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FF:1355-25E4

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Name:stomach, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11104
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
tissuestomach
dev stage25 days neonate
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  SAMD00005716
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11104 CAGE DRX009098 DRR009972
Accession ID Mm9

Library idBAMCTSS
CNhs11104 DRZ001397 DRZ002780
Accession ID Mm10

Library idBAMCTSS
CNhs11104 DRZ012747 DRZ014130
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

CNhs11104

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.3
1001 0.0966
1002 0.322
1003 0.0426
1004 0
1005 0.0328
1006 0.0351
1007 -0.0222
1008 0
1009 0.243
101 -0.0783
1010 0
1011 -0.0339
1012 0
1013 0.33
1014 0
1015 -0.237
1016 -0.154
1017 0.252
1018 0.617
1019 0
102 0
1020 0
1021 0
1022 0.363
1023 0
1024 0.145
1025 0.72
1026 0
1027 7.687337e-4
1028 0
1029 0.135
103 0.216
1030 0
1031 0.0211
1032 0.271
1033 -0.0665
1034 0.41
1035 0
1036 -0.0983
1037 0
1038 0.121
1039 0.388
104 0
1040 0.0928
1041 0.101



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: CNhs11104
Jaspar motif P-value
MA0002.2 0.356
MA0003.1 0.226
MA0004.1 0.481
MA0006.1 0.0616
MA0007.1 0.149
MA0009.1 0.0279
MA0014.1 0.362
MA0017.1 0.755
MA0018.2 0.00343
MA0019.1 0.556
MA0024.1 9.45939e-5
MA0025.1 0.301
MA0027.1 0.41
MA0028.1 0.0392
MA0029.1 0.856
MA0030.1 0.0345
MA0031.1 0.0124
MA0035.2 0.251
MA0038.1 0.671
MA0039.2 3.39725e-4
MA0040.1 0.512
MA0041.1 0.374
MA0042.1 0.255
MA0043.1 2.49607e-4
MA0046.1 2.00532e-9
MA0047.2 6.16337e-11
MA0048.1 0.442
MA0050.1 0.116
MA0051.1 0.457
MA0052.1 0.032
MA0055.1 0.148
MA0057.1 0.0398
MA0058.1 0.251
MA0059.1 0.505
MA0060.1 0.00125
MA0061.1 0.997
MA0062.2 0.00127
MA0065.2 0.0902
MA0066.1 0.314
MA0067.1 0.921
MA0068.1 0.0814
MA0069.1 0.106
MA0070.1 0.834
MA0071.1 0.304
MA0072.1 0.791
MA0073.1 0.961
MA0074.1 0.528
MA0076.1 0.0121
MA0077.1 0.161
MA0078.1 0.0644
MA0079.2 0.0541
MA0080.2 0.766
MA0081.1 0.0475
MA0083.1 3.28332e-7
MA0084.1 0.998
MA0087.1 0.514
MA0088.1 0.713
MA0090.1 6.15806e-4
MA0091.1 0.926
MA0092.1 0.174
MA0093.1 0.405
MA0099.2 7.34574e-13
MA0100.1 0.0225
MA0101.1 0.563
MA0102.2 0.337
MA0103.1 1.83476e-5
MA0104.2 0.101
MA0105.1 0.908
MA0106.1 0.0243
MA0107.1 0.65
MA0108.2 1.72586e-8
MA0111.1 0.492
MA0112.2 2.9478e-4
MA0113.1 0.468
MA0114.1 0.733
MA0115.1 0.0937
MA0116.1 0.526
MA0117.1 0.873
MA0119.1 0.147
MA0122.1 0.964
MA0124.1 0.663
MA0125.1 0.0955
MA0131.1 0.185
MA0135.1 0.324
MA0136.1 0.0978
MA0137.2 0.933
MA0138.2 0.0278
MA0139.1 0.172
MA0140.1 0.797
MA0141.1 0.524
MA0142.1 0.107
MA0143.1 0.0339
MA0144.1 0.463
MA0145.1 0.00116
MA0146.1 0.169
MA0147.1 0.0975
MA0148.1 1.51974e-11
MA0149.1 0.371
MA0150.1 0.256
MA0152.1 0.299
MA0153.1 1.30667e-7
MA0154.1 0.0413
MA0155.1 0.868
MA0156.1 0.232
MA0157.1 0.0257
MA0159.1 0.104
MA0160.1 0.966
MA0162.1 0.404
MA0163.1 0.72
MA0164.1 0.57
MA0258.1 0.0178
MA0259.1 0.0948



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: CNhs11104
Novel motif P-value
1 0.337
10 0.903
100 0.548
101 0.847
102 0.367
103 0.177
104 0.6
105 0.26
106 0.00239
107 0.0205
108 0.785
109 0.123
11 0.579
110 0.528
111 0.267
112 0.328
113 0.815
114 0.999
115 0.797
116 0.37
117 0.716
118 0.272
119 0.0123
12 0.967
120 0.951
121 0.741
122 0.556
123 0.493
124 0.739
125 0.781
126 0.109
127 0.715
128 0.011
129 0.868
13 0.0192
130 0.978
131 0.731
132 0.775
133 0.52
134 0.724
135 0.399
136 0.503
137 0.45
138 0.294
139 0.0892
14 0.44
140 0.0781
141 0.264
142 0.979
143 0.0609
144 0.261
145 0.18
146 0.101
147 0.805
148 0.764
149 0.0199
15 0.328
150 0.351
151 0.407
152 0.00796
153 0.774
154 0.856
155 0.889
156 0.00331
157 0.135
158 0.772
159 0.934
160 0.32
161 0.486
162 0.335
163 0.939
164 0.887
165 0.394
166 0.137
167 0.37
168 0.0662
169 0.0049
17 0.028
18 0.49
19 0.1
2 0.175
20 0.286
21 0.847
22 0.243
23 0.187
24 0.119
25 0.835
26 0.0779
27 0.574
28 0.673
29 0.909
3 0.598
30 0.167
31 0.492
32 0.0159
33 0.804
34 0.537
35 0.623
36 0.548
37 0.0443
38 0.61
39 0.258
4 0.00481
40 0.587
41 0.318
42 0.859
43 0.258
44 0.592
45 0.206
46 0.316
47 0.471
48 0.606
49 0.309
5 0.527
50 0.578
51 0.543
52 0.0348
53 0.428
54 0.276
55 0.242
56 0.356
57 0.663
58 0.465
59 0.201
6 0.312
60 0.03
61 0.365
62 0.4
63 0.125
64 0.981
65 0.329
66 0.927
67 0.689
68 0.584
69 0.943
7 0.176
70 0.0455
71 0.22
72 0.73
73 0.0306
74 0.838
75 0.639
76 0.111
77 0.0164
78 0.112
79 0.635
8 0.474
80 0.506
81 0.373
82 0.159
83 0.931
84 0.517
85 0.0246
86 0.36
87 0.222
88 0.446
89 0.137
9 0.345
90 0.872
91 0.891
92 0.146
93 0.9
94 0.405
95 0.183
96 0.066
97 0.0198
98 0.674
99 0.0618



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: CNhs11104


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)
0000945 (stomach)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
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)
0010039 (food storage organ)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)
0001041 (foregut)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000309 (mouse neonate N25 sample)
0011493 (mouse stomach- neonate N25 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)