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FF:758-6D5

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Name:kidney, neonate N10
Species:Mouse (Mus musculus)
Library ID:CNhs11206
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 stage10 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  SAMD00005505
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11206 CAGE DRX009010 DRR009884
Accession ID Mm9

Library idBAMCTSS
CNhs11206 DRZ001309 DRZ002692
Accession ID Mm10

Library idBAMCTSS
CNhs11206 DRZ012659 DRZ014042
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

CNhs11206

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.00962
1001 0.104
1002 0.691
1003 --0.00321
1004 0
1005 0
1006 --0.0988
1007 0.112
1008 0
1009 0.0897
101 --0.0384
1010 0
1011 --0.0201
1012 0.0266
1013 0.277
1014 0.0263
1015 --0.0369
1016 0.181
1017 0
1018 0.0517
1019 0
102 0
1020 0
1021 0
1022 0.288
1023 0
1024 0.14
1025 0
1026 0
1027 0
1028 0
1029 0.231
103 0.0615
1030 0.0266
1031 0.241
1032 0.193
1033 --0.0235
1034 0.0979
1035 0.0517
1036 --0.0855
1037 0
1038 0.21
1039 0.167
104 0
1040 0.305
1041 0.0266



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: CNhs11206

Jaspar motif P-value
MA0002.2 0.016
MA0003.1 0.256
MA0004.1 0.435
MA0006.1 0.0471
MA0007.1 0.636
MA0009.1 0.562
MA0014.1 0.425
MA0017.1 2.67397e-9
MA0018.2 3.08214e-5
MA0019.1 0.215
MA0024.1 0.619
MA0025.1 0.694
MA0027.1 0.488
MA0028.1 0.376
MA0029.1 0.352
MA0030.1 0.00476
MA0031.1 0.011
MA0035.2 7.73336e-4
MA0038.1 0.575
MA0039.2 0.0428
MA0040.1 0.964
MA0041.1 0.543
MA0042.1 0.918
MA0043.1 0.012
MA0046.1 7.35536e-132
MA0047.2 0.0135
MA0048.1 0.368
MA0050.1 0.84
MA0051.1 0.683
MA0052.1 0.00296
MA0055.1 0.135
MA0057.1 0.873
MA0058.1 0.428
MA0059.1 0.00874
MA0060.1 0.359
MA0061.1 0.119
MA0062.2 0.00931
MA0065.2 0.0725
MA0066.1 0.188
MA0067.1 0.285
MA0068.1 0.361
MA0069.1 0.172
MA0070.1 0.855
MA0071.1 0.588
MA0072.1 0.594
MA0073.1 0.542
MA0074.1 0.822
MA0076.1 0.289
MA0077.1 0.301
MA0078.1 0.00128
MA0079.2 0.122
MA0080.2 0.0754
MA0081.1 0.361
MA0083.1 0.203
MA0084.1 0.869
MA0087.1 0.383
MA0088.1 0.648
MA0090.1 7.35474e-4
MA0091.1 0.0915
MA0092.1 0.0859
MA0093.1 0.459
MA0099.2 0.0616
MA0100.1 0.0505
MA0101.1 0.582
MA0102.2 0.43
MA0103.1 0.363
MA0104.2 0.00135
MA0105.1 0.00256
MA0106.1 0.886
MA0107.1 0.836
MA0108.2 0.0156
MA0111.1 0.225
MA0112.2 0.31
MA0113.1 0.363
MA0114.1 2.80232e-10
MA0115.1 0.238
MA0116.1 1.95966e-4
MA0117.1 0.432
MA0119.1 0.707
MA0122.1 0.42
MA0124.1 0.655
MA0125.1 0.329
MA0131.1 0.686
MA0135.1 0.767
MA0136.1 0.00531
MA0137.2 0.914
MA0138.2 0.251
MA0139.1 0.909
MA0140.1 0.00624
MA0141.1 0.0642
MA0142.1 0.0154
MA0143.1 0.713
MA0144.1 0.522
MA0145.1 1.75271e-4
MA0146.1 0.518
MA0147.1 1.02071e-4
MA0148.1 0.0915
MA0149.1 0.842
MA0150.1 0.456
MA0152.1 0.0209
MA0153.1 2.04009e-58
MA0154.1 0.971
MA0155.1 0.328
MA0156.1 0.107
MA0157.1 0.112
MA0159.1 0.538
MA0160.1 0.471
MA0162.1 0.499
MA0163.1 0.00978
MA0164.1 0.582
MA0258.1 0.308
MA0259.1 0.0503



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: CNhs11206

Novel motif P-value
1 0.0782
10 0.0666
100 0.811
101 0.614
102 0.176
103 0.918
104 0.642
105 0.69
106 0.706
107 0.11
108 0.0294
109 0.97
11 0.261
110 0.721
111 0.0726
112 0.472
113 0.889
114 0.0261
115 0.511
116 0.144
117 0.012
118 0.0342
119 0.771
12 0.631
120 0.178
121 0.813
122 0.335
123 0.0495
124 0.26
125 0.101
126 0.587
127 0.105
128 0.637
129 0.782
13 0.0466
130 0.0761
131 0.524
132 0.755
133 0.276
134 0.585
135 0.94
136 0.0847
137 0.0356
138 0.00705
139 0.333
14 0.384
140 0.971
141 0.642
142 0.201
143 0.237
144 0.0854
145 0.556
146 0.535
147 0.522
148 0.525
149 0.898
15 0.676
150 0.15
151 0.219
152 0.0574
153 0.685
154 0.863
155 0.42
156 0.347
157 0.516
158 0.498
159 0.288
160 0.647
161 0.995
162 0.282
163 0.955
164 0.263
165 0.151
166 0.669
167 0.352
168 0.932
169 0.128
17 0.997
18 0.00397
19 0.0506
2 0.154
20 0.711
21 0.42
22 0.244
23 0.98
24 0.62
25 0.465
26 0.845
27 0.807
28 0.844
29 0.0729
3 0.569
30 0.224
31 0.658
32 0.0158
33 0.622
34 0.447
35 0.0188
36 0.0876
37 0.918
38 0.829
39 0.455
4 0.926
40 0.924
41 0.109
42 0.361
43 0.315
44 0.28
45 0.339
46 0.245
47 0.193
48 0.665
49 0.207
5 0.173
50 0.737
51 0.88
52 0.0683
53 0.837
54 0.477
55 0.664
56 0.318
57 0.438
58 0.978
59 0.58
6 0.781
60 0.229
61 0.886
62 0.253
63 0.657
64 0.291
65 0.585
66 0.701
67 0.0446
68 0.204
69 0.583
7 0.894
70 0.171
71 0.0432
72 0.288
73 0.876
74 0.222
75 0.115
76 0.246
77 0.506
78 0.961
79 0.218
8 0.0291
80 0.113
81 0.207
82 0.139
83 0.174
84 0.607
85 0.713
86 0.924
87 0.256
88 0.308
89 0.603
9 0.972
90 0.297
91 0.99
92 0.243
93 0.722
94 0.0816
95 0.421
96 0.462
97 0.321
98 0.9
99 0.736



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: CNhs11206


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)
0000305 (mouse neonate N10 sample)
0011419 (mouse kidney- neonate N10 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)