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FF:683-20E5

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Name:lung, neonate N06
Species:Mouse (Mus musculus)
Library ID:CNhs11212
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 stage6 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  SAMD00005933
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11212 CAGE DRX009038 DRR009912
Accession ID Mm9

Library idBAMCTSS
CNhs11212 DRZ001337 DRZ002720
Accession ID Mm10

Library idBAMCTSS
CNhs11212 DRZ012687 DRZ014070
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11212

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0318
1001 0.145
1002 -0.0623
1003 0.15
1004 0
1005 0.173
1006 0.0636
1007 0.147
1008 0.0636
1009 0.428
101 -0.0207
1010 0
1011 -0.0142
1012 0.0636
1013 -0.0195
1014 0.0831
1015 -0.012
1016 0.205
1017 0
1018 0
1019 0
102 0
1020 0
1021 -0.00561
1022 0.0999
1023 0
1024 0.594
1025 1.285
1026 0
1027 0
1028 0
1029 0.487
103 0.187
1030 0.0636
1031 0.568
1032 0.0549
1033 0
1034 0.168
1035 0
1036 -0.0446
1037 0
1038 0.567
1039 -0.049
104 0
1040 0.531
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: CNhs11212
Jaspar motif P-value
MA0002.2 0.319
MA0003.1 0.1
MA0004.1 0.0135
MA0006.1 0.0349
MA0007.1 0.0535
MA0009.1 0.954
MA0014.1 0.933
MA0017.1 4.11734e-5
MA0018.2 0.00367
MA0019.1 0.562
MA0024.1 0.43
MA0025.1 0.866
MA0027.1 0.422
MA0028.1 0.00136
MA0029.1 0.9
MA0030.1 0.0159
MA0031.1 0.0245
MA0035.2 0.107
MA0038.1 0.893
MA0039.2 0.026
MA0040.1 0.471
MA0041.1 0.311
MA0042.1 0.487
MA0043.1 0.359
MA0046.1 1.07895e-9
MA0047.2 1.32094e-5
MA0048.1 0.756
MA0050.1 0.0368
MA0051.1 0.12
MA0052.1 0.0914
MA0055.1 0.607
MA0057.1 0.755
MA0058.1 0.00161
MA0059.1 4.31961e-5
MA0060.1 0.00787
MA0061.1 0.702
MA0062.2 0.00184
MA0065.2 0.00135
MA0066.1 0.0362
MA0067.1 0.497
MA0068.1 0.755
MA0069.1 0.757
MA0070.1 0.909
MA0071.1 0.00317
MA0072.1 0.0436
MA0073.1 0.669
MA0074.1 0.273
MA0076.1 8.7368e-4
MA0077.1 0.342
MA0078.1 0.00816
MA0079.2 0.065
MA0080.2 2.35562e-4
MA0081.1 0.281
MA0083.1 2.88279e-6
MA0084.1 0.741
MA0087.1 0.546
MA0088.1 0.284
MA0090.1 0.0129
MA0091.1 0.477
MA0092.1 0.746
MA0093.1 0.00993
MA0099.2 0.0535
MA0100.1 0.493
MA0101.1 0.477
MA0102.2 0.451
MA0103.1 0.0122
MA0104.2 6.0077e-5
MA0105.1 0.0343
MA0106.1 0.146
MA0107.1 0.0334
MA0108.2 0.831
MA0111.1 0.913
MA0112.2 0.0744
MA0113.1 0.613
MA0114.1 7.53432e-7
MA0115.1 0.00506
MA0116.1 0.0328
MA0117.1 0.207
MA0119.1 0.378
MA0122.1 0.172
MA0124.1 0.144
MA0125.1 0.325
MA0131.1 0.512
MA0135.1 0.801
MA0136.1 0.476
MA0137.2 0.579
MA0138.2 0.132
MA0139.1 0.9
MA0140.1 0.344
MA0141.1 4.52091e-7
MA0142.1 0.341
MA0143.1 0.951
MA0144.1 0.649
MA0145.1 0.00304
MA0146.1 0.928
MA0147.1 3.5889e-6
MA0148.1 1.07242e-4
MA0149.1 0.65
MA0150.1 0.00202
MA0152.1 0.667
MA0153.1 1.05985e-5
MA0154.1 0.625
MA0155.1 0.301
MA0156.1 0.0428
MA0157.1 0.0365
MA0159.1 5.84476e-4
MA0160.1 1.31606e-4
MA0162.1 0.506
MA0163.1 0.00225
MA0164.1 0.312
MA0258.1 0.0112
MA0259.1 0.0233



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: CNhs11212
Novel motif P-value
1 0.244
10 0.0844
100 0.191
101 0.553
102 0.731
103 0.502
104 0.696
105 0.884
106 0.0892
107 0.00666
108 0.659
109 0.155
11 0.0952
110 0.231
111 0.0658
112 0.614
113 0.873
114 0.0883
115 0.411
116 0.399
117 0.0103
118 0.346
119 0.862
12 0.46
120 0.0954
121 0.231
122 0.81
123 0.65
124 0.352
125 0.531
126 0.861
127 0.633
128 0.0997
129 0.58
13 0.449
130 0.012
131 0.0359
132 0.808
133 0.628
134 0.508
135 0.302
136 0.981
137 0.244
138 0.149
139 0.184
14 0.807
140 0.464
141 0.822
142 0.696
143 0.393
144 0.712
145 0.88
146 0.921
147 0.46
148 0.821
149 0.264
15 0.513
150 0.365
151 0.844
152 0.122
153 0.766
154 0.489
155 0.705
156 0.00113
157 0.868
158 0.832
159 0.0353
160 0.258
161 0.592
162 0.333
163 0.84
164 0.727
165 0.367
166 0.153
167 0.354
168 0.973
169 0.305
17 0.463
18 0.00535
19 0.152
2 0.162
20 0.189
21 0.924
22 0.402
23 0.221
24 0.725
25 0.177
26 0.619
27 0.715
28 0.769
29 0.0569
3 0.235
30 0.568
31 0.422
32 0.121
33 0.593
34 0.495
35 0.00563
36 0.369
37 0.958
38 0.563
39 0.183
4 0.78
40 0.988
41 0.331
42 0.625
43 0.706
44 0.0272
45 0.256
46 0.388
47 0.301
48 0.225
49 0.244
5 0.653
50 0.405
51 0.893
52 0.12
53 0.362
54 0.943
55 0.827
56 0.745
57 0.308
58 0.741
59 0.54
6 0.746
60 0.199
61 0.692
62 0.278
63 0.967
64 0.113
65 0.859
66 0.181
67 0.887
68 0.174
69 0.532
7 0.84
70 0.0257
71 0.178
72 0.258
73 0.628
74 0.945
75 0.0201
76 0.5
77 0.564
78 0.155
79 0.772
8 0.0642
80 0.658
81 0.14
82 0.403
83 0.823
84 0.494
85 0.886
86 0.761
87 0.0083
88 0.609
89 0.674
9 0.336
90 0.0126
91 0.662
92 0.52
93 0.472
94 0.344
95 0.351
96 0.328
97 0.696
98 0.582
99 0.353



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: CNhs11212


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000312 (mouse neonate N6 sample)
0011402 (mouse lung- neonate N06 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)