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FF:1385-42H1

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Name:kidney, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11203
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 stage30 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

Accession numbers
MethodSample accession id
CAGE  SAMD00005811
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11203 CAGE DRX009013 DRR009887
Accession ID Mm9

Library idBAMCTSS
CNhs11203 DRZ001312 DRZ002695
Accession ID Mm10

Library idBAMCTSS
CNhs11203 DRZ012662 DRZ014045
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

CNhs11203

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0505
1001 0.0849
1002 0.276
1003 --0.0712
1004 0
1005 0.0569
1006 --0.0258
1007 --0.0382
1008 0
1009 0.0796
101 --0.101
1010 0
1011 --0.0212
1012 0
1013 0.44
1014 --0.0851
1015 --0.279
1016 --0.171
1017 0
1018 0.0505
1019 0
102 0
1020 0
1021 0
1022 0.46
1023 0
1024 0.151
1025 0.0347
1026 0
1027 0
1028 0
1029 0.0266
103 --0.0461
1030 0
1031 --0.0667
1032 0.331
1033 --0.016
1034 0.55
1035 0.0505
1036 --0.181
1037 0
1038 0.0634
1039 0.563
104 0
1040 0.0767
1041 0.0958



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: CNhs11203

Jaspar motif P-value
MA0002.2 0.44
MA0003.1 0.167
MA0004.1 0.368
MA0006.1 0.0259
MA0007.1 0.161
MA0009.1 0.2
MA0014.1 0.125
MA0017.1 2.75044e-24
MA0018.2 4.3287e-4
MA0019.1 0.237
MA0024.1 3.23945e-6
MA0025.1 0.108
MA0027.1 0.28
MA0028.1 0.766
MA0029.1 0.737
MA0030.1 0.00707
MA0031.1 3.96572e-5
MA0035.2 0.00833
MA0038.1 0.574
MA0039.2 0.00208
MA0040.1 0.183
MA0041.1 0.484
MA0042.1 0.491
MA0043.1 0.0109
MA0046.1 3.87088e-152
MA0047.2 2.44663e-4
MA0048.1 0.775
MA0050.1 0.341
MA0051.1 0.163
MA0052.1 0.0147
MA0055.1 0.232
MA0057.1 0.395
MA0058.1 0.18
MA0059.1 0.573
MA0060.1 0.166
MA0061.1 0.431
MA0062.2 0.321
MA0065.2 4.11967e-14
MA0066.1 0.885
MA0067.1 0.593
MA0068.1 0.258
MA0069.1 0.451
MA0070.1 0.949
MA0071.1 7.42148e-4
MA0072.1 0.0724
MA0073.1 0.787
MA0074.1 0.241
MA0076.1 0.89
MA0077.1 0.165
MA0078.1 0.00219
MA0079.2 0.245
MA0080.2 0.234
MA0081.1 0.591
MA0083.1 0.01
MA0084.1 0.643
MA0087.1 0.16
MA0088.1 0.337
MA0090.1 0.00279
MA0091.1 0.0717
MA0092.1 0.0915
MA0093.1 0.388
MA0099.2 0.79
MA0100.1 0.0189
MA0101.1 0.558
MA0102.2 0.805
MA0103.1 0.00205
MA0104.2 0.105
MA0105.1 0.27
MA0106.1 0.535
MA0107.1 0.521
MA0108.2 0.00314
MA0111.1 0.476
MA0112.2 0.0101
MA0113.1 0.11
MA0114.1 8.99282e-32
MA0115.1 4.80393e-4
MA0116.1 0.468
MA0117.1 0.564
MA0119.1 0.0679
MA0122.1 0.442
MA0124.1 0.43
MA0125.1 0.913
MA0131.1 0.583
MA0135.1 0.0878
MA0136.1 0.0813
MA0137.2 0.582
MA0138.2 0.504
MA0139.1 0.255
MA0140.1 0.0111
MA0141.1 1.70506e-10
MA0142.1 0.00237
MA0143.1 0.998
MA0144.1 0.17
MA0145.1 3.55991e-4
MA0146.1 0.0709
MA0147.1 0.0514
MA0148.1 5.01966e-4
MA0149.1 0.0246
MA0150.1 0.0184
MA0152.1 0.0949
MA0153.1 1.77109e-66
MA0154.1 0.129
MA0155.1 0.537
MA0156.1 0.359
MA0157.1 0.00104
MA0159.1 0.0108
MA0160.1 1.5805e-6
MA0162.1 0.242
MA0163.1 0.759
MA0164.1 0.417
MA0258.1 0.0203
MA0259.1 0.163



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: CNhs11203

Novel motif P-value
1 0.904
10 0.734
100 0.882
101 0.689
102 0.221
103 0.0975
104 0.452
105 0.66
106 0.143
107 0.17
108 0.0508
109 0.00748
11 0.238
110 0.257
111 0.963
112 0.118
113 0.728
114 0.829
115 0.937
116 0.392
117 0.596
118 0.275
119 0.0786
12 0.91
120 0.406
121 0.856
122 0.0785
123 0.041
124 0.22
125 0.159
126 0.304
127 0.237
128 0.178
129 0.736
13 3.39565e-5
130 0.173
131 0.687
132 0.871
133 0.193
134 0.552
135 0.43
136 0.00412
137 0.0954
138 0.125
139 0.729
14 0.179
140 0.265
141 0.81
142 0.836
143 0.362
144 0.0742
145 0.178
146 0.257
147 0.411
148 0.883
149 0.228
15 0.274
150 0.198
151 0.82
152 0.0366
153 0.652
154 0.835
155 0.899
156 0.0153
157 0.213
158 0.596
159 0.659
160 0.57
161 0.437
162 0.344
163 0.311
164 0.997
165 0.00852
166 0.624
167 0.818
168 0.799
169 0.0137
17 0.058
18 0.049
19 0.0244
2 0.109
20 0.933
21 0.817
22 0.0252
23 0.633
24 0.114
25 0.771
26 0.515
27 0.502
28 0.512
29 0.715
3 0.462
30 0.157
31 0.598
32 0.319
33 0.897
34 0.508
35 0.421
36 0.668
37 0.0264
38 0.444
39 0.386
4 0.673
40 0.215
41 0.36
42 0.611
43 0.506
44 0.669
45 0.11
46 0.826
47 0.381
48 0.184
49 0.433
5 0.513
50 0.728
51 0.798
52 0.0396
53 0.945
54 0.975
55 0.995
56 0.993
57 0.442
58 0.291
59 0.717
6 0.996
60 0.0376
61 0.92
62 0.381
63 0.262
64 0.951
65 0.349
66 0.713
67 0.0223
68 0.947
69 0.486
7 0.188
70 0.28
71 0.766
72 0.437
73 0.0356
74 0.232
75 0.58
76 0.375
77 0.0542
78 0.0987
79 0.37
8 0.755
80 0.465
81 0.366
82 0.297
83 0.424
84 0.0711
85 0.061
86 0.461
87 0.134
88 0.58
89 0.466
9 0.967
90 0.612
91 0.502
92 0.98
93 0.548
94 0.0652
95 0.252
96 0.538
97 0.384
98 0.338
99 0.248



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: CNhs11203


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011483 (mouse kidney- neonate N30 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)