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FF:718-18A9

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Name:stomach, neonate N07, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuestomach
dev stage7 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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs11210

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.0345
10 0
100 0
1000 0.161
1001 0.0957
1002 0.323
1003 0.11
1004 0
1005 0.132
1006 0.0962
1007 0.0315
1008 0
1009 0.191
101 --0.0161
1010 0.0664
1011 0.0655
1012 0.0159
1013 0.179
1014 0.175
1015 --0.0407
1016 0.0762
1017 0.0962
1018 0.334
1019 0.0664
102 0
1020 0
1021 0
1022 0.281
1023 0
1024 0.138
1025 0.826
1026 0
1027 0.0352
1028 0.0345
1029 0.235
103 0.355
1030 0
1031 0.312
1032 0.188
1033 --0.0396
1034 0.284
1035 0.0664
1036 --0.0588
1037 0
1038 0.179
1039 0.112
104 0
1040 0.147
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
no result for this sample


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: CNhs11210

Jaspar motif P-value
MA0002.2 0.858
MA0003.1 0.133
MA0004.1 0.255
MA0006.1 0.0543
MA0007.1 0.924
MA0009.1 0.412
MA0014.1 0.963
MA0017.1 0.00145
MA0018.2 1.05774e-4
MA0019.1 0.601
MA0024.1 0.0431
MA0025.1 0.398
MA0027.1 0.0632
MA0028.1 8.95519e-6
MA0029.1 0.887
MA0030.1 5.05533e-4
MA0031.1 0.0207
MA0035.2 0.0995
MA0038.1 0.989
MA0039.2 0.00317
MA0040.1 0.597
MA0041.1 0.461
MA0042.1 0.267
MA0043.1 0.00189
MA0046.1 1.3569e-56
MA0047.2 1.59747e-12
MA0048.1 0.47
MA0050.1 0.0959
MA0051.1 0.538
MA0052.1 0.426
MA0055.1 0.0432
MA0057.1 0.0843
MA0058.1 0.0381
MA0059.1 0.049
MA0060.1 0.0267
MA0061.1 0.883
MA0062.2 8.04541e-11
MA0065.2 8.90416e-4
MA0066.1 0.397
MA0067.1 0.259
MA0068.1 0.362
MA0069.1 0.0421
MA0070.1 0.657
MA0071.1 0.32
MA0072.1 0.703
MA0073.1 0.847
MA0074.1 0.899
MA0076.1 2.0303e-6
MA0077.1 0.27
MA0078.1 0.153
MA0079.2 0.021
MA0080.2 0.107
MA0081.1 0.00169
MA0083.1 1.56913e-9
MA0084.1 0.897
MA0087.1 0.0756
MA0088.1 0.479
MA0090.1 0.011
MA0091.1 0.209
MA0092.1 0.0706
MA0093.1 0.178
MA0099.2 1.66115e-6
MA0100.1 0.00319
MA0101.1 0.375
MA0102.2 0.613
MA0103.1 0.00383
MA0104.2 0.0288
MA0105.1 0.857
MA0106.1 0.187
MA0107.1 0.787
MA0108.2 2.39243e-9
MA0111.1 0.929
MA0112.2 0.0184
MA0113.1 0.466
MA0114.1 9.3969e-6
MA0115.1 0.666
MA0116.1 0.843
MA0117.1 0.262
MA0119.1 0.059
MA0122.1 0.205
MA0124.1 0.941
MA0125.1 0.808
MA0131.1 0.161
MA0135.1 0.369
MA0136.1 9.66533e-5
MA0137.2 0.879
MA0138.2 0.0714
MA0139.1 0.452
MA0140.1 0.891
MA0141.1 0.302
MA0142.1 0.0201
MA0143.1 0.977
MA0144.1 0.404
MA0145.1 0.00107
MA0146.1 0.421
MA0147.1 0.0124
MA0148.1 2.10633e-15
MA0149.1 0.529
MA0150.1 0.788
MA0152.1 0.989
MA0153.1 4.35342e-31
MA0154.1 0.0854
MA0155.1 0.338
MA0156.1 4.24954e-4
MA0157.1 0.0136
MA0159.1 0.925
MA0160.1 0.343
MA0162.1 0.615
MA0163.1 0.69
MA0164.1 0.847
MA0258.1 0.32
MA0259.1 0.0351



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: CNhs11210

Novel motif P-value
1 0.963
10 0.395
100 0.465
101 0.709
102 0.327
103 0.196
104 0.966
105 0.381
106 0.00101
107 0.00124
108 0.888
109 0.477
11 0.938
110 0.771
111 0.947
112 0.344
113 0.894
114 0.555
115 0.903
116 0.403
117 0.102
118 0.221
119 0.116
12 0.753
120 0.384
121 0.962
122 0.273
123 0.468
124 0.617
125 0.3
126 0.222
127 0.991
128 0.00419
129 0.823
13 0.0641
130 0.223
131 0.418
132 0.435
133 0.335
134 0.818
135 0.306
136 0.456
137 0.617
138 0.0195
139 0.415
14 0.427
140 0.152
141 0.69
142 0.692
143 0.015
144 0.221
145 0.305
146 0.0433
147 0.855
148 0.742
149 0.0974
15 0.977
150 0.379
151 0.59
152 0.00708
153 0.854
154 0.865
155 0.479
156 0.0116
157 0.048
158 0.227
159 0.498
160 0.146
161 0.838
162 0.174
163 0.399
164 0.799
165 0.778
166 0.0796
167 0.146
168 0.0931
169 0.00754
17 0.091
18 0.546
19 0.0278
2 0.0108
20 0.111
21 0.396
22 0.168
23 0.144
24 0.283
25 0.357
26 0.0386
27 0.554
28 0.854
29 0.326
3 0.846
30 0.112
31 0.548
32 0.035
33 0.963
34 0.623
35 0.285
36 0.14
37 0.344
38 0.711
39 0.0978
4 0.278
40 0.77
41 0.16
42 0.835
43 0.255
44 0.735
45 0.156
46 0.493
47 0.762
48 0.966
49 0.407
5 0.497
50 0.53
51 0.433
52 0.0139
53 0.237
54 0.247
55 0.995
56 0.442
57 0.837
58 0.684
59 0.376
6 0.53
60 0.0273
61 0.412
62 0.853
63 0.288
64 0.752
65 0.394
66 0.689
67 0.594
68 0.143
69 0.653
7 0.521
70 1
71 0.494
72 0.807
73 0.258
74 0.747
75 0.683
76 0.0273
77 0.0165
78 0.273
79 0.717
8 0.912
80 0.561
81 0.681
82 0.297
83 0.995
84 0.554
85 0.225
86 0.565
87 0.429
88 0.178
89 0.236
9 0.18
90 0.31
91 0.748
92 0.242
93 0.423
94 0.163
95 0.55
96 0.658
97 0.155
98 0.823
99 0.0386



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: CNhs11210


FANTOM5 (FF) ontology


Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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
0000061 (anatomical structure)
0000062 (organ)
0000077 (mixed endoderm/mesoderm-derived structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000945 (stomach)
0001007 (digestive system)
0001041 (foregut)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003104 (mesenchyme)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)
0009142 (entire embryonic mesenchyme)

FF: FANTOM5
NA

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

NA