
MA0069.10.686
MA0070.10.121
MA0071.10.1
MA0072.10.491
MA0073.10.778
MA0074.10.527
MA0076.10.0574
MA0077.10.196
MA0078.10.393
MA0079.20.658
MA0080.22.58896e-5
MA0081.10.75
MA0083.10.76
MA0084.10.305
MA0087.10.263
MA0088.10.243
MA0090.10.678
MA0091.10.718
MA0092.10.832
MA0093.10.577
MA0099.26.51633e-8
MA0100.10.691
MA0101.13.36269e-8
MA0102.20.435
MA0103.18.97431e-9
MA0104.20.972
MA0105.10.0527
MA0106.10.198
MA0107.15.19768e-8
MA0108.23.08393e-5
MA0111.10.508
MA0112.20.0461
MA0113.10.816
MA0114.11.65353e-27
MA0115.17.85144e-12
MA0116.10.341
MA0117.10.441
MA0119.10.281
MA0122.10.964
MA0124.10.42
MA0125.10.856
MA0131.10.867
MA0135.10.167
MA0136.17.90358e-10
MA0137.20.00324
MA0138.20.729
MA0139.10.224
MA0140.10.103
MA0141.13.38426e-5
MA0142.10.139
MA0143.10.0514
MA0144.15.37654e-4
MA0145.10.0302
MA0146.10.222
MA0147.10.781
MA0148.10.00129
MA0149.10.0162
MA0150.10.0488
MA0152.10.057
MA0153.11.58466e-35
MA0154.10.174
MA0155.10.555
MA0156.11.73224e-5
MA0157.10.799
MA0159.11.23679e-4
MA0160.11.53059e-4
MA0162.10.913
MA0163.10.36
MA0164.10.565
MA0258.10.186
MA0259.10.976



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: CNhs13210

Novel motifP-value
10.239
100.186
1000.627
1010.552
1020.977
1030.91
1040.942
1050.408
1060.0116
1070.151
1080.543
1090.0423
110.219
1100.433
1110.271
1120.0515
1130.0875
1140.311
1150.821
1160.0962
1170.0151
1180.707
1190.208
120.341
1200.487
1210.247
1220.907
1230.0673
1240.0829
1250.296
1260.00505
1270.277
1280.143
1290.407
131.17612e-5
1300.864
1310.581
1320.808
1330.627
1340.706
1350.0305
1367.02375e-4
1370.501
1380.541
1390.523
140.877
1400.857
1410.312
1420.486
1430.292
1440.056
1450.0622
1460.265
1470.907
1480.804
1490.514
150.259
1500.422
1510.716
1520.0167
1530.462
1540.855
1550.461
1560.0539
1570.359
1580.813
1590.685
1600.575
1610.668
1620.596
1630.251
1640.0998
1650.193
1660.522
1670.494
1680.422
1690.0849
170.0428
180.695
190.564
20.823
200.261
210.61
220.537
230.995
240.494
250.388
260.00505
270.802
280.567
290.0376
30.292
300.463
310.726
320.555
330.207
340.787
350.945
360.365
370.0575
380.714
390.483
40.152
400.124
410.159
420.746
430.639
440.246
450.525
460.339
470.615
480.316
490.898
50.9
500.656
510.897
520.177
530.332
540.618
550.838
560.566
570.871
580.39
590.476
60.927
600.0313
610.252
620.329
630.218
640.915
650.508
660.578
670.635
680.13
690.964
70.0664
700.0204
710.115
720.411
730.012
740.206
750.0129
760.643
770.0533
780.0575
791
80.267
800.663
810.632
820.449
830.842
840.149
850.224
860.102
870.00129
880.186
890.43
90.837
900.24
910.824
920.918
930.143
940.735
950.00553
960.854
970.724
980.664
990.47



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: CNhs13210


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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