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FF:434-16F8

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Name:kidney, embryo E15
Species:Mouse (Mus musculus)
Library ID:CNhs10997
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
tissuekidney
dev stage15 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  SAMD00005060
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10997 CAGE DRX009005 DRR009879
Accession ID Mm9

Library idBAMCTSS
CNhs10997 DRZ001304 DRZ002687
Accession ID Mm10

Library idBAMCTSS
CNhs10997 DRZ012654 DRZ014037
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
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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

CNhs10997

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0.0367
1000 --0.00761
1001 --0.00676
1002 0.266
1003 --0.087
1004 0
1005 --0.0724
1006 --0.0815
1007 0.13
1008 0
1009 --0.0102
101 0.134
1010 0.047
1011 0
1012 0
1013 --0.188
1014 0.196
1015 0.214
1016 0.162
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.047
1022 --0.0655
1023 0
1024 0.0736
1025 0.169
1026 0.0599
1027 0
1028 0.047
1029 0.219
103 0.0982
1030 0
1031 0.335
1032 --0.0645
1033 0
1034 0
1035 0.00898
1036 0.192
1037 0
1038 0.0282
1039 --0.0467
104 0
1040 0.0754
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: CNhs10997

Jaspar motif P-value
MA0002.2 3.78415e-4
MA0003.1 0.146
MA0004.1 0.72
MA0006.1 0.661
MA0007.1 0.511
MA0009.1 0.553
MA0014.1 0.546
MA0017.1 0.0787
MA0018.2 0.102
MA0019.1 0.937
MA0024.1 6.19678e-8
MA0025.1 1.66802e-4
MA0027.1 0.0515
MA0028.1 0.267
MA0029.1 0.98
MA0030.1 0.24
MA0031.1 0.00263
MA0035.2 0.0727
MA0038.1 0.0562
MA0039.2 0.0303
MA0040.1 0.322
MA0041.1 0.219
MA0042.1 0.451
MA0043.1 0.418
MA0046.1 4.54147e-22
MA0047.2 0.111
MA0048.1 0.0015
MA0050.1 2.32933e-4
MA0051.1 3.71033e-5
MA0052.1 2.67693e-5
MA0055.1 0.00533
MA0057.1 0.104
MA0058.1 0.699
MA0059.1 0.683
MA0060.1 1.33753e-9
MA0061.1 0.0785
MA0062.2 0.484
MA0065.2 0.00221
MA0066.1 0.0997
MA0067.1 0.232
MA0068.1 0.912
MA0069.1 0.23
MA0070.1 0.676
MA0071.1 0.057
MA0072.1 0.0148
MA0073.1 0.606
MA0074.1 0.567
MA0076.1 0.479
MA0077.1 0.751
MA0078.1 0.547
MA0079.2 0.0817
MA0080.2 2.58903e-10
MA0081.1 0.121
MA0083.1 0.805
MA0084.1 0.258
MA0087.1 0.168
MA0088.1 0.945
MA0090.1 0.703
MA0091.1 0.95
MA0092.1 0.501
MA0093.1 0.758
MA0099.2 1.32065e-5
MA0100.1 0.724
MA0101.1 0.457
MA0102.2 0.0477
MA0103.1 0.0112
MA0104.2 0.976
MA0105.1 0.149
MA0106.1 0.591
MA0107.1 0.145
MA0108.2 0.236
MA0111.1 0.588
MA0112.2 0.00116
MA0113.1 0.855
MA0114.1 0.0928
MA0115.1 0.355
MA0116.1 0.041
MA0117.1 0.0565
MA0119.1 0.0724
MA0122.1 0.969
MA0124.1 0.88
MA0125.1 0.794
MA0131.1 0.286
MA0135.1 0.35
MA0136.1 1.8694e-8
MA0137.2 0.0949
MA0138.2 0.00159
MA0139.1 0.197
MA0140.1 0.681
MA0141.1 0.0386
MA0142.1 0.575
MA0143.1 0.186
MA0144.1 0.133
MA0145.1 0.0406
MA0146.1 0.055
MA0147.1 0.975
MA0148.1 0.13
MA0149.1 0.0639
MA0150.1 0.00163
MA0152.1 0.0465
MA0153.1 2.16367e-9
MA0154.1 0.0117
MA0155.1 0.993
MA0156.1 0.00159
MA0157.1 0.0111
MA0159.1 0.0317
MA0160.1 0.0164
MA0162.1 0.981
MA0163.1 0.231
MA0164.1 0.517
MA0258.1 0.00125
MA0259.1 0.83



