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FF:1288-20C7

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Name:kidney, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs11001
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 stage18 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  SAMD00005277
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11001 CAGE DRX009008 DRR009882
Accession ID Mm9

Library idBAMCTSS
CNhs11001 DRZ001307 DRZ002690
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11001

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.051
1002 0.546
1003 0.00188
1004 0
1005 --0.0389
1006 --0.0464
1007 0.0846
1008 0
1009 0.0615
101 0.0371
1010 0
1011 0.0324
1012 0
1013 0.143
1014 0.156
1015 0.142
1016 0.117
1017 0
1018 0
1019 0
102 0
1020 0
1021 --0.0487
1022 0.077
1023 0
1024 0.077
1025 0.142
1026 0
1027 0
1028 0.077
1029 0.351
103 0.111
1030 0
1031 0.29
1032 0.0701
1033 0.133
1034 0
1035 0.077
1036 0.06
1037 0
1038 0.0307
1039 0.0744
104 0
1040 0.173
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: CNhs11001

Jaspar motif P-value
MA0002.2 0.00202
MA0003.1 0.689
MA0004.1 0.687
MA0006.1 0.332
MA0007.1 0.683
MA0009.1 0.568
MA0014.1 0.803
MA0017.1 0.00452
MA0018.2 2.40895e-5
MA0019.1 0.328
MA0024.1 7.92733e-4
MA0025.1 0.00383
MA0027.1 0.998
MA0028.1 0.51
MA0029.1 0.207
MA0030.1 0.702
MA0031.1 0.689
MA0035.2 8.87645e-6
MA0038.1 0.388
MA0039.2 0.553
MA0040.1 0.545
MA0041.1 0.25
MA0042.1 0.638
MA0043.1 0.0023
MA0046.1 1.18331e-88
MA0047.2 0.623
MA0048.1 3.7845e-4
MA0050.1 0.124
MA0051.1 0.0596
MA0052.1 1.87829e-5
MA0055.1 4.29493e-4
MA0057.1 0.645
MA0058.1 0.566
MA0059.1 0.819
MA0060.1 0.00328
MA0061.1 0.101
MA0062.2 2.3339e-4
MA0065.2 0.991
MA0066.1 0.463
MA0067.1 0.116
MA0068.1 0.979
MA0069.1 0.0653
MA0070.1 0.739
MA0071.1 0.475
MA0072.1 0.0586
MA0073.1 0.682
MA0074.1 0.634
MA0076.1 0.154
MA0077.1 0.34
MA0078.1 0.0329
MA0079.2 0.208
MA0080.2 3.64623e-5
MA0081.1 0.0797
MA0083.1 0.501
MA0084.1 0.755
MA0087.1 0.928
MA0088.1 0.915
MA0090.1 0.0211
MA0091.1 0.575
MA0092.1 0.524
MA0093.1 0.655
MA0099.2 9.54234e-4
MA0100.1 0.0803
MA0101.1 0.379
MA0102.2 0.0779
MA0103.1 0.723
MA0104.2 0.184
MA0105.1 0.397
MA0106.1 0.677
MA0107.1 0.204
MA0108.2 0.0148
MA0111.1 0.774
MA0112.2 0.492
MA0113.1 0.566
MA0114.1 8.50727e-4
MA0115.1 0.923
MA0116.1 0.112
MA0117.1 0.0156
MA0119.1 0.501
MA0122.1 0.367
MA0124.1 0.896
MA0125.1 0.736
MA0131.1 0.65
MA0135.1 0.55
MA0136.1 1.13604e-7
MA0137.2 0.318
MA0138.2 0.00761
MA0139.1 0.928
MA0140.1 6.0058e-4
MA0141.1 0.596
MA0142.1 0.0932
MA0143.1 0.512
MA0144.1 0.429
MA0145.1 0.302
MA0146.1 0.415
MA0147.1 0.155
MA0148.1 0.56
MA0149.1 0.317
MA0150.1 0.0201
MA0152.1 0.0237
MA0153.1 1.31386e-38
MA0154.1 0.699
MA0155.1 0.286
MA0156.1 6.48259e-5
MA0157.1 0.796
MA0159.1 0.475
MA0160.1 0.416
MA0162.1 0.204
MA0163.1 0.575
MA0164.1 0.985
MA0258.1 0.0684
MA0259.1 0.651



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: CNhs11001

Novel motif P-value
1 0.0597
10 0.963
100 0.493
101 0.527
102 0.494
103 0.563
104 0.524
105 0.913
106 0.709
107 0.476
108 0.281
109 0.602
11 0.18
110 0.852
111 0.0688
112 0.55
113 0.719
114 0.00717
115 0.831
116 0.311
117 0.0774
118 0.269
119 0.963
12 0.583
120 0.241
121 0.505
122 0.956
123 0.0983
124 0.506
125 0.147
126 0.394
127 0.0801
128 0.752
129 0.583
13 0.0468
130 0.256
131 0.298
132 0.636
133 0.55
134 0.63
135 0.847
136 0.266
137 0.284
138 0.0258
139 0.226
14 0.492
140 0.999
141 0.998
142 0.0917
143 0.37
144 0.196
145 0.386
146 0.553
147 0.145
148 0.711
149 0.606
15 0.254
150 0.229
151 0.0163
152 0.407
153 0.475
154 0.359
155 0.639
156 0.0244
157 0.815
158 0.517
159 0.279
160 0.157
161 0.769
162 0.672
163 0.0881
164 0.194
165 0.21
166 0.156
167 0.746
168 0.656
169 0.252
17 0.622
18 0.0312
19 0.0578
2 0.461
20 0.712
21 0.926
22 0.599
23 0.264
24 0.635
25 0.198
26 0.656
27 0.915
28 0.276
29 0.478
3 0.821
30 0.666
31 0.414
32 0.0329
33 0.929
34 0.807
35 0.0861
36 0.131
37 0.994
38 0.608
39 0.325
4 0.965
40 0.412
41 0.0482
42 0.675
43 0.354
44 0.291
45 0.818
46 0.512
47 0.218
48 0.409
49 0.278
5 0.264
50 0.525
51 0.786
52 0.408
53 0.773
54 0.242
55 0.303
56 0.277
57 0.933
58 0.763
59 0.373
6 0.932
60 0.86
61 0.352
62 0.0969
63 0.347
64 0.571
65 0.244
66 0.479
67 0.0546
68 0.054
69 0.735
7 0.905
70 0.0449
71 0.73
72 0.441
73 0.487
74 0.927
75 0.231
76 0.921
77 0.888
78 0.821
79 0.481
8 0.224
80 0.0351
81 0.164
82 0.0607
83 0.293
84 0.59
85 0.185
86 0.563
87 7.63323e-4
88 0.502
89 0.296
9 0.768
90 0.426
91 0.753
92 0.242
93 0.75
94 0.39
95 0.179
96 0.65
97 0.735
98 0.384
99 0.515



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: CNhs11001


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)
0000302 (mouse embryonic day 18 sample)
0011512 (mouse kidney- embryo E18 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)