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FF:464-22A5

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Name:kidney, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs10584
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 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  SAMD00005783
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10584 CAGE DRX009006 DRR009880
Accession ID Mm9

Library idBAMCTSS
CNhs10584 DRZ001305 DRZ002688
Accession ID Mm10

Library idBAMCTSS
CNhs10584 DRZ012655 DRZ014038
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 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

CNhs10584

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 -0.0355
1001 -0.0631
1002 0.0614
1003 -0.123
1004 0
1005 -0.201
1006 -0.143
1007 0.137
1008 0
1009 0.0681
101 0.0864
1010 0
1011 -0.00937
1012 0
1013 -0.0717
1014 0
1015 0.21
1016 0.111
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 -0.0704
1023 0
1024 0
1025 0
1026 0.0674
1027 -0.048
1028 0
1029 -0.148
103 0
1030 0
1031 0.338
1032 0.086
1033 -0.0665
1034 0
1035 0
1036 0.042
1037 0
1038 -0.0289
1039 -0.129
104 0
1040 0.166
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: CNhs10584
Jaspar motif P-value
MA0002.2 0.0369
MA0003.1 0.6
MA0004.1 0.535
MA0006.1 0.793
MA0007.1 0.862
MA0009.1 0.344
MA0014.1 0.147
MA0017.1 0.851
MA0018.2 0.0736
MA0019.1 0.451
MA0024.1 6.63102e-7
MA0025.1 0.0386
MA0027.1 0.829
MA0028.1 0.935
MA0029.1 0.21
MA0030.1 0.599
MA0031.1 0.838
MA0035.2 7.80504e-4
MA0038.1 0.041
MA0039.2 0.908
MA0040.1 0.796
MA0041.1 0.204
MA0042.1 0.611
MA0043.1 0.204
MA0046.1 1.82509e-56
MA0047.2 0.412
MA0048.1 0.0837
MA0050.1 1.15639e-6
MA0051.1 6.03886e-4
MA0052.1 3.7009e-5
MA0055.1 0.0387
MA0057.1 0.494
MA0058.1 0.494
MA0059.1 0.358
MA0060.1 8.07892e-9
MA0061.1 0.687
MA0062.2 0.123
MA0065.2 0.0894
MA0066.1 0.136
MA0067.1 0.24
MA0068.1 0.946
MA0069.1 0.206
MA0070.1 0.779
MA0071.1 0.144
MA0072.1 0.145
MA0073.1 0.905
MA0074.1 0.979
MA0076.1 0.858
MA0077.1 0.301
MA0078.1 0.918
MA0079.2 0.967
MA0080.2 0.00189
MA0081.1 0.364
MA0083.1 0.98
MA0084.1 0.174
MA0087.1 0.847
MA0088.1 0.846
MA0090.1 0.328
MA0091.1 0.29
MA0092.1 0.734
MA0093.1 0.508
MA0099.2 0.0253
MA0100.1 0.515
MA0101.1 0.392
MA0102.2 0.0864
MA0103.1 0.302
MA0104.2 0.0656
MA0105.1 0.343
MA0106.1 0.139
MA0107.1 0.59
MA0108.2 0.0747
MA0111.1 0.646
MA0112.2 0.00959
MA0113.1 0.296
MA0114.1 0.81
MA0115.1 0.369
MA0116.1 0.00773
MA0117.1 0.0213
MA0119.1 0.0745
MA0122.1 0.734
MA0124.1 0.992
MA0125.1 0.842
MA0131.1 0.691
MA0135.1 0.361
MA0136.1 0.00333
MA0137.2 0.339
MA0138.2 0.00849
MA0139.1 0.279
MA0140.1 0.0357
MA0141.1 0.175
MA0142.1 0.219
MA0143.1 0.13
MA0144.1 0.717
MA0145.1 0.546
MA0146.1 0.34
MA0147.1 0.0869
MA0148.1 0.573
MA0149.1 0.0373
MA0150.1 0.0217
MA0152.1 0.0855
MA0153.1 7.76624e-34
MA0154.1 0.11
MA0155.1 0.12
MA0156.1 0.107
MA0157.1 0.513
MA0159.1 0.0413
MA0160.1 0.336
MA0162.1 0.359
MA0163.1 0.0753
MA0164.1 0.938
MA0258.1 0.00883
MA0259.1 0.606



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: CNhs10584
Novel motif P-value
1 0.00482
10 0.638
100 0.714
101 0.996
102 0.545
103 0.108
104 0.62
105 0.893
106 0.4
107 0.882
108 0.936
109 0.121
11 0.0993
110 0.523
111 0.00766
112 0.483
113 0.986
114 0.00649
115 0.0727
116 0.32
117 0.0546
118 0.0496
119 0.441
12 0.972
120 0.201
121 0.858
122 0.629
123 0.0175
124 0.935
125 0.236
126 0.997
127 0.288
128 0.117
129 0.531
13 0.84
130 0.351
131 0.234
132 0.74
133 0.649
134 0.227
135 0.862
136 0.0897
137 0.295
138 0.186
139 0.00677
14 0.684
140 0.48
141 0.889
142 0.153
143 0.536
144 0.24
145 0.912
146 0.95
147 0.774
148 0.597
149 0.484
15 0.0912
150 0.185
151 0.101
152 0.973
153 0.845
154 0.611
155 0.943
156 0.107
157 0.877
158 0.997
159 0.873
160 0.532
161 0.21
162 0.756
163 0.0793
164 0.424
165 0.808
166 0.49
167 0.133
168 0.329
169 0.988
17 0.531
18 0.108
19 0.571
2 0.659
20 0.942
21 0.554
22 0.792
23 0.0998
24 0.704
25 0.347
26 0.547
27 0.817
28 0.111
29 0.284
3 0.182
30 0.387
31 0.343
32 0.083
33 0.463
34 0.861
35 0.0199
36 0.19
37 0.157
38 0.727
39 0.567
4 0.752
40 0.707
41 0.233
42 0.432
43 0.145
44 0.0287
45 0.931
46 0.307
47 0.0455
48 0.171
49 0.0978
5 0.0959
50 0.418
51 0.659
52 0.687
53 0.899
54 0.192
55 0.54
56 0.341
57 0.143
58 0.25
59 0.187
6 0.978
60 0.976
61 0.916
62 0.063
63 0.279
64 0.665
65 0.268
66 0.579
67 0.409
68 0.0956
69 0.365
7 0.511
70 0.00287
71 0.377
72 0.531
73 0.198
74 0.954
75 0.071
76 0.351
77 0.696
78 0.779
79 0.757
8 0.0813
80 0.3
81 0.149
82 0.0559
83 0.344
84 0.318
85 0.13
86 0.674
87 0.113
88 0.765
89 0.502
9 0.688
90 0.0705
91 0.381
92 0.0325
93 0.565
94 0.321
95 0.124
96 0.326
97 0.436
98 0.401
99 0.779



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: CNhs10584


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)
0000299 (mouse embryonic day 16 sample)
0011363 (mouse kidney- 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:0003104 (mesenchyme)
UBERON:0003918 (kidney mesenchyme)
UBERON:0007687 (kidney field)
FF:0000294 (mouse embryonic day 11 sample)