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FF:463-22H4

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Name:intestine, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs10585
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
tissueintestine
dev stage16 days embryo
sexmixture
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  SAMD00005161
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10585 CAGE DRX008993 DRR009867
Accession ID Mm9

Library idBAMCTSS
CNhs10585 DRZ001292 DRZ002675
Accession ID Mm10

Library idBAMCTSS
CNhs10585 DRZ012642 DRZ014025
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sample
Ranked 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 sample
Ranked 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

CNhs10585

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.107
1001 0.0627
1002 0.321
1003 -0.038
1004 0
1005 0.038
1006 -0.0706
1007 0.0044
1008 0
1009 0.0155
101 0.059
1010 0.205
1011 -0.0923
1012 0
1013 0.0177
1014 0.218
1015 0.0279
1016 0.0522
1017 0
1018 0.205
1019 0
102 0
1020 0
1021 0
1022 -0.0704
1023 0
1024 -0.0101
1025 0.776
1026 0
1027 0.0318
1028 0
1029 0.27
103 0.116
1030 0
1031 0.278
1032 0.134
1033 0
1034 0
1035 0.0282
1036 -0.00386
1037 0
1038 0.0146
1039 -0.0982
104 0
1040 0
1041 0



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs10585
Jaspar motif P-value
MA0002.2 0.492
MA0003.1 0.259
MA0004.1 0.0872
MA0006.1 0.108
MA0007.1 0.633
MA0009.1 0.865
MA0014.1 0.94
MA0017.1 1.70269e-25
MA0018.2 3.08014e-4
MA0019.1 0.151
MA0024.1 0.001
MA0025.1 0.0284
MA0027.1 0.372
MA0028.1 0.0638
MA0029.1 0.867
MA0030.1 0.662
MA0031.1 0.919
MA0035.2 9.37987e-7
MA0038.1 0.0738
MA0039.2 0.00542
MA0040.1 0.567
MA0041.1 0.571
MA0042.1 0.546
MA0043.1 0.0136
MA0046.1 1.89447e-90
MA0047.2 8.56919e-4
MA0048.1 0.229
MA0050.1 0.00952
MA0051.1 0.0353
MA0052.1 1.77495e-5
MA0055.1 0.313
MA0057.1 0.795
MA0058.1 0.0209
MA0059.1 0.692
MA0060.1 2.74001e-5
MA0061.1 0.945
MA0062.2 0.00631
MA0065.2 4.96742e-6
MA0066.1 0.802
MA0067.1 0.084
MA0068.1 0.37
MA0069.1 0.0915
MA0070.1 0.646
MA0071.1 0.528
MA0072.1 0.157
MA0073.1 0.895
MA0074.1 0.0412
MA0076.1 0.0229
MA0077.1 0.55
MA0078.1 0.685
MA0079.2 0.43
MA0080.2 0.339
MA0081.1 0.0228
MA0083.1 0.0201
MA0084.1 0.922
MA0087.1 0.605
MA0088.1 0.504
MA0090.1 0.205
MA0091.1 0.82
MA0092.1 0.504
MA0093.1 0.0431
MA0099.2 0.456
MA0100.1 0.00231
MA0101.1 0.288
MA0102.2 0.265
MA0103.1 1.28349e-4
MA0104.2 0.747
MA0105.1 0.709
MA0106.1 0.357
MA0107.1 0.218
MA0108.2 0.68
MA0111.1 0.403
MA0112.2 0.152
MA0113.1 0.563
MA0114.1 1.241e-38
MA0115.1 1.34759e-5
MA0116.1 0.54
MA0117.1 0.114
MA0119.1 0.702
MA0122.1 0.548
MA0124.1 0.455
MA0125.1 0.668
MA0131.1 0.556
MA0135.1 0.00953
MA0136.1 0.763
MA0137.2 0.921
MA0138.2 0.465
MA0139.1 0.0428
MA0140.1 0.0171
MA0141.1 0.0491
MA0142.1 0.285
MA0143.1 0.4
MA0144.1 0.314
MA0145.1 0.178
MA0146.1 0.289
MA0147.1 0.304
MA0148.1 6.14761e-5
MA0149.1 0.873
MA0150.1 0.0439
MA0152.1 0.652
MA0153.1 9.39258e-58
MA0154.1 0.0914
MA0155.1 0.00944
MA0156.1 0.32
MA0157.1 0.465
MA0159.1 0.164
MA0160.1 0.276
MA0162.1 0.236
MA0163.1 0.0867
MA0164.1 0.482
MA0258.1 0.986
MA0259.1 0.671



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs10585
Novel motif P-value
1 0.828
10 0.825
100 0.462
101 0.693
102 0.25
103 0.747
104 0.959
105 0.379
106 0.0538
107 0.0274
108 0.94
109 0.864
11 0.956
110 0.558
111 0.906
112 0.388
113 0.217
114 0.283
115 0.597
116 0.964
117 0.416
118 0.587
119 0.524
12 0.507
120 0.726
121 0.925
122 0.824
123 0.215
124 0.512
125 0.621
126 0.0393
127 0.795
128 0.738
129 0.886
13 1.74716e-4
130 0.257
131 0.914
132 0.429
133 0.119
134 0.39
135 0.419
136 0.407
137 0.45
138 0.0199
139 0.98
14 0.559
140 0.0371
141 0.418
142 0.48
143 0.0489
144 0.29
145 0.272
146 0.0274
147 0.302
148 0.857
149 0.363
15 0.744
150 0.358
151 0.703
152 0.0763
153 0.097
154 0.365
155 0.991
156 0.319
157 0.625
158 0.374
159 0.0311
160 0.0186
161 0.551
162 0.967
163 0.462
164 0.692
165 0.698
166 0.49
167 0.642
168 0.189
169 0.271
17 0.586
18 0.0429
19 0.0509
2 0.287
20 0.423
21 0.955
22 0.267
23 0.684
24 0.351
25 0.522
26 0.0885
27 0.632
28 0.222
29 0.966
3 0.801
30 0.19
31 0.636
32 0.77
33 0.0921
34 0.355
35 0.499
36 0.836
37 0.381
38 0.999
39 0.314
4 0.369
40 0.154
41 0.181
42 0.696
43 0.903
44 0.501
45 0.0798
46 0.785
47 0.983
48 0.94
49 0.226
5 0.555
50 0.391
51 0.752
52 0.0268
53 0.623
54 0.941
55 0.128
56 0.905
57 0.0926
58 0.956
59 0.673
6 0.869
60 0.145
61 0.265
62 0.118
63 0.889
64 0.949
65 0.908
66 0.79
67 0.0649
68 0.469
69 0.337
7 0.151
70 0.284
71 0.433
72 0.767
73 0.814
74 0.895
75 0.973
76 0.168
77 0.0373
78 0.401
79 0.287
8 0.466
80 0.148
81 0.367
82 0.787
83 0.391
84 0.399
85 0.919
86 0.484
87 0.858
88 0.579
89 0.664
9 0.792
90 0.431
91 0.148
92 0.977
93 0.386
94 0.0331
95 0.924
96 0.113
97 0.288
98 0.643
99 0.0661



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

library id: CNhs10585


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)
0000922 (embryo)
0000160 (intestine)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
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)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000299 (mouse embryonic day 16 sample)
0011362 (mouse intestine- embryo E16 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)
FF:0000294 (mouse embryonic day 11 sample)