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FF:1359-25C7

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Name:lung, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11119
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 stage25 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  SAMD00005110
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11119 CAGE DRX009042 DRR009916
Accession ID Mm9

Library idBAMCTSS
CNhs11119 DRZ001341 DRZ002724
Accession ID Mm10

Library idBAMCTSS
CNhs11119 DRZ012691 DRZ014074
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

CNhs11119

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0.061
100 0
1000 0.125
1001 0.239
1002 --0.0136
1003 0.127
1004 0
1005 0.171
1006 0.202
1007 0.0478
1008 0
1009 0.365
101 --0.0861
1010 0
1011 --0.0314
1012 0.181
1013 0.0727
1014 0.129
1015 --0.182
1016 0.0533
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.156
1023 0
1024 0.589
1025 1.121
1026 0
1027 0
1028 0.0692
1029 0.473
103 0.175
1030 0.407
1031 0.287
1032 0.0642
1033 0
1034 0.228
1035 0.0692
1036 --0.157
1037 0.019
1038 0.508
1039 0.0897
104 0
1040 0.491
1041 0.344



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: CNhs11119

Jaspar motif P-value
MA0002.2 0.294
MA0003.1 0.0946
MA0004.1 0.0747
MA0006.1 0.0458
MA0007.1 0.311
MA0009.1 0.364
MA0014.1 0.688
MA0017.1 0.202
MA0018.2 1.48844e-5
MA0019.1 0.898
MA0024.1 7.6534e-4
MA0025.1 0.791
MA0027.1 0.665
MA0028.1 0.0117
MA0029.1 0.72
MA0030.1 0.376
MA0031.1 0.0677
MA0035.2 0.0876
MA0038.1 0.668
MA0039.2 0.00326
MA0040.1 0.56
MA0041.1 0.257
MA0042.1 0.503
MA0043.1 0.00212
MA0046.1 1.63639e-9
MA0047.2 6.40277e-5
MA0048.1 0.857
MA0050.1 7.01164e-8
MA0051.1 1.9027e-4
MA0052.1 0.0615
MA0055.1 0.818
MA0057.1 0.277
MA0058.1 0.05
MA0059.1 0.0874
MA0060.1 8.97089e-10
MA0061.1 0.0223
MA0062.2 0.0152
MA0065.2 0.863
MA0066.1 0.876
MA0067.1 0.683
MA0068.1 0.939
MA0069.1 0.655
MA0070.1 0.532
MA0071.1 0.285
MA0072.1 0.341
MA0073.1 0.801
MA0074.1 0.566
MA0076.1 0.00459
MA0077.1 0.0116
MA0078.1 0.00438
MA0079.2 0.0609
MA0080.2 7.75867e-10
MA0081.1 0.194
MA0083.1 0.0337
MA0084.1 0.816
MA0087.1 0.562
MA0088.1 0.725
MA0090.1 0.0891
MA0091.1 0.623
MA0092.1 0.484
MA0093.1 0.0695
MA0099.2 0.273
MA0100.1 0.137
MA0101.1 0.143
MA0102.2 0.366
MA0103.1 0.93
MA0104.2 0.00285
MA0105.1 0.178
MA0106.1 0.0223
MA0107.1 0.00522
MA0108.2 0.433
MA0111.1 0.438
MA0112.2 0.0134
MA0113.1 0.87
MA0114.1 0.0345
MA0115.1 0.0971
MA0116.1 0.14
MA0117.1 0.378
MA0119.1 0.0369
MA0122.1 0.242
MA0124.1 0.52
MA0125.1 0.0519
MA0131.1 0.22
MA0135.1 0.263
MA0136.1 0.0068
MA0137.2 0.917
MA0138.2 0.828
MA0139.1 0.0648
MA0140.1 0.824
MA0141.1 0.0694
MA0142.1 0.869
MA0143.1 0.287
MA0144.1 0.345
MA0145.1 0.00151
MA0146.1 0.323
MA0147.1 0.00168
MA0148.1 1.71498e-4
MA0149.1 0.65
MA0150.1 0.37
MA0152.1 0.213
MA0153.1 3.11583e-7
MA0154.1 0.00366
MA0155.1 0.158
MA0156.1 0.0013
MA0157.1 0.0645
MA0159.1 0.83
MA0160.1 0.0888
MA0162.1 0.16
MA0163.1 0.74
MA0164.1 0.401
MA0258.1 0.242
MA0259.1 0.0108



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: CNhs11119

Novel motif P-value
1 0.641
10 0.815
100 0.26
101 0.496
102 0.588
103 0.282
104 0.619
105 0.439
106 9.21095e-4
107 0.00577
108 0.667
109 0.172
11 0.859
110 0.867
111 0.867
112 0.201
113 0.975
114 0.386
115 0.535
116 0.914
117 0.326
118 0.812
119 0.0804
12 0.681
120 0.169
121 0.638
122 0.815
123 0.96
124 0.579
125 0.449
126 0.292
127 0.223
128 0.00447
129 0.0879
13 0.0147
130 0.00761
131 0.126
132 0.338
133 0.463
134 0.744
135 0.583
136 0.337
137 0.326
138 0.0496
139 0.643
14 0.29
140 0.561
141 0.265
142 0.315
143 0.611
144 0.721
145 0.168
146 0.819
147 0.825
148 0.306
149 0.125
15 0.414
150 0.145
151 0.181
152 0.0251
153 0.583
154 0.321
155 0.678
156 0.357
157 0.975
158 0.915
159 0.0333
160 0.0752
161 0.466
162 0.403
163 0.852
164 0.568
165 0.766
166 0.235
167 0.764
168 0.945
169 0.00869
17 0.345
18 0.155
19 0.036
2 0.129
20 0.374
21 0.617
22 0.103
23 0.0333
24 0.316
25 0.324
26 0.0626
27 0.867
28 0.52
29 0.511
3 0.454
30 0.86
31 0.884
32 0.714
33 0.74
34 0.421
35 0.315
36 0.871
37 0.0403
38 0.199
39 0.076
4 0.715
40 0.61
41 0.392
42 0.607
43 0.135
44 0.577
45 0.169
46 0.687
47 0.629
48 0.894
49 0.261
5 0.521
50 0.321
51 0.659
52 0.0668
53 0.402
54 0.806
55 0.895
56 0.356
57 0.998
58 0.586
59 0.0478
6 0.923
60 0.0336
61 0.739
62 0.803
63 0.142
64 0.716
65 0.201
66 0.105
67 0.491
68 0.632
69 0.986
7 0.346
70 0.437
71 0.308
72 0.91
73 0.145
74 0.475
75 0.751
76 0.718
77 0.23
78 0.861
79 0.616
8 0.883
80 0.811
81 0.858
82 0.329
83 0.253
84 0.279
85 0.0422
86 0.826
87 0.0206
88 0.979
89 0.343
9 0.154
90 0.642
91 0.167
92 0.136
93 0.595
94 0.864
95 0.656
96 0.813
97 0.847
98 0.704
99 0.259



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: CNhs11119


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)
0000309 (mouse neonate N25 sample)
0011488 (mouse lung- neonate N25 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)