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FF:411-4I9

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Name:kidney, embryo E14
Species:Mouse (Mus musculus)
Library ID:CNhs10606
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 stage14 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  SAMD00005957
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10606 CAGE DRX009004 DRR009878
Accession ID Mm9

Library idBAMCTSS
CNhs10606 DRZ001303 DRZ002686
Accession ID Mm10

Library idBAMCTSS
CNhs10606 DRZ012653 DRZ014036
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 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

CNhs10606

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.00177
1001 --0.0749
1002 0.126
1003 --0.0754
1004 0
1005 --0.0575
1006 --0.108
1007 0.141
1008 0
1009 --0.0145
101 0.0657
1010 0
1011 0
1012 0
1013 --0.143
1014 0.14
1015 0.307
1016 0.226
1017 0
1018 0
1019 0
102 0
1020 0.0754
1021 0.14
1022 --0.109
1023 0
1024 --0.0496
1025 0.0348
1026 0
1027 0
1028 0
1029 --0.148
103 0.0223
1030 0
1031 0.359
1032 --0.0175
1033 0.00893
1034 0
1035 0
1036 0.081
1037 0
1038 --0.166
1039 --0.104
104 0
1040 0.0558
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: CNhs10606

Jaspar motif P-value
MA0002.2 0.149
MA0003.1 0.379
MA0004.1 0.659
MA0006.1 0.901
MA0007.1 0.55
MA0009.1 0.312
MA0014.1 0.336
MA0017.1 0.031
MA0018.2 0.317
MA0019.1 0.32
MA0024.1 4.63847e-6
MA0025.1 0.477
MA0027.1 0.0733
MA0028.1 0.00113
MA0029.1 0.396
MA0030.1 0.585
MA0031.1 0.297
MA0035.2 0.0876
MA0038.1 0.0439
MA0039.2 0.672
MA0040.1 0.902
MA0041.1 0.198
MA0042.1 0.676
MA0043.1 0.0775
MA0046.1 5.15563e-8
MA0047.2 0.361
MA0048.1 0.0139
MA0050.1 7.65232e-8
MA0051.1 4.2583e-5
MA0052.1 0.0263
MA0055.1 6.61729e-4
MA0057.1 0.63
MA0058.1 0.332
MA0059.1 0.248
MA0060.1 1.38014e-17
MA0061.1 0.343
MA0062.2 0.00276
MA0065.2 0.21
MA0066.1 0.167
MA0067.1 0.118
MA0068.1 0.818
MA0069.1 0.143
MA0070.1 0.214
MA0071.1 0.445
MA0072.1 0.0424
MA0073.1 0.833
MA0074.1 0.193
MA0076.1 0.00356
MA0077.1 0.0345
MA0078.1 0.703
MA0079.2 0.691
MA0080.2 0.00316
MA0081.1 0.833
MA0083.1 0.0165
MA0084.1 0.531
MA0087.1 0.949
MA0088.1 0.698
MA0090.1 0.456
MA0091.1 0.628
MA0092.1 0.387
MA0093.1 0.612
MA0099.2 0.0653
MA0100.1 0.766
MA0101.1 0.734
MA0102.2 0.119
MA0103.1 0.0728
MA0104.2 0.126
MA0105.1 0.764
MA0106.1 0.137
MA0107.1 0.565
MA0108.2 0.0774
MA0111.1 0.55
MA0112.2 0.00817
MA0113.1 0.739
MA0114.1 0.0644
MA0115.1 0.434
MA0116.1 0.453
MA0117.1 0.0502
MA0119.1 0.0229
MA0122.1 0.964
MA0124.1 0.736
MA0125.1 0.422
MA0131.1 0.108
MA0135.1 0.0111
MA0136.1 0.713
MA0137.2 0.932
MA0138.2 0.011
MA0139.1 0.658
MA0140.1 0.05
MA0141.1 0.0939
MA0142.1 0.452
MA0143.1 0.126
MA0144.1 0.888
MA0145.1 0.731
MA0146.1 0.488
MA0147.1 0.0904
MA0148.1 0.027
MA0149.1 0.109
MA0150.1 0.00459
MA0152.1 0.96
MA0153.1 7.41388e-4
MA0154.1 0.0244
MA0155.1 0.0991
MA0156.1 0.626
MA0157.1 0.214
MA0159.1 0.234
MA0160.1 0.243
MA0162.1 0.41
MA0163.1 0.791
MA0164.1 0.779
MA0258.1 0.00438
MA0259.1 0.488



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: CNhs10606

Novel motif P-value
1 0.0143
10 0.344
100 0.659
101 0.664
102 0.946
103 0.0373
104 0.963
105 0.445
106 0.031
107 0.291
108 0.731
109 0.927
11 0.383
110 0.834
111 0.0118
112 0.21
113 0.382
114 0.00704
115 0.765
116 0.62
117 0.9
118 0.243
119 0.172
12 0.812
120 0.766
121 0.462
122 0.697
123 0.0751
124 0.552
125 0.271
126 0.837
127 0.0116
128 0.121
129 0.0746
13 0.793
130 0.621
131 0.78
132 0.42
133 0.815
134 0.306
135 0.572
136 0.0568
137 0.263
138 0.28
139 0.00147
14 0.202
140 0.0295
141 0.427
142 0.0126
143 0.656
144 0.478
145 0.957
146 0.904
147 0.361
148 0.34
149 0.299
15 0.109
150 0.586
151 0.0765
152 0.316
153 0.116
154 0.42
155 0.528
156 0.132
157 0.93
158 0.389
159 0.0614
160 0.995
161 0.431
162 0.922
163 0.058
164 0.427
165 0.916
166 0.324
167 0.132
168 0.391
169 0.867
17 0.217
18 0.426
19 0.775
2 0.759
20 0.508
21 0.575
22 0.821
23 0.0122
24 0.612
25 0.441
26 0.756
27 0.816
28 0.157
29 0.834
3 0.279
30 0.65
31 0.375
32 0.345
33 0.333
34 0.657
35 0.054
36 0.91
37 0.434
38 0.491
39 0.844
4 0.966
40 0.421
41 0.574
42 0.392
43 0.135
44 0.707
45 0.788
46 0.278
47 0.334
48 0.479
49 0.0601
5 0.0832
50 0.346
51 0.373
52 0.666
53 0.671
54 0.245
55 0.433
56 0.322
57 0.376
58 0.206
59 0.578
6 0.724
60 0.447
61 0.942
62 0.053
63 0.281
64 0.935
65 0.379
66 0.113
67 0.429
68 0.237
69 0.541
7 0.423
70 0.0164
71 0.691
72 0.787
73 0.637
74 0.672
75 0.551
76 0.719
77 0.714
78 0.779
79 0.556
8 0.621
80 0.111
81 0.295
82 0.105
83 0.193
84 0.424
85 0.0161
86 0.982
87 0.0541
88 0.981
89 0.288
9 0.456
90 0.00158
91 0.335
92 0.0306
93 0.533
94 0.136
95 0.947
96 0.174
97 0.673
98 0.287
99 0.778



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: CNhs10606


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)
0000296 (mouse embryonic day 14 sample)
0011341 (mouse kidney- embryo E14 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)