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FF:1353-25F3

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Name:kidney, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11122
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 stage25 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  SAMD00005166
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11122 CAGE DRX009012 DRR009886
Accession ID Mm9

Library idBAMCTSS
CNhs11122 DRZ001311 DRZ002694
Accession ID Mm10

Library idBAMCTSS
CNhs11122 DRZ012661 DRZ014044
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

CNhs11122

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.169
1002 0.572
1003 --0.0841
1004 0
1005 0
1006 0
1007 --0.0261
1008 0
1009 0.00611
101 --0.0788
1010 0
1011 0
1012 0.0207
1013 0.392
1014 --0.0218
1015 --0.239
1016 --0.153
1017 0
1018 0.118
1019 0
102 0
1020 0
1021 --0.0487
1022 0.422
1023 0
1024 0.341
1025 0
1026 0
1027 0
1028 0.0633
1029 0.239
103 0
1030 0
1031 --0.0365
1032 0.419
1033 --0.00316
1034 0.478
1035 0.0633
1036 --0.265
1037 0
1038 0.0955
1039 0.526
104 0
1040 0.162
1041 0.119



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: CNhs11122

Jaspar motif P-value
MA0002.2 0.124
MA0003.1 0.254
MA0004.1 0.574
MA0006.1 0.0418
MA0007.1 0.448
MA0009.1 0.324
MA0014.1 0.115
MA0017.1 4.4864e-22
MA0018.2 2.6847e-6
MA0019.1 0.273
MA0024.1 5.06949e-5
MA0025.1 0.961
MA0027.1 0.539
MA0028.1 0.814
MA0029.1 0.493
MA0030.1 0.0303
MA0031.1 0.00176
MA0035.2 0.00151
MA0038.1 0.396
MA0039.2 0.0216
MA0040.1 0.523
MA0041.1 0.336
MA0042.1 0.591
MA0043.1 2.88617e-4
MA0046.1 5.9426e-131
MA0047.2 0.00229
MA0048.1 0.362
MA0050.1 0.0747
MA0051.1 0.102
MA0052.1 0.00455
MA0055.1 0.335
MA0057.1 0.434
MA0058.1 0.421
MA0059.1 0.904
MA0060.1 0.0134
MA0061.1 0.68
MA0062.2 0.0493
MA0065.2 1.69466e-12
MA0066.1 0.537
MA0067.1 0.442
MA0068.1 0.715
MA0069.1 0.472
MA0070.1 0.796
MA0071.1 0.00482
MA0072.1 0.366
MA0073.1 0.875
MA0074.1 0.4
MA0076.1 0.486
MA0077.1 0.0334
MA0078.1 0.00169
MA0079.2 0.756
MA0080.2 0.104
MA0081.1 0.442
MA0083.1 0.046
MA0084.1 0.669
MA0087.1 0.468
MA0088.1 0.195
MA0090.1 0.0012
MA0091.1 0.35
MA0092.1 0.0697
MA0093.1 0.566
MA0099.2 0.768
MA0100.1 0.0227
MA0101.1 0.437
MA0102.2 0.679
MA0103.1 0.00151
MA0104.2 0.0887
MA0105.1 0.707
MA0106.1 0.308
MA0107.1 0.507
MA0108.2 8.57584e-5
MA0111.1 0.817
MA0112.2 5.3993e-4
MA0113.1 0.415
MA0114.1 2.54851e-27
MA0115.1 6.09359e-4
MA0116.1 0.766
MA0117.1 0.823
MA0119.1 0.0176
MA0122.1 0.322
MA0124.1 0.619
MA0125.1 0.472
MA0131.1 0.338
MA0135.1 0.839
MA0136.1 0.00428
MA0137.2 0.981
MA0138.2 0.972
MA0139.1 0.136
MA0140.1 0.0179
MA0141.1 1.56514e-9
MA0142.1 0.00475
MA0143.1 0.911
MA0144.1 0.618
MA0145.1 4.9839e-4
MA0146.1 0.175
MA0147.1 0.0627
MA0148.1 0.00426
MA0149.1 0.0239
MA0150.1 0.0656
MA0152.1 0.05
MA0153.1 6.46744e-57
MA0154.1 0.0722
MA0155.1 0.379
MA0156.1 0.143
MA0157.1 0.0286
MA0159.1 0.0197
MA0160.1 4.03364e-5
MA0162.1 0.16
MA0163.1 0.59
MA0164.1 0.554
MA0258.1 0.00554
MA0259.1 0.137



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: CNhs11122

Novel motif P-value
1 0.42
10 0.711
100 0.963
101 0.933
102 0.304
103 0.0224
104 0.609
105 0.62
106 0.122
107 0.102
108 0.0262
109 0.0226
11 0.263
110 0.21
111 0.67
112 0.0923
113 0.691
114 0.379
115 0.887
116 0.463
117 0.775
118 0.375
119 0.0849
12 0.847
120 0.268
121 0.716
122 0.299
123 0.0464
124 0.482
125 0.546
126 0.381
127 0.305
128 0.153
129 0.929
13 6.66475e-6
130 0.125
131 0.683
132 0.823
133 0.157
134 0.58
135 0.419
136 0.259
137 0.119
138 0.0364
139 0.341
14 0.176
140 0.234
141 0.701
142 0.831
143 0.361
144 0.148
145 0.131
146 0.492
147 0.57
148 0.481
149 0.285
15 0.184
150 0.178
151 0.488
152 0.0665
153 0.652
154 0.493
155 0.882
156 0.174
157 0.199
158 0.986
159 0.129
160 0.199
161 0.647
162 0.375
163 0.545
164 0.792
165 0.0171
166 0.804
167 0.762
168 0.926
169 0.00483
17 0.0412
18 0.0981
19 0.00466
2 0.204
20 0.798
21 0.835
22 0.0275
23 0.336
24 0.303
25 0.769
26 0.205
27 0.521
28 0.545
29 0.948
3 0.247
30 0.337
31 0.618
32 0.285
33 0.838
34 0.655
35 0.796
36 0.92
37 0.0412
38 0.329
39 0.402
4 0.701
40 0.356
41 0.253
42 0.886
43 0.287
44 0.816
45 0.261
46 0.694
47 0.44
48 0.226
49 0.177
5 0.851
50 0.965
51 0.61
52 0.0651
53 0.981
54 0.96
55 0.886
56 0.999
57 0.913
58 0.221
59 0.93
6 0.914
60 0.0298
61 0.489
62 0.313
63 0.345
64 0.982
65 0.311
66 0.424
67 0.103
68 0.81
69 0.667
7 0.0652
70 0.19
71 0.363
72 0.871
73 0.111
74 0.348
75 0.554
76 0.536
77 0.0814
78 0.0772
79 0.402
8 0.896
80 0.367
81 0.557
82 0.385
83 0.599
84 0.325
85 0.0201
86 0.528
87 0.254
88 0.726
89 0.736
9 0.756
90 0.327
91 0.41
92 0.607
93 0.813
94 0.203
95 0.575
96 0.34
97 0.368
98 0.33
99 0.376



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: CNhs11122


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)
0000309 (mouse neonate N25 sample)
0011482 (mouse kidney- neonate N25 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)