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FF:458-17B6

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Name:lung, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs10998
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 stage16 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  SAMD00005297
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10998 CAGE DRX009034 DRR009908
Accession ID Mm9

Library idBAMCTSS
CNhs10998 DRZ001333 DRZ002716
Accession ID Mm10

Library idBAMCTSS
CNhs10998 DRZ012683 DRZ014066
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

CNhs10998

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0577
1001 0.0168
1002 0.0363
1003 0.0915
1004 0
1005 -0.0818
1006 -0.143
1007 0.109
1008 0
1009 0.213
101 0.0608
1010 0
1011 0
1012 0
1013 -0.128
1014 0.487
1015 0.154
1016 0.2
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.0916
1023 0
1024 0.0746
1025 1.121
1026 0
1027 0
1028 0
1029 0.283
103 0.147
1030 0
1031 0.391
1032 -0.00941
1033 0.0503
1034 0.0916
1035 0
1036 0.194
1037 0
1038 0.125
1039 -0.117
104 0
1040 0.253
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: CNhs10998
Jaspar motif P-value
MA0002.2 0.00173
MA0003.1 0.492
MA0004.1 0.467
MA0006.1 0.881
MA0007.1 0.594
MA0009.1 0.748
MA0014.1 0.442
MA0017.1 4.21473e-5
MA0018.2 0.0141
MA0019.1 0.403
MA0024.1 2.66236e-8
MA0025.1 0.165
MA0027.1 0.165
MA0028.1 0.203
MA0029.1 0.651
MA0030.1 0.693
MA0031.1 0.227
MA0035.2 1.03672e-4
MA0038.1 0.464
MA0039.2 0.206
MA0040.1 0.548
MA0041.1 0.215
MA0042.1 0.351
MA0043.1 0.47
MA0046.1 1.03235e-8
MA0047.2 0.281
MA0048.1 2.32686e-4
MA0050.1 0.033
MA0051.1 0.0061
MA0052.1 0.0114
MA0055.1 1.66934e-4
MA0057.1 0.371
MA0058.1 0.242
MA0059.1 0.866
MA0060.1 0.00453
MA0061.1 0.14
MA0062.2 0.859
MA0065.2 2.31151e-4
MA0066.1 0.149
MA0067.1 0.0951
MA0068.1 0.949
MA0069.1 0.611
MA0070.1 0.719
MA0071.1 0.0169
MA0072.1 0.00772
MA0073.1 0.596
MA0074.1 0.301
MA0076.1 0.615
MA0077.1 0.677
MA0078.1 0.317
MA0079.2 0.15
MA0080.2 3.11992e-4
MA0081.1 0.386
MA0083.1 0.12
MA0084.1 0.555
MA0087.1 0.389
MA0088.1 0.655
MA0090.1 0.201
MA0091.1 0.837
MA0092.1 0.985
MA0093.1 0.439
MA0099.2 1.40392e-5
MA0100.1 0.385
MA0101.1 0.46
MA0102.2 0.848
MA0103.1 0.0143
MA0104.2 0.316
MA0105.1 0.178
MA0106.1 0.137
MA0107.1 0.355
MA0108.2 0.00292
MA0111.1 0.609
MA0112.2 0.0578
MA0113.1 0.425
MA0114.1 8.26718e-6
MA0115.1 0.00629
MA0116.1 0.98
MA0117.1 0.00681
MA0119.1 0.465
MA0122.1 0.733
MA0124.1 0.533
MA0125.1 0.902
MA0131.1 0.305
MA0135.1 0.166
MA0136.1 4.77776e-4
MA0137.2 0.13
MA0138.2 8.09726e-6
MA0139.1 0.928
MA0140.1 0.0384
MA0141.1 3.31588e-4
MA0142.1 0.433
MA0143.1 0.491
MA0144.1 0.234
MA0145.1 0.414
MA0146.1 0.557
MA0147.1 0.304
MA0148.1 0.622
MA0149.1 0.33
MA0150.1 1.375e-5
MA0152.1 0.568
MA0153.1 4.75115e-5
MA0154.1 0.148
MA0155.1 0.162
MA0156.1 0.203
MA0157.1 0.34
MA0159.1 0.00533
MA0160.1 1.27878e-4
MA0162.1 0.602
MA0163.1 0.664
MA0164.1 0.97
MA0258.1 0.00455
MA0259.1 0.63



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: CNhs10998
Novel motif P-value
1 0.159
10 0.701
100 0.587
101 0.964
102 0.63
103 0.857
104 0.429
105 0.749
106 0.54
107 0.806
108 0.618
109 0.223
11 0.16
110 0.983
111 0.145
112 0.239
113 0.469
114 0.0588
115 0.496
116 0.932
117 0.857
118 0.924
119 0.199
12 0.421
120 0.158
121 0.766
122 0.76
123 0.323
124 0.778
125 0.471
126 0.56
127 0.552
128 0.502
129 0.121
13 0.00651
130 0.0175
131 0.707
132 0.876
133 0.648
134 0.417
135 0.417
136 0.674
137 0.793
138 0.291
139 0.0143
14 0.291
140 0.778
141 0.497
142 0.867
143 0.55
144 0.836
145 0.672
146 0.108
147 0.596
148 0.154
149 0.84
15 0.203
150 0.341
151 0.0469
152 0.256
153 0.502
154 0.413
155 0.566
156 0.029
157 0.877
158 0.785
159 0.0259
160 0.134
161 0.822
162 0.932
163 0.0247
164 0.621
165 0.266
166 0.182
167 0.603
168 0.7
169 0.853
17 0.197
18 0.0242
19 0.734
2 0.409
20 0.397
21 0.36
22 0.674
23 0.159
24 0.819
25 0.149
26 0.0639
27 0.147
28 0.366
29 0.531
3 0.568
30 0.536
31 0.17
32 0.058
33 0.846
34 0.775
35 0.118
36 0.537
37 0.743
38 0.912
39 0.301
4 0.761
40 0.504
41 0.193
42 0.926
43 0.38
44 0.0318
45 0.26
46 0.569
47 0.353
48 0.208
49 0.229
5 0.606
50 0.442
51 0.694
52 0.947
53 0.698
54 0.229
55 0.814
56 0.374
57 0.85
58 0.464
59 0.439
6 0.629
60 0.815
61 0.602
62 0.0975
63 0.572
64 0.373
65 0.298
66 0.717
67 0.499
68 0.202
69 0.699
7 0.903
70 0.00497
71 0.452
72 0.0764
73 0.149
74 0.647
75 0.404
76 0.391
77 0.293
78 0.209
79 0.83
8 0.391
80 0.111
81 0.029
82 0.288
83 0.665
84 0.0745
85 0.0812
86 0.577
87 0.00203
88 0.338
89 0.213
9 0.886
90 0.0827
91 0.988
92 0.0724
93 0.728
94 0.423
95 0.65
96 0.402
97 0.173
98 0.343
99 0.879



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: CNhs10998


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)
0000299 (mouse embryonic day 16 sample)
0011357 (mouse lung- embryo E16 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)