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FF:11851-124I6

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Name:CD326+ enterocyte isolated from mice, treated with RANKL, day03, pool2
Species:Mouse (Mus musculus)
Library ID:CNhs13233
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :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_Ep+_b
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004692
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13233 CAGE DRX008763 DRR009635
Accession ID Mm9

Library idBAMCTSS
CNhs13233 DRZ001060 DRZ002445
Accession ID Mm10

Library idBAMCTSS
CNhs13233 DRZ012410 DRZ013795
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

CNhs13233

00
10
100
1000
1000-0.0355
1001-0.0631
1002-0.116
1003-0.175
10040
10051.037
1006-0.269
10070.134
10080.893
1009-0.19
101-0.478
10100
1011-0.298
10120
10130.406
1014-0.0874
1015-0.479
1016-0.465
10170
10180.744
10190
1020
10200
10210
1022-0.0704
10230
1024-0.307
10250
10260
1027-0.048
10280
1029-0.176
103-0.0887
10300
1031-0.819
10321.16
10330
10340
10350
1036-0.254
10370
10380.19
1039-0.1
1040
1040-0.687
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: CNhs13233

Jaspar motifP-value
MA0002.20.0209
MA0003.10.462
MA0004.10.994
MA0006.10.0305
MA0007.10.25
MA0009.10.082
MA0014.10.045
MA0017.13.35925e-31
MA0018.20.126
MA0019.10.0332
MA0024.14.64553e-6
MA0025.10.371
MA0027.10.827
MA0028.10.19
MA0029.10.946
MA0030.10.344
MA0031.10.155
MA0035.27.34492e-6
MA0038.10.324
MA0039.21.36521e-5
MA0040.10.0695
MA0041.10.217
MA0042.10.255
MA0043.10.247
MA0046.14.217e-52
MA0047.20.0184
MA0048.10.29
MA0050.11.54369e-4
MA0051.12.14905e-6
MA0052.10.925
MA0055.10.268
MA0057.10.083
MA0058.10.834
MA0059.10.227
MA0060.10.12
MA0061.10.00428
MA0062.28.47813e-4
MA0065.26.45114e-16
MA0066.10.16
MA0067.10.373
MA0068.10.114
MA0069.10.647
MA0070.10.459
MA0071.10.0206
MA0072.10.71
MA0073.10.98
MA0074.10.318
MA0076.10.285
MA0077.10.481
MA0078.10.745
MA0079.20.0715
MA0080.21.02959e-4
MA0081.10.792
MA0083.10.82
MA0084.10.216
MA0087.10.362
MA0088.10.94
MA0090.10.384
MA0091.10.0418
MA0092.10.524
MA0093.10.951
MA0099.21.00415e-13
MA0100.10.589
MA0101.16.29262e-6
MA0102.20.78
MA0103.11.36819e-6
MA0104.20.0238
MA0105.10.723
MA0106.10.592
MA0107.13.08643e-6
MA0108.22.58478e-4
MA0111.10.289
MA0112.20.0193
MA0113.10.952
MA0114.13.87727e-40
MA0115.14.89658e-18
MA0116.10.757
MA0117.10.178
MA0119.10.114
MA0122.10.857
MA0124.10.451
MA0125.10.86
MA0131.10.466
MA0135.10.173
MA0136.12.06075e-7
MA0137.20.0393
MA0138.20.932
MA0139.10.495
MA0140.10.116
MA0141.11.14424e-7
MA0142.10.0246
MA0143.10.0603
MA0144.10.00392
MA0145.10.00589
MA0146.10.0577
MA0147.10.0206
MA0148.10.0282
MA0149.10.0438
MA0150.10.00436
MA0152.10.202
MA0153.13.47036e-40
MA0154.10.0887
MA0155.10.739
MA0156.12.17193e-4
MA0157.10.992
MA0159.10.00187
MA0160.15.94681e-6
MA0162.10.866
MA0163.10.7
MA0164.10.815
MA0258.10.149
MA0259.10.343



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: CNhs13233

Novel motifP-value
10.274
100.596
1000.994
1010.893
1020.894
1030.98
1040.713
1050.0999
1060.0104
1070.162
1080.566
1090.112
110.23
1100.64
1110.132
1120.0421
1130.26
1140.12
1150.634
1160.103
1170.109
1180.544
1190.119
120.663
1200.667
1210.339
1220.689
1230.112
1240.196
1250.585
1260.0971
1270.212
1280.0367
1290.199
135.08485e-5
1300.755
1310.969
1320.453
1330.484
1340.735
1350.151
1360.00725
1370.615
1380.139
1390.468
140.577
1400.806
1410.136
1420.579
1430.126
1440.255
1450.165
1460.241
1470.58
1480.922
1490.945
150.208
1500.269
1510.986
1520.0188
1530.643
1540.546
1550.512
1560.136
1570.399
1580.379
1590.685
1600.498
1610.83
1620.913
1630.0308
1640.268
1650.243
1660.823
1670.908
1680.927
1690.0848
170.0363
180.848
190.358
20.607
200.295
210.938
220.215
230.168
240.894
250.534
260.0436
270.629
280.204
290.367
30.296
300.222
310.821
320.258
330.282
340.856
350.881
360.732
370.0211
380.401
390.462
40.362
400.377
410.16
420.871
430.338
440.28
450.209
460.613
470.8
480.442
490.445
50.907
500.359
510.643
520.096
530.514
540.317
550.374
560.569
570.542
580.309
590.305
60.707
600.0237
610.632
620.326
630.119
640.912
650.324
660.858
670.364
680.0364
690.973
70.0707
700.018
710.476
720.368
730.0103
740.635
750.0572
760.876
770.0488
780.0276
790.804
80.77
800.989
810.768
820.0982
830.712
840.059
850.119
860.144
870.0104
880.203
890.522
90.983
900.774
910.854
920.623
930.248
940.648
950.00832
960.823
970.807
980.671
990.601



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: CNhs13233


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)
0011113 (mouse CD326-positive enterocyte isolated from mice- treated with RANKL- day03 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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