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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;11848
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11848
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;11848
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11848
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%2520enterocyte%252c%2520pool1.CNhs13542.11848-124I3.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%2520enterocyte%252c%2520pool1.CNhs13542.11848-124I3.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%2520enterocyte%252c%2520pool1.CNhs13542.11848-124I3.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD326%252b%2520enterocyte%252c%2520pool1.CNhs13542.11848-124I3.mm10.nobarcode.ctss.bed.gz

Revision as of 17:13, 4 August 2017


Name:CD326+ enterocyte, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs13542
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 numberCont_Ep+_a
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005789
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13542 CAGE DRX008787 DRR009659
Accession ID Mm9

Library idBAMCTSS
CNhs13542 DRZ001084 DRZ002469
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

CNhs13542

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.175
10040
10050.115
1006-0.395
10070.128
10081.174
1009-0.19
101-0.503
10100
1011-0.337
10120
10130.301
1014-0.0874
1015-0.555
1016-0.564
10170
10180.605
10190
1020
10200
10210.205
10220
10230
1024-0.307
10250
10260
1027-0.048
10280
1029-0.0989
103-0.0887
10300
1031-1.033
10320.767
10330.205
10340
10350
1036-0.00185
10370
10380.403
1039-0.177
1040
1040-0.567
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: CNhs13542

Jaspar motifP-value
MA0002.20.0196
MA0003.10.586
MA0004.10.766
MA0006.10.0307
MA0007.10.181
MA0009.10.0899
MA0014.10.0675
MA0017.18.69498e-42
MA0018.20.0201
MA0019.10.0853
MA0024.15.02691e-5
MA0025.10.266
MA0027.10.193
MA0028.10.171
MA0029.10.681
MA0030.10.167
MA0031.10.0331
MA0035.29.11225e-7
MA0038.10.409
MA0039.21.04471e-4
MA0040.10.0721
MA0041.10.138
MA0042.10.15
MA0043.10.456
MA0046.11.54514e-49
MA0047.20.0237
MA0048.10.179
MA0050.15.22759e-4
MA0051.12.93592e-6
MA0052.10.567
MA0055.10.236
MA0057.10.1
MA0058.10.729
MA0059.10.405
MA0060.10.881
MA0061.10.973
MA0062.20.00438
MA0065.23.63821e-19
MA0066.10.242
MA0067.10.315
MA0068.10.0446
MA0069.10.673
MA0070.10.275
MA0071.10.00306
MA0072.10.163
MA0073.10.625
MA0074.10.165
MA0076.10.173
MA0077.10.592
MA0078.10.823
MA0079.20.189
MA0080.20.0241
MA0081.10.625
MA0083.10.741
MA0084.10.233
MA0087.10.543
MA0088.10.67
MA0090.10.884
MA0091.10.0514
MA0092.10.998
MA0093.10.816
MA0099.27.13174e-7
MA0100.10.704
MA0101.10.418
MA0102.20.914
MA0103.11.34547e-6
MA0104.20.0323
MA0105.10.11
MA0106.10.834
MA0107.10.587
MA0108.20.159
MA0111.10.759
MA0112.20.0222
MA0113.10.507
MA0114.11.14884e-57
MA0115.11.23856e-18
MA0116.10.119
MA0117.10.113
MA0119.10.0818
MA0122.10.763
MA0124.10.485
MA0125.10.794
MA0131.10.94
MA0135.10.0381
MA0136.14.54542e-4
MA0137.20.555
MA0138.20.777
MA0139.10.557
MA0140.10.0159
MA0141.11.01921e-10
MA0142.10.0271
MA0143.10.0677
MA0144.10.054
MA0145.10.0131
MA0146.10.0718
MA0147.10.0283
MA0148.10.0212
MA0149.10.0242
MA0150.10.0349
MA0152.10.0623
MA0153.17.01368e-42
MA0154.10.44
MA0155.10.43
MA0156.10.00669
MA0157.10.501
MA0159.15.07436e-4
MA0160.11.27352e-7
MA0162.10.469
MA0163.10.611
MA0164.10.708
MA0258.10.0616
MA0259.10.617



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: CNhs13542

Novel motifP-value
10.264
100.433
1000.649
1010.9
1020.646
1030.833
1040.735
1050.371
1060.12
1070.435
1080.447
1090.347
110.259
1100.505
1110.0838
1120.0401
1130.185
1140.0609
1150.724
1160.334
1170.0417
1180.556
1190.245
120.701
1200.777
1210.439
1220.941
1230.0691
1240.102
1250.45
1260.0647
1270.486
1280.256
1290.511
138.34769e-6
1300.569
1310.974
1320.42
1330.224
1340.895
1350.0702
1360.00809
1370.402
1380.234
1390.211
140.685
1400.758
1410.687
1420.504
1430.143
1440.309
1450.461
1460.482
1470.795
1480.959
1490.436
150.221
1500.369
1510.828
1520.0671
1530.574
1540.587
1550.57
1560.199
1570.414
1580.259
1590.79
1600.45
1610.857
1620.793
1630.0879
1640.234
1650.92
1660.451
1670.852
1680.681
1690.201
170.115
180.628
190.702
20.834
200.205
210.75
220.304
230.195
240.984
250.242
260.0473
270.732
280.234
290.378
30.311
300.304
310.965
320.509
330.248
340.816
350.756
360.678
370.0248
380.675
390.58
40.367
400.278
410.257
420.749
430.665
440.536
450.365
460.613
470.86
480.55
490.364
50.849
500.706
510.852
520.171
530.327
540.388
550.31
560.717
570.571
580.338
590.518
60.966
600.0404
610.476
620.257
630.356
640.996
650.426
660.78
670.147
680.0242
690.839
70.0209
700.00975
710.436
720.697
730.0187
740.494
750.0463
760.756
770.0932
780.0119
790.928
80.941
800.688
810.9
820.142
830.738
840.0183
850.0985
860.0645
870.0101
880.166
890.679
90.725
900.807
910.475
920.762
930.164
940.29
950.0732
960.808
970.844
980.957
990.618



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: CNhs13542


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)
0011149 (mouse CD326-positive enterocyte 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
CL:0000223 (endodermal cell)

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