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FF:432-17C5

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Name:lung, embryo E15
Species:Mouse (Mus musculus)
Library ID:CNhs11020
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
tissuelung
dev stage15 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  SAMD00005866
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11020 CAGE DRX009033 DRR009907
Accession ID Mm9

Library idBAMCTSS
CNhs11020 DRZ001332 DRZ002715
Accession ID Mm10

Library idBAMCTSS
CNhs11020 DRZ012682 DRZ014065
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 sample
Ranked 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 sample
Ranked 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

CNhs11020

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.0241
1002 0.128
1003 0.0665
1004 0
1005 -0.096
1006 -0.138
1007 0.0915
1008 0
1009 0.15
101 0.115
1010 0
1011 0
1012 0
1013 -0.17
1014 0.364
1015 0.226
1016 0.21
1017 0
1018 0
1019 0
102 0
1020 0
1021 -0.00109
1022 -0.0484
1023 0
1024 0.0956
1025 0.919
1026 0
1027 0.043
1028 0
1029 0.306
103 0.13
1030 0
1031 0.394
1032 -0.0504
1033 0.00159
1034 0
1035 0
1036 0.223
1037 0
1038 0.158
1039 -0.0991
104 0
1040 0.206
1041 0



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs11020
Jaspar motif P-value
MA0002.2 0.0037
MA0003.1 0.371
MA0004.1 0.627
MA0006.1 0.897
MA0007.1 0.285
MA0009.1 0.548
MA0014.1 0.333
MA0017.1 1.14548e-4
MA0018.2 0.0799
MA0019.1 0.529
MA0024.1 4.34845e-9
MA0025.1 0.163
MA0027.1 0.0295
MA0028.1 0.11
MA0029.1 0.637
MA0030.1 0.223
MA0031.1 0.0104
MA0035.2 0.00446
MA0038.1 0.127
MA0039.2 0.0318
MA0040.1 0.496
MA0041.1 0.202
MA0042.1 0.302
MA0043.1 0.94
MA0046.1 2.82406e-10
MA0047.2 0.708
MA0048.1 9.5677e-4
MA0050.1 2.12865e-4
MA0051.1 4.28927e-4
MA0052.1 0.0575
MA0055.1 0.00148
MA0057.1 0.224
MA0058.1 0.548
MA0059.1 0.757
MA0060.1 2.31021e-5
MA0061.1 0.0852
MA0062.2 0.702
MA0065.2 2.61974e-4
MA0066.1 0.0181
MA0067.1 0.136
MA0068.1 0.973
MA0069.1 0.615
MA0070.1 0.351
MA0071.1 0.0169
MA0072.1 0.003
MA0073.1 0.592
MA0074.1 0.521
MA0076.1 0.288
MA0077.1 0.492
MA0078.1 0.529
MA0079.2 0.0703
MA0080.2 4.66735e-5
MA0081.1 0.575
MA0083.1 0.0172
MA0084.1 0.683
MA0087.1 0.693
MA0088.1 0.641
MA0090.1 0.273
MA0091.1 0.816
MA0092.1 0.626
MA0093.1 0.612
MA0099.2 1.15773e-5
MA0100.1 0.643
MA0101.1 0.5
MA0102.2 0.673
MA0103.1 0.00388
MA0104.2 0.842
MA0105.1 0.038
MA0106.1 0.642
MA0107.1 0.309
MA0108.2 0.0644
MA0111.1 0.35
MA0112.2 0.0052
MA0113.1 0.175
MA0114.1 8.2418e-5
MA0115.1 0.0501
MA0116.1 0.504
MA0117.1 0.0293
MA0119.1 0.507
MA0122.1 0.365
MA0124.1 0.312
MA0125.1 0.943
MA0131.1 0.256
MA0135.1 0.178
MA0136.1 3.59743e-4
MA0137.2 0.049
MA0138.2 3.63063e-6
MA0139.1 0.413
MA0140.1 0.178
MA0141.1 0.00101
MA0142.1 0.666
MA0143.1 0.244
MA0144.1 0.175
MA0145.1 0.118
MA0146.1 0.561
MA0147.1 0.903
MA0148.1 0.625
MA0149.1 0.0641
MA0150.1 4.94858e-5
MA0152.1 0.0685
MA0153.1 1.37683e-5
MA0154.1 0.031
MA0155.1 0.371
MA0156.1 0.234
MA0157.1 0.164
MA0159.1 0.00614
MA0160.1 0.0012
MA0162.1 0.867
MA0163.1 0.923
MA0164.1 0.942
MA0258.1 4.21311e-4
MA0259.1 0.638



