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FF:10260-104C8

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Name:Ileum epithelium, treated with RANKL, day03, pool3
Species:Mouse (Mus musculus)
Library ID:CNhs13234
Sample type:tissues
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
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

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
Accession ID Mm10

Library idBAMCTSS
CNhs13234 DRZ012568 DRZ013951
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.
Analyst:NA

link to dataset.
data

CNhs13234

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0631
1002 --0.116
1003 --0.175
1004 0
1005 1.103
1006 --0.292
1007 --0.0978
1008 1.695
1009 --0.2
101 --0.0744
1010 0
1011 --0.298
1012 0
1013 0.46
1014 --0.0874
1015 --0.278
1016 --0.479
1017 0
1018 0.658
1019 0
102 0
1020 0
1021 0
1022 --0.0395
1023 0
1024 --0.237
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.0606
103 --0.0887
1030 0
1031 --0.685
1032 0.797
1033 0.087
1034 0
1035 0
1036 0.171
1037 0
1038 --0.136
1039 --0.0243
104 0.087
1040 --0.617
1041 0



Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs13234

Jaspar motif P-value
MA0002.2 0.0045
MA0003.1 0.2
MA0004.1 0.639
MA0006.1 0.134
MA0007.1 0.212
MA0009.1 0.128
MA0014.1 0.136
MA0017.1 6.60303e-17
MA0018.2 0.56
MA0019.1 0.231
MA0024.1 0.236
MA0025.1 0.167
MA0027.1 0.941
MA0028.1 0.00175
MA0029.1 0.509
MA0030.1 0.773
MA0031.1 0.65
MA0035.2 0.0027
MA0038.1 0.739
MA0039.2 8.73542e-5
MA0040.1 0.0344
MA0041.1 0.361
MA0042.1 0.561
MA0043.1 0.543
MA0046.1 7.58674e-43
MA0047.2 0.0317
MA0048.1 0.301
MA0050.1 5.57877e-5
MA0051.1 6.54702e-5
MA0052.1 0.00375
MA0055.1 0.0983
MA0057.1 0.0628
MA0058.1 0.648
MA0059.1 0.445
MA0060.1 0.312
MA0061.1 0.0121
MA0062.2 7.38546e-8
MA0065.2 4.39535e-10
MA0066.1 0.0786
MA0067.1 0.649
MA0068.1 0.19
MA0069.1 0.761
MA0070.1 0.0621
MA0071.1 0.211
MA0072.1 0.979
MA0073.1 0.761
MA0074.1 0.394
MA0076.1 0.0063
MA0077.1 0.88
MA0078.1 0.734
MA0079.2 0.629
MA0080.2 1.6297e-8
MA0081.1 0.283
MA0083.1 0.00551
MA0084.1 0.457
MA0087.1 0.329
MA0088.1 0.0978
MA0090.1 0.93
MA0091.1 0.865
MA0092.1 0.734
MA0093.1 0.682
MA0099.2 5.91584e-10
MA0100.1 0.778
MA0101.1 3.93515e-4
MA0102.2 0.625
MA0103.1 2.23412e-7
MA0104.2 0.793
MA0105.1 0.0353
MA0106.1 0.218
MA0107.1 8.76946e-4
MA0108.2 0.1
MA0111.1 0.737
MA0112.2 9.89002e-4
MA0113.1 0.245
MA0114.1 7.79195e-18
MA0115.1 1.05904e-11
MA0116.1 0.0563
MA0117.1 0.469
MA0119.1 0.243
MA0122.1 0.989
MA0124.1 0.175
MA0125.1 0.484
MA0131.1 0.967
MA0135.1 0.834
MA0136.1 5.5859e-17
MA0137.2 2.21405e-4
MA0138.2 0.592
MA0139.1 0.0804
MA0140.1 0.259
MA0141.1 4.36769e-5
MA0142.1 0.172
MA0143.1 0.0931
MA0144.1 5.02537e-4
MA0145.1 0.0173
MA0146.1 0.143
MA0147.1 0.905
MA0148.1 0.0257
MA0149.1 0.00644
MA0150.1 0.0095
MA0152.1 0.106
MA0153.1 6.55911e-35
MA0154.1 0.0582
MA0155.1 0.761
MA0156.1 1.36516e-9
MA0157.1 0.35
MA0159.1 5.07153e-4
MA0160.1 0.00211
MA0162.1 0.354
MA0163.1 0.0531
MA0164.1 0.575
MA0258.1 0.0414
MA0259.1 0.837



FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs13234

Novel motif P-value
1 0.0983
10 0.0873
100 0.719
101 0.976
102 0.94
103 0.296
104 0.98
105 0.282
106 0.03
107 0.277
108 0.899
109 0.0148
11 0.0958
110 0.178
111 0.162
112 0.0199
113 0.328
114 0.23
115 0.875
116 0.131
117 0.0164
118 0.683
119 0.121
12 0.624
120 0.407
121 0.426
122 0.827
123 0.0671
124 0.248
125 0.408
126 0.046
127 0.116
128 0.224
129 0.12
13 1.51766e-4
130 0.84
131 0.743
132 0.636
133 0.882
134 0.95
135 0.223
136 0.0141
137 0.884
138 0.233
139 0.0907
14 0.702
140 0.241
141 0.109
142 0.828
143 0.698
144 0.126
145 0.0878
146 0.242
147 0.773
148 0.482
149 0.688
15 0.117
150 0.438
151 0.842
152 0.0491
153 0.865
154 0.918
155 0.25
156 0.114
157 0.491
158 0.629
159 0.658
160 0.822
161 0.55
162 0.71
163 0.233
164 0.0661
165 0.0375
166 0.371
167 0.563
168 0.824
169 0.0195
17 0.0296
18 0.897
19 0.308
2 0.933
20 0.297
21 0.945
22 0.333
23 0.913
24 0.31
25 0.475
26 0.00604
27 0.887
28 0.341
29 0.0494
3 0.116
30 0.576
31 0.933
32 0.214
33 0.164
34 0.848
35 0.754
36 0.19
37 0.0426
38 0.383
39 0.284
4 0.329
40 0.101
41 0.212
42 0.616
43 0.296
44 0.127
45 0.494
46 0.236
47 0.238
48 0.12
49 0.309
5 0.59
50 0.371
51 0.732
52 0.211
53 0.527
54 0.606
55 0.653
56 0.434
57 0.892
58 0.312
59 0.187
6 0.399
60 0.0548
61 0.171
62 0.222
63 0.0997
64 0.567
65 0.255
66 0.908
67 0.595
68 0.112
69 0.939
7 0.0874
70 0.00497
71 0.0766
72 0.211
73 0.0294
74 0.879
75 0.0181
76 0.633
77 0.105
78 0.0332
79 0.983
8 0.132
80 0.873
81 0.922
82 0.161
83 0.045
84 0.522
85 0.106
86 0.193
87 0.00873
88 0.258
89 0.122
9 0.927
90 0.0775
91 0.916
92 0.573
93 0.297
94 0.697
95 0.00416
96 0.621
97 0.977
98 0.458
99 0.198



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs13234


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
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)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)