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FF:879-12E4

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Name:urinary bladder, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10481
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
tissueurinary bladder
dev stageadult
sexmale
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  SAMD00005219
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10481 CAGE DRX009127 DRR010001
Accession ID Mm9

Library idBAMCTSS
CNhs10481 DRZ001426 DRZ002809
Accession ID Mm10

Library idBAMCTSS
CNhs10481 DRZ012776 DRZ014159
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

CNhs10481

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.433
1001 0.203
1002 0.0404
1003 0.137
1004 0
1005 0.0378
1006 0.131
1007 --0.0227
1008 0
1009 0.479
101 --0.0409
1010 0
1011 --0.0286
1012 0
1013 0.0764
1014 --0.0084
1015 --0.211
1016 0.00527
1017 0
1018 0.569
1019 0
102 0
1020 0
1021 0
1022 0.128
1023 0
1024 0.204
1025 0.879
1026 0
1027 0
1028 0.0767
1029 0.117
103 0.142
1030 0
1031 0.268
1032 0.158
1033 0
1034 0.211
1035 0
1036 --0.225
1037 0
1038 0.137
1039 0.103
104 0
1040 0.353
1041 0.911



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: CNhs10481

Jaspar motif P-value
MA0002.2 0.774
MA0003.1 0.0767
MA0004.1 0.239
MA0006.1 0.192
MA0007.1 0.517
MA0009.1 0.581
MA0014.1 0.373
MA0017.1 0.0149
MA0018.2 0.0669
MA0019.1 0.344
MA0024.1 1.81159e-10
MA0025.1 0.709
MA0027.1 0.84
MA0028.1 0.00461
MA0029.1 0.917
MA0030.1 0.021
MA0031.1 0.011
MA0035.2 0.106
MA0038.1 0.357
MA0039.2 0.0326
MA0040.1 0.142
MA0041.1 0.35
MA0042.1 0.459
MA0043.1 0.206
MA0046.1 7.31234e-4
MA0047.2 1.0603e-4
MA0048.1 0.0743
MA0050.1 4.77429e-7
MA0051.1 5.20781e-4
MA0052.1 0.625
MA0055.1 0.0702
MA0057.1 0.544
MA0058.1 0.0793
MA0059.1 0.0024
MA0060.1 1.09057e-8
MA0061.1 0.794
MA0062.2 2.46182e-4
MA0065.2 0.43
MA0066.1 0.405
MA0067.1 0.855
MA0068.1 0.108
MA0069.1 0.807
MA0070.1 0.757
MA0071.1 0.0803
MA0072.1 0.111
MA0073.1 0.766
MA0074.1 0.618
MA0076.1 0.00273
MA0077.1 0.169
MA0078.1 0.22
MA0079.2 0.012
MA0080.2 0.593
MA0081.1 0.221
MA0083.1 7.88648e-22
MA0084.1 0.797
MA0087.1 0.678
MA0088.1 0.548
MA0090.1 0.00324
MA0091.1 0.376
MA0092.1 0.5
MA0093.1 0.218
MA0099.2 3.52693e-4
MA0100.1 0.0142
MA0101.1 0.911
MA0102.2 0.888
MA0103.1 0.736
MA0104.2 0.0513
MA0105.1 0.167
MA0106.1 0.119
MA0107.1 0.673
MA0108.2 0.47
MA0111.1 0.958
MA0112.2 0.124
MA0113.1 0.827
MA0114.1 0.015
MA0115.1 0.0715
MA0116.1 0.685
MA0117.1 0.898
MA0119.1 0.786
MA0122.1 0.472
MA0124.1 0.34
MA0125.1 0.586
MA0131.1 0.145
MA0135.1 0.277
MA0136.1 0.426
MA0137.2 0.767
MA0138.2 0.122
MA0139.1 0.425
MA0140.1 3.84257e-4
MA0141.1 8.35194e-5
MA0142.1 0.539
MA0143.1 0.498
MA0144.1 0.716
MA0145.1 9.31332e-4
MA0146.1 0.627
MA0147.1 0.0137
MA0148.1 0.0012
MA0149.1 0.391
MA0150.1 0.202
MA0152.1 0.43
MA0153.1 1.53714e-7
MA0154.1 0.361
MA0155.1 0.268
MA0156.1 0.847
MA0157.1 0.00321
MA0159.1 0.998
MA0160.1 0.0189
MA0162.1 0.844
MA0163.1 0.221
MA0164.1 0.919
MA0258.1 0.888
MA0259.1 0.0353



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: CNhs10481

Novel motif P-value
1 0.496
10 0.099
100 0.0923
101 0.604
102 0.835
103 0.582
104 0.322
105 0.237
106 0.0289
107 0.0978
108 0.745
109 0.838
11 0.53
110 0.82
111 0.599
112 0.4
113 0.531
114 0.601
115 0.65
116 0.209
117 0.0233
118 0.0762
119 0.394
12 0.487
120 0.942
121 0.889
122 0.709
123 0.295
124 0.156
125 0.398
126 0.591
127 0.318
128 0.0649
129 0.181
13 0.751
130 0.199
131 0.854
132 0.777
133 0.637
134 0.22
135 0.915
136 0.693
137 0.872
138 0.0191
139 0.308
14 0.442
140 0.0565
141 0.262
142 0.994
143 0.527
144 0.844
145 0.629
146 0.104
147 0.776
148 0.866
149 0.0426
15 0.96
150 0.375
151 0.339
152 0.00965
153 0.755
154 0.631
155 0.278
156 0.0259
157 0.771
158 0.425
159 0.894
160 0.536
161 0.911
162 0.795
163 0.0517
164 0.672
165 0.704
166 0.00113
167 0.122
168 0.102
169 0.0756
17 0.175
18 0.281
19 0.122
2 0.018
20 0.0386
21 0.6
22 0.329
23 0.135
24 0.364
25 0.0584
26 0.594
27 0.467
28 0.691
29 0.107
3 0.414
30 0.355
31 0.754
32 0.508
33 0.429
34 0.596
35 0.198
36 0.0445
37 0.469
38 0.889
39 0.155
4 0.295
40 0.255
41 0.0757
42 0.354
43 0.65
44 0.304
45 0.0475
46 0.616
47 0.88
48 0.938
49 0.888
5 0.838
50 0.49
51 0.712
52 0.0594
53 0.105
54 0.682
55 0.973
56 0.901
57 0.349
58 0.946
59 0.383
6 0.485
60 0.056
61 0.851
62 0.556
63 0.55
64 0.685
65 0.827
66 0.83
67 0.609
68 0.0175
69 0.948
7 0.754
70 0.136
71 0.377
72 0.23
73 0.118
74 0.532
75 0.14
76 0.0341
77 0.382
78 0.821
79 0.914
8 0.128
80 0.652
81 0.174
82 0.224
83 0.89
84 0.618
85 0.463
86 0.645
87 0.632
88 0.602
89 0.232
9 0.231
90 0.046
91 0.871
92 0.308
93 0.0212
94 0.0855
95 0.544
96 0.686
97 0.216
98 0.952
99 0.602



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: CNhs10481


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)
0007023 (adult organism)
0001255 (urinary bladder)
0002100 (trunk)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0002323 (body cavity)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0001556 (lower urinary tract)
0001008 (renal system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011437 (mouse urinary bladder- adult 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:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)