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs11020
Novel motif P-value
1 0.248
10 0.715
100 0.763
101 0.739
102 0.933
103 0.702
104 0.64
105 0.662
106 0.189
107 0.644
108 0.69
109 0.148
11 0.126
110 0.824
111 0.0697
112 0.129
113 0.567
114 0.0305
115 0.531
116 0.997
117 0.822
118 0.724
119 0.0718
12 0.534
120 0.148
121 0.74
122 0.735
123 0.166
124 0.846
125 0.595
126 0.826
127 0.451
128 0.147
129 0.0676
13 0.108
130 0.0253
131 0.314
132 0.924
133 0.659
134 0.459
135 0.819
136 0.962
137 0.887
138 0.762
139 0.00833
14 0.322
140 0.473
141 0.46
142 0.865
143 0.676
144 0.707
145 0.968
146 0.101
147 0.314
148 0.243
149 0.338
15 0.138
150 0.766
151 0.0483
152 0.177
153 0.362
154 0.722
155 0.887
156 0.335
157 0.958
158 0.845
159 0.0208
160 0.239
161 0.997
162 0.824
163 0.0366
164 0.716
165 0.214
166 0.158
167 0.927
168 0.456
169 0.372
17 0.15
18 0.0752
19 0.708
2 0.378
20 0.476
21 0.408
22 0.495
23 0.0602
24 0.668
25 0.234
26 0.0531
27 0.18
28 0.234
29 0.616
3 0.283
30 0.475
31 0.219
32 0.0944
33 0.933
34 0.679
35 0.155
36 0.528
37 0.352
38 0.544
39 0.578
4 0.633
40 0.396
41 0.224
42 0.604
43 0.266
44 0.0222
45 0.198
46 0.52
47 0.261
48 0.145
49 0.191
5 0.461
50 0.539
51 0.654
52 0.569
53 0.655
54 0.24
55 0.544
56 0.355
57 0.968
58 0.282
59 0.251
6 0.755
60 0.307
61 0.862
62 0.0599
63 0.358
64 0.309
65 0.164
66 0.77
67 0.419
68 0.155
69 0.731
7 0.876
70 7.17346e-4
71 0.544
72 0.132
73 0.0954
74 0.646
75 0.366
76 0.322
77 0.164
78 0.462
79 0.87
8 0.462
80 0.147
81 0.113
82 0.13
83 0.912
84 0.248
85 0.036
86 0.406
87 0.00466
88 0.354
89 0.245
9 0.749
90 0.0383
91 0.69
92 0.065
93 0.979
94 0.774
95 0.366
96 0.387
97 0.187
98 0.204
99 0.993



de novo motifs identified by HOMER in promoters active in this sample
Summary:The result of HOMER in this sample is shown.
Analyst:NA

library id: CNhs11020


FANTOM5 (FF) ontology


Direct parent terms

part_of relathionship
UBERON:0000310 breast

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)
0002048 (lung)
0000310 (breast)
0002100 (trunk)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0005177 (trunk region element)
0000117 (respiratory tube)
0000171 (respiration organ)
0000464 (anatomical space)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0000065 (respiratory tract)
0000170 (pair of lungs)
0001004 (respiratory system)
0001443 (chest)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

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)
0000298 (mouse embryonic day 15 sample)
0011348 (mouse lung- embryo E15 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:0001041 (foregut)
UBERON:0008947 (respiratory primordium)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)