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FF:1287-20I6

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Name:lung, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs10583
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 stage18 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  SAMD00005648
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10583 CAGE DRX009036 DRR009910
Accession ID Mm9

Library idBAMCTSS
CNhs10583 DRZ001335 DRZ002718
Accession ID Mm10

Library idBAMCTSS
CNhs10583 DRZ012685 DRZ014068
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

CNhs10583

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0454
1001 0.0496
1002 -0.0137
1003 0.0821
1004 0
1005 0.0927
1006 0
1007 0.0808
1008 0
1009 0.307
101 -0.0911
1010 0
1011 -0.0539
1012 0
1013 0.0161
1014 0.0927
1015 -0.0607
1016 0.148
1017 0
1018 0.171
1019 0
102 0
1020 0.0927
1021 -0.0487
1022 0.0726
1023 0
1024 0.542
1025 1.051
1026 0
1027 0
1028 0
1029 0.0864
103 0.0966
1030 0
1031 0.437
1032 -0.0838
1033 0
1034 0.299
1035 0
1036 -0.183
1037 0
1038 0.427
1039 -0.0359
104 0
1040 0.397
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: CNhs10583
Jaspar motif P-value
MA0002.2 0.0905
MA0003.1 0.0712
MA0004.1 0.0199
MA0006.1 0.0497
MA0007.1 0.31
MA0009.1 0.953
MA0014.1 0.736
MA0017.1 8.57076e-4
MA0018.2 0.00816
MA0019.1 0.583
MA0024.1 0.122
MA0025.1 0.209
MA0027.1 0.802
MA0028.1 0.0618
MA0029.1 0.808
MA0030.1 0.00228
MA0031.1 0.00284
MA0035.2 0.0647
MA0038.1 0.187
MA0039.2 0.00408
MA0040.1 0.442
MA0041.1 0.945
MA0042.1 0.78
MA0043.1 0.912
MA0046.1 0.458
MA0047.2 2.05155e-10
MA0048.1 0.653
MA0050.1 0.0531
MA0051.1 0.0475
MA0052.1 0.0213
MA0055.1 0.215
MA0057.1 0.575
MA0058.1 0.00511
MA0059.1 3.38948e-5
MA0060.1 0.7
MA0061.1 0.761
MA0062.2 0.0196
MA0065.2 0.0397
MA0066.1 0.0266
MA0067.1 0.329
MA0068.1 0.279
MA0069.1 0.317
MA0070.1 0.318
MA0071.1 0.0089
MA0072.1 0.201
MA0073.1 0.822
MA0074.1 0.433
MA0076.1 0.0651
MA0077.1 0.437
MA0078.1 0.0256
MA0079.2 0.0108
MA0080.2 0.105
MA0081.1 0.729
MA0083.1 3.18959e-4
MA0084.1 0.684
MA0087.1 0.278
MA0088.1 0.45
MA0090.1 0.00452
MA0091.1 0.151
MA0092.1 0.85
MA0093.1 0.0281
MA0099.2 0.0706
MA0100.1 0.972
MA0101.1 0.789
MA0102.2 0.191
MA0103.1 0.372
MA0104.2 2.1977e-4
MA0105.1 0.27
MA0106.1 0.316
MA0107.1 0.147
MA0108.2 0.031
MA0111.1 0.989
MA0112.2 0.195
MA0113.1 0.623
MA0114.1 2.53942e-4
MA0115.1 0.0152
MA0116.1 0.299
MA0117.1 0.0724
MA0119.1 0.1
MA0122.1 0.0935
MA0124.1 0.302
MA0125.1 0.728
MA0131.1 0.335
MA0135.1 0.12
MA0136.1 0.896
MA0137.2 0.93
MA0138.2 0.277
MA0139.1 0.473
MA0140.1 0.668
MA0141.1 5.19195e-7
MA0142.1 0.349
MA0143.1 0.952
MA0144.1 0.614
MA0145.1 0.00244
MA0146.1 0.309
MA0147.1 1.90183e-5
MA0148.1 7.79001e-9
MA0149.1 0.555
MA0150.1 0.00223
MA0152.1 0.907
MA0153.1 0.853
MA0154.1 0.279
MA0155.1 0.089
MA0156.1 0.237
MA0157.1 0.0344
MA0159.1 0.0183
MA0160.1 0.00573
MA0162.1 0.407
MA0163.1 0.105
MA0164.1 0.388
MA0258.1 0.0171
MA0259.1 0.0933



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: CNhs10583
Novel motif P-value
1 0.115
10 0.108
100 0.408
101 0.671
102 0.914
103 0.633
104 0.886
105 0.706
106 0.131
107 0.0757
108 0.998
109 0.989
11 0.211
110 0.713
111 0.169
112 0.442
113 0.731
114 0.429
115 0.513
116 0.826
117 0.0155
118 0.406
119 0.51
12 0.379
120 0.07
121 0.337
122 0.999
123 0.747
124 0.582
125 0.528
126 0.847
127 0.585
128 0.266
129 0.819
13 0.0198
130 0.0199
131 0.0286
132 0.48
133 0.775
134 0.399
135 0.849
136 0.0309
137 0.84
138 0.243
139 0.187
14 0.759
140 0.141
141 0.454
142 0.752
143 0.185
144 0.904
145 0.746
146 0.966
147 0.554
148 0.225
149 0.131
15 0.344
150 0.165
151 0.465
152 0.0133
153 0.486
154 0.471
155 0.962
156 0.00831
157 0.655
158 0.655
159 0.187
160 0.233
161 0.647
162 0.428
163 0.715
164 0.93
165 0.697
166 0.346
167 0.0106
168 0.988
169 0.143
17 0.645
18 0.00152
19 0.243
2 0.0918
20 0.358
21 0.931
22 0.216
23 0.366
24 0.374
25 0.0975
26 0.385
27 0.895
28 0.981
29 0.25
3 0.549
30 0.374
31 0.325
32 0.085
33 0.72
34 0.635
35 0.0024
36 0.372
37 0.552
38 0.685
39 0.25
4 0.484
40 0.702
41 0.409
42 0.686
43 0.901
44 0.0291
45 0.107
46 0.276
47 0.261
48 0.22
49 0.151
5 0.746
50 0.228
51 0.798
52 0.121
53 0.632
54 0.804
55 0.688
56 0.966
57 0.261
58 0.786
59 0.202
6 0.748
60 0.253
61 0.654
62 0.294
63 0.732
64 0.232
65 0.876
66 0.317
67 0.949
68 0.225
69 0.361
7 0.772
70 0.0552
71 0.441
72 0.272
73 0.343
74 0.993
75 0.146
76 0.413
77 0.341
78 0.221
79 0.977
8 0.125
80 0.503
81 0.0573
82 0.763
83 0.262
84 0.712
85 0.812
86 0.918
87 0.963
88 0.779
89 0.752
9 0.463
90 8.62297e-4
91 0.851
92 0.254
93 0.992
94 0.0403
95 0.507
96 0.0792
97 0.723
98 0.722
99 0.466



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: CNhs10583


FANTOM5 (FF) ontology


Direct parent terms

part_of relathionship
UBERON:0000170 pair of lungs

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)
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)
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)
0000302 (mouse embryonic day 18 sample)
0011513 (mouse lung- embryo E18 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)