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FF:750-23E6

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Name:lung, neonate N10
Species:Mouse (Mus musculus)
Library ID:CNhs11219
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 stage10 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  SAMD00005871
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11219 CAGE DRX009040 DRR009914
Accession ID Mm9

Library idBAMCTSS
CNhs11219 DRZ001339 DRZ002722
Accession ID Mm10

Library idBAMCTSS
CNhs11219 DRZ012689 DRZ014072
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

CNhs11219

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0643
1001 0.165
1002 --0.0845
1003 0.184
1004 0
1005 0.0813
1006 0.149
1007 0.103
1008 0
1009 0.415
101 --0.0689
1010 0
1011 --0.0835
1012 0.0643
1013 0.0055
1014 0.0847
1015 0.058
1016 0.352
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0156
1022 0.0109
1023 0
1024 0.562
1025 1.22
1026 0
1027 0.00328
1028 0
1029 0.455
103 0.228
1030 0.255
1031 0.533
1032 0.0856
1033 --0.0752
1034 0.12
1035 0.0643
1036 --0.194
1037 0
1038 0.698
1039 --0.0641
104 0
1040 0.522
1041 0.255



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: CNhs11219

Jaspar motif P-value
MA0002.2 0.389
MA0003.1 0.288
MA0004.1 0.023
MA0006.1 0.0373
MA0007.1 0.172
MA0009.1 0.783
MA0014.1 0.929
MA0017.1 4.84668e-5
MA0018.2 0.00577
MA0019.1 0.756
MA0024.1 0.206
MA0025.1 0.573
MA0027.1 0.45
MA0028.1 0.00137
MA0029.1 0.607
MA0030.1 0.0118
MA0031.1 0.0282
MA0035.2 0.00777
MA0038.1 0.778
MA0039.2 0.0554
MA0040.1 0.562
MA0041.1 0.349
MA0042.1 0.738
MA0043.1 0.224
MA0046.1 2.71266e-8
MA0047.2 4.82481e-6
MA0048.1 0.828
MA0050.1 0.0219
MA0051.1 0.0551
MA0052.1 0.238
MA0055.1 0.845
MA0057.1 0.678
MA0058.1 0.0039
MA0059.1 7.61001e-5
MA0060.1 0.00121
MA0061.1 0.696
MA0062.2 6.57742e-4
MA0065.2 0.00159
MA0066.1 0.196
MA0067.1 0.613
MA0068.1 0.591
MA0069.1 0.955
MA0070.1 0.978
MA0071.1 0.00609
MA0072.1 0.0427
MA0073.1 0.627
MA0074.1 0.715
MA0076.1 5.35948e-4
MA0077.1 0.418
MA0078.1 0.0109
MA0079.2 0.0408
MA0080.2 0.00542
MA0081.1 0.275
MA0083.1 4.07066e-6
MA0084.1 0.887
MA0087.1 0.753
MA0088.1 0.102
MA0090.1 0.0137
MA0091.1 0.304
MA0092.1 0.896
MA0093.1 0.0191
MA0099.2 0.0451
MA0100.1 0.162
MA0101.1 0.38
MA0102.2 0.677
MA0103.1 0.0187
MA0104.2 1.45973e-4
MA0105.1 0.037
MA0106.1 0.147
MA0107.1 0.0116
MA0108.2 0.966
MA0111.1 0.778
MA0112.2 0.0399
MA0113.1 0.445
MA0114.1 1.38439e-6
MA0115.1 0.00334
MA0116.1 0.00963
MA0117.1 0.206
MA0119.1 0.449
MA0122.1 0.285
MA0124.1 0.122
MA0125.1 0.185
MA0131.1 0.281
MA0135.1 0.579
MA0136.1 0.886
MA0137.2 0.312
MA0138.2 0.372
MA0139.1 0.608
MA0140.1 0.146
MA0141.1 2.87719e-6
MA0142.1 0.395
MA0143.1 0.841
MA0144.1 0.882
MA0145.1 0.0098
MA0146.1 0.795
MA0147.1 1.22156e-5
MA0148.1 1.95608e-4
MA0149.1 0.638
MA0150.1 8.42972e-4
MA0152.1 0.274
MA0153.1 1.62036e-6
MA0154.1 0.681
MA0155.1 0.507
MA0156.1 0.161
MA0157.1 0.101
MA0159.1 0.00172
MA0160.1 1.55929e-4
MA0162.1 0.764
MA0163.1 9.27748e-4
MA0164.1 0.504
MA0258.1 0.0132
MA0259.1 0.019



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: CNhs11219

Novel motif P-value
1 0.176
10 0.0512
100 0.187
101 0.721
102 0.839
103 0.295
104 0.774
105 0.416
106 0.0846
107 0.00872
108 0.638
109 0.3
11 0.107
110 0.125
111 0.0628
112 0.882
113 0.875
114 0.161
115 0.369
116 0.275
117 0.0125
118 0.302
119 0.965
12 0.496
120 0.131
121 0.168
122 0.596
123 0.991
124 0.586
125 0.672
126 0.691
127 0.196
128 0.0563
129 0.812
13 0.891
130 0.0344
131 0.0886
132 0.438
133 0.366
134 0.777
135 0.359
136 0.871
137 0.44
138 0.0957
139 0.237
14 0.732
140 0.998
141 0.749
142 0.82
143 0.457
144 0.792
145 0.923
146 0.942
147 0.389
148 0.82
149 0.371
15 0.376
150 0.326
151 0.728
152 0.0389
153 0.542
154 0.685
155 0.664
156 0.4
157 0.713
158 0.879
159 0.0413
160 0.498
161 0.713
162 0.287
163 0.714
164 0.493
165 0.19
166 0.0782
167 0.521
168 0.748
169 0.462
17 0.483
18 0.00632
19 0.295
2 0.33
20 0.378
21 0.915
22 0.495
23 0.221
24 0.761
25 0.0479
26 0.507
27 0.543
28 0.836
29 0.0364
3 0.223
30 0.565
31 0.466
32 0.299
33 0.448
34 0.462
35 0.0107
36 0.186
37 0.739
38 0.629
39 0.174
4 0.782
40 0.777
41 0.292
42 0.534
43 0.995
44 0.0303
45 0.253
46 0.314
47 0.245
48 0.176
49 0.416
5 0.71
50 0.341
51 0.828
52 0.0886
53 0.582
54 0.948
55 0.666
56 0.884
57 0.175
58 0.646
59 0.62
6 0.636
60 0.246
61 0.743
62 0.195
63 0.91
64 0.12
65 0.958
66 0.166
67 0.865
68 0.33
69 0.21
7 0.687
70 0.0679
71 0.0641
72 0.441
73 0.989
74 0.915
75 0.0271
76 0.613
77 0.425
78 0.192
79 0.982
8 0.0496
80 0.451
81 0.0567
82 0.414
83 0.854
84 0.862
85 0.952
86 0.692
87 0.0043
88 0.728
89 0.378
9 0.424
90 0.00693
91 0.576
92 0.827
93 0.577
94 0.269
95 0.45
96 0.106
97 0.581
98 0.272
99 0.595



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: CNhs11219


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)
0000305 (mouse neonate N10 sample)
0011415 (mouse lung- neonate N10 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)