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|library_id=CNhs13234
|library_id=CNhs13234
|library_id_phase_based=2:CNhs13234
|library_id_phase_based=2:CNhs13234
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.LQhCAGE/Ileum%2520epithelium%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool3.CNhs13234.10260-104C8.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.LQhCAGE/Ileum%2520epithelium%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool3.CNhs13234.10260-104C8.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.LQhCAGE/Ileum%2520epithelium%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool3.CNhs13234.10260-104C8.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.LQhCAGE/Ileum%2520epithelium%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool3.CNhs13234.10260-104C8.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.LQhCAGE/Ileum%2520epithelium%252c%2520treated%2520with%2520RANKL%252c%2520day03%252c%2520pool3.CNhs13234.10260-104C8.mm9.nobarcode.rdna.fa.gz
|name=Ileum epithelium, treated with RANKL, day03, pool3
|name=Ileum epithelium, treated with RANKL, day03, pool3
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 14:12, 17 May 2017


Name:Ileum epithelium, treated with RANKL, day03, pool3
Species:Mouse (Mus musculus)
Library ID:CNhs13234
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainBalb/c
tissueileum
dev stageNA
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationShinji Fukuda (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberR-3day_ileum_c
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005036
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13234 CAGE DRX008919 DRR009793
Accession ID Mm9

Library idBAMCTSS
CNhs13234 DRZ001218 DRZ002601
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

CNhs13234

00
10
100
1000
1000-0.0355
1001-0.0631
1002-0.116
1003-0.175
10040
10051.103
1006-0.292
1007-0.0978
10081.695
1009-0.2
101-0.0744
10100
1011-0.298
10120
10130.46
1014-0.0874
1015-0.278
1016-0.479
10170
10180.658
10190
1020
10200
10210
1022-0.0395
10230
1024-0.237
1025-0.0611
10260
1027-0.048
10280
1029-0.0606
103-0.0887
10300
1031-0.685
10320.797
10330.087
10340
10350
10360.171
10370
1038-0.136
1039-0.0243
1040.087
1040-0.617
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: CNhs13234

Jaspar motifP-value
MA0002.20.0045
MA0003.10.2
MA0004.10.639
MA0006.10.134
MA0007.10.212
MA0009.10.128
MA0014.10.136
MA0017.16.60303e-17
MA0018.20.56
MA0019.10.231
MA0024.10.236
MA0025.10.167
MA0027.10.941
MA0028.10.00175
MA0029.10.509
MA0030.10.773
MA0031.10.65
MA0035.20.0027
MA0038.10.739
MA0039.28.73542e-5
MA0040.10.0344
MA0041.10.361
MA0042.10.561
MA0043.10.543
MA0046.17.58674e-43
MA0047.20.0317
MA0048.10.301
MA0050.15.57877e-5
MA0051.16.54702e-5
MA0052.10.00375
MA0055.10.0983
MA0057.10.0628
MA0058.10.648
MA0059.10.445
MA0060.10.312
MA0061.10.0121
MA0062.27.38546e-8
MA0065.24.39535e-10
MA0066.10.0786
MA0067.10.649
MA0068.10.19
MA0069.10.761
MA0070.10.0621
MA0071.10.211
MA0072.10.979
MA0073.10.761
MA0074.10.394
MA0076.10.0063
MA0077.10.88
MA0078.10.734
MA0079.20.629
MA0080.21.6297e-8
MA0081.10.283
MA0083.10.00551
MA0084.10.457
MA0087.10.329
MA0088.10.0978
MA0090.10.93
MA0091.10.865
MA0092.10.734
MA0093.10.682
MA0099.25.91584e-10
MA0100.10.778
MA0101.13.93515e-4
MA0102.20.625
MA0103.12.23412e-7
MA0104.20.793
MA0105.10.0353
MA0106.10.218
MA0107.18.76946e-4
MA0108.20.1
MA0111.10.737
MA0112.29.89002e-4
MA0113.10.245
MA0114.17.79195e-18
MA0115.11.05904e-11
MA0116.10.0563
MA0117.10.469
MA0119.10.243
MA0122.10.989
MA0124.10.175
MA0125.10.484
MA0131.10.967
MA0135.10.834
MA0136.15.5859e-17
MA0137.22.21405e-4
MA0138.20.592
MA0139.10.0804
MA0140.10.259
MA0141.14.36769e-5
MA0142.10.172
MA0143.10.0931
MA0144.15.02537e-4
MA0145.10.0173
MA0146.10.143
MA0147.10.905
MA0148.10.0257
MA0149.10.00644
MA0150.10.0095
MA0152.10.106
MA0153.16.55911e-35
MA0154.10.0582
MA0155.10.761
MA0156.11.36516e-9
MA0157.10.35
MA0159.15.07153e-4
MA0160.10.00211
MA0162.10.354
MA0163.10.0531
MA0164.10.575
MA0258.10.0414
MA0259.10.837



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: CNhs13234

Novel motifP-value
10.0983
100.0873
1000.719
1010.976
1020.94
1030.296
1040.98
1050.282
1060.03
1070.277
1080.899
1090.0148
110.0958
1100.178
1110.162
1120.0199
1130.328
1140.23
1150.875
1160.131
1170.0164
1180.683
1190.121
120.624
1200.407
1210.426
1220.827
1230.0671
1240.248
1250.408
1260.046
1270.116
1280.224
1290.12
131.51766e-4
1300.84
1310.743
1320.636
1330.882
1340.95
1350.223
1360.0141
1370.884
1380.233
1390.0907
140.702
1400.241
1410.109
1420.828
1430.698
1440.126
1450.0878
1460.242
1470.773
1480.482
1490.688
150.117
1500.438
1510.842
1520.0491
1530.865
1540.918
1550.25
1560.114
1570.491
1580.629
1590.658
1600.822
1610.55
1620.71
1630.233
1640.0661
1650.0375
1660.371
1670.563
1680.824
1690.0195
170.0296
180.897
190.308
20.933
200.297
210.945
220.333
230.913
240.31
250.475
260.00604
270.887
280.341
290.0494
30.116
300.576
310.933
320.214
330.164
340.848
350.754
360.19
370.0426
380.383
390.284
40.329
400.101
410.212
420.616
430.296
440.127
450.494
460.236
470.238
480.12
490.309
50.59
500.371
510.732
520.211
530.527
540.606
550.653
560.434
570.892
580.312
590.187
60.399
600.0548
610.171
620.222
630.0997
640.567
650.255
660.908
670.595
680.112
690.939
70.0874
700.00497
710.0766
720.211
730.0294
740.879
750.0181
760.633
770.105
780.0332
790.983
80.132
800.873
810.922
820.161
830.045
840.522
850.106
860.193
870.00873
880.258
890.122
90.927
900.0775
910.916
920.573
930.297
940.697
950.00416
960.621
970.977
980.458
990.198



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: CNhs13234


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)
0002108 (small intestine)
0000160 (intestine)
0000331 (ileal mucosa)
0000483 (epithelium)
0002116 (ileum)
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)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0001204 (mucosa of small intestine)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0001262 (wall of intestine)
0004786 (gastrointestinal system mucosa)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)
0001168 (wall of small intestine)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0000383 (3 days sample)
0000627 (RANK ligand treatment sample)
0011478 (mouse Ileum epithelium 3days after RANKL 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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