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FF:860-29I3

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Name:intestinal mucosa, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10506
Sample type:developmental
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueintestinal mucosa
dev stageadult
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005876
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10506 CAGE DRX008988 DRR009862
Accession ID Mm9

Library idBAMCTSS
CNhs10506 DRZ001287 DRZ002670
Accession ID Mm10

Library idBAMCTSS
CNhs10506 DRZ012637 DRZ014020
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
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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

CNhs10506

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 0.0102
1002 --0.116
1003 --0.102
1004 0
1005 0.35
1006 --0.143
1007 --0.104
1008 0.798
1009 --0.19
101 --0.375
1010 0
1011 --0.145
1012 0
1013 0.41
1014 0
1015 --0.54
1016 --0.379
1017 0
1018 0.666
1019 0
102 0
1020 0
1021 --0.0487
1022 0.0211
1023 0
1024 --0.307
1025 0
1026 0
1027 --0.048
1028 0
1029 0.483
103 --0.0861
1030 0
1031 --0.972
1032 0.635
1033 --0.0396
1034 0.203
1035 0
1036 --0.436
1037 0
1038 0.0449
1039 --0.0905
104 0
1040 --0.676
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: CNhs10506

Jaspar motif P-value
MA0002.2 4.45167e-4
MA0003.1 0.346
MA0004.1 0.636
MA0006.1 0.0606
MA0007.1 0.384
MA0009.1 0.26
MA0014.1 0.289
MA0017.1 5.6012e-27
MA0018.2 0.166
MA0019.1 0.298
MA0024.1 5.15593e-4
MA0025.1 0.799
MA0027.1 0.263
MA0028.1 0.844
MA0029.1 0.641
MA0030.1 0.618
MA0031.1 0.4
MA0035.2 3.78852e-6
MA0038.1 0.138
MA0039.2 4.247e-4
MA0040.1 0.0444
MA0041.1 0.366
MA0042.1 0.259
MA0043.1 0.0615
MA0046.1 8.27811e-44
MA0047.2 0.00474
MA0048.1 0.583
MA0050.1 8.84252e-8
MA0051.1 6.99028e-7
MA0052.1 8.74771e-4
MA0055.1 0.362
MA0057.1 0.0702
MA0058.1 0.547
MA0059.1 0.753
MA0060.1 3.38685e-5
MA0061.1 0.353
MA0062.2 0.126
MA0065.2 8.00267e-15
MA0066.1 0.0665
MA0067.1 0.537
MA0068.1 0.00666
MA0069.1 0.46
MA0070.1 0.223
MA0071.1 0.127
MA0072.1 0.297
MA0073.1 0.905
MA0074.1 0.135
MA0076.1 0.986
MA0077.1 0.767
MA0078.1 0.674
MA0079.2 0.636
MA0080.2 2.28524e-6
MA0081.1 0.654
MA0083.1 0.034
MA0084.1 0.265
MA0087.1 0.454
MA0088.1 0.469
MA0090.1 0.642
MA0091.1 0.941
MA0092.1 0.428
MA0093.1 0.62
MA0099.2 8.98089e-5
MA0100.1 0.323
MA0101.1 0.715
MA0102.2 0.131
MA0103.1 3.92535e-6
MA0104.2 0.0696
MA0105.1 0.314
MA0106.1 0.839
MA0107.1 0.836
MA0108.2 0.52
MA0111.1 0.847
MA0112.2 1.04135e-5
MA0113.1 0.484
MA0114.1 1.94385e-29
MA0115.1 1.59586e-16
MA0116.1 0.409
MA0117.1 0.454
MA0119.1 0.0174
MA0122.1 0.76
MA0124.1 0.263
MA0125.1 0.742
MA0131.1 0.416
MA0135.1 0.228
MA0136.1 8.45297e-7
MA0137.2 0.381
MA0138.2 0.376
MA0139.1 0.0305
MA0140.1 0.00968
MA0141.1 6.44861e-7
MA0142.1 0.905
MA0143.1 0.15
MA0144.1 0.0597
MA0145.1 0.00322
MA0146.1 0.109
MA0147.1 0.0972
MA0148.1 1.88116e-4
MA0149.1 0.0112
MA0150.1 0.0367
MA0152.1 0.0543
MA0153.1 4.75446e-36
MA0154.1 0.0258
MA0155.1 0.686
MA0156.1 3.55098e-4
MA0157.1 0.95
MA0159.1 3.09495e-4
MA0160.1 9.73291e-4
MA0162.1 0.604
MA0163.1 0.121
MA0164.1 0.907
MA0258.1 9.12915e-4
MA0259.1 0.273



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: CNhs10506

Novel motif P-value
1 0.0831
10 0.133
100 0.872
101 0.845
102 0.893
103 0.116
104 0.899
105 0.258
106 0.0445
107 0.0857
108 0.802
109 0.124
11 0.116
110 0.253
111 0.0159
112 0.0144
113 0.88
114 0.0113
115 0.813
116 0.446
117 0.0883
118 0.383
119 0.0393
12 0.725
120 0.627
121 0.674
122 0.544
123 0.358
124 0.922
125 0.576
126 0.164
127 0.157
128 0.0785
129 0.126
13 0.00276
130 0.744
131 0.42
132 0.599
133 0.66
134 0.911
135 0.536
136 0.277
137 0.518
138 0.318
139 0.0404
14 0.477
140 0.166
141 0.0758
142 0.268
143 0.604
144 0.282
145 0.194
146 0.32
147 0.68
148 0.351
149 0.699
15 0.117
150 0.404
151 0.262
152 0.0878
153 0.878
154 0.962
155 0.242
156 0.596
157 0.648
158 0.439
159 0.531
160 0.552
161 0.45
162 0.987
163 0.101
164 0.0745
165 0.409
166 0.386
167 0.853
168 0.807
169 0.0155
17 0.0921
18 0.474
19 0.145
2 0.503
20 0.893
21 0.892
22 0.286
23 0.12
24 0.559
25 0.494
26 0.0113
27 0.492
28 0.294
29 0.199
3 0.158
30 0.542
31 0.622
32 0.0673
33 0.236
34 0.925
35 0.309
36 0.947
37 0.0273
38 0.369
39 0.47
4 0.27
40 0.257
41 0.507
42 0.393
43 0.247
44 0.216
45 0.377
46 0.207
47 0.283
48 0.256
49 0.151
5 0.338
50 0.708
51 0.58
52 0.187
53 0.796
54 0.4
55 0.489
56 0.425
57 0.94
58 0.27
59 0.18
6 0.859
60 0.0523
61 0.378
62 0.178
63 0.201
64 0.555
65 0.178
66 0.548
67 0.353
68 0.0108
69 0.611
7 0.0627
70 0.0138
71 0.108
72 0.543
73 0.09
74 0.724
75 0.0551
76 0.988
77 0.0692
78 0.0577
79 0.809
8 0.228
80 0.972
81 0.608
82 0.0343
83 0.322
84 0.173
85 0.0528
86 0.0511
87 0.407
88 0.524
89 0.267
9 0.736
90 0.0538
91 0.224
92 0.206
93 0.141
94 0.866
95 0.188
96 0.626
97 0.595
98 0.371
99 0.226



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: CNhs10506


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)
0000160 (intestine)
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)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0001262 (wall of intestine)
0004786 (gastrointestinal system mucosa)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011436 (mouse intestinal mucosa- adult 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)