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: CNhs10997

Novel motif P-value
1 0.11
10 0.643
100 0.731
101 0.497
102 0.785
103 0.262
104 0.723
105 0.422
106 0.0593
107 0.654
108 0.597
109 0.228
11 0.129
110 0.762
111 0.0132
112 0.178
113 0.538
114 0.00132
115 0.572
116 0.666
117 0.33
118 0.265
119 0.178
12 0.681
120 0.23
121 0.325
122 0.791
123 0.0953
124 0.578
125 0.218
126 0.871
127 0.0372
128 0.0909
129 0.26
13 0.903
130 0.269
131 0.408
132 0.25
133 0.404
134 0.448
135 0.977
136 0.676
137 0.898
138 0.0569
139 0.00977
14 0.267
140 0.68
141 0.487
142 0.648
143 0.462
144 0.655
145 0.898
146 0.382
147 0.437
148 0.593
149 0.0589
15 0.076
150 0.894
151 0.0371
152 0.188
153 0.952
154 0.406
155 0.817
156 0.314
157 0.611
158 0.65
159 0.71
160 0.727
161 0.331
162 0.882
163 0.0207
164 0.504
165 0.473
166 0.226
167 0.996
168 0.664
169 0.0886
17 0.152
18 0.229
19 0.944
2 0.715
20 0.633
21 0.959
22 0.429
23 0.0467
24 0.445
25 0.241
26 0.68
27 0.473
28 0.225
29 0.705
3 0.39
30 0.745
31 0.343
32 0.0428
33 0.839
34 0.612
35 0.237
36 0.272
37 0.225
38 0.38
39 0.723
4 0.488
40 0.305
41 0.0466
42 0.534
43 0.172
44 0.0891
45 0.257
46 0.303
47 0.165
48 0.248
49 0.135
5 0.194
50 0.866
51 0.527
52 0.666
53 0.621
54 0.33
55 0.314
56 0.237
57 0.874
58 0.23
59 0.0671
6 0.682
60 0.255
61 0.925
62 0.0399
63 0.126
64 0.54
65 0.122
66 0.819
67 0.254
68 0.0696
69 0.552
7 0.403
70 1.68741e-4
71 0.519
72 0.161
73 0.0871
74 0.964
75 0.0719
76 0.768
77 0.265
78 0.33
79 0.342
8 0.4
80 0.0762
81 0.147
82 0.0296
83 0.427
84 0.206
85 0.0127
86 0.373
87 0.0162
88 0.935
89 0.0779
9 0.599
90 0.291
91 0.822
92 0.143
93 0.773
94 0.976
95 0.0848
96 0.372
97 0.795
98 0.157
99 0.989



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: CNhs10997


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)
0002113 (kidney)
0002100 (trunk)
0000479 (tissue)
0000062 (organ)
0000475 (organism subdivision)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0009569 (subdivision of trunk)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0005172 (abdomen element)
0005173 (abdominal segment element)
0011143 (upper urinary tract)
0001008 (renal system)
0002417 (abdominal segment of trunk)
0000916 (abdomen)

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)
0000298 (mouse embryonic day 15 sample)
0011350 (mouse kidney- embryo E15 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:0003104 (mesenchyme)
UBERON:0003918 (kidney mesenchyme)
UBERON:0007687 (kidney field)
FF:0000294 (mouse embryonic day 11 sample)