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FF:715-19A3

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Name:lung, neonate N07
Species:Mouse (Mus musculus)
Library ID:CNhs11111
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 stage7 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  SAMD00005558
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11111 CAGE DRX009039 DRR009913
Accession ID Mm9

Library idBAMCTSS
CNhs11111 DRZ001338 DRZ002721
Accession ID Mm10

Library idBAMCTSS
CNhs11111 DRZ012688 DRZ014071
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

CNhs11111

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0869
1001 0.146
1002 -0.0798
1003 0.327
1004 0
1005 0.048
1006 0.0764
1007 0.0873
1008 0
1009 0.446
101 -0.0507
1010 0
1011 -0.108
1012 0.0869
1013 -0.0407
1014 0.231
1015 -0.0272
1016 0.31
1017 0
1018 0.0869
1019 0
102 0
1020 0
1021 0
1022 0.0353
1023 0
1024 0.717
1025 1.319
1026 0
1027 0
1028 0
1029 0.436
103 0.276
1030 0.0869
1031 0.566
1032 0.0971
1033 -0.022
1034 0.159
1035 0
1036 0.0101
1037 0
1038 0.598
1039 0.0755
104 0
1040 0.502
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: CNhs11111
Jaspar motif P-value
MA0002.2 0.196
MA0003.1 0.123
MA0004.1 0.00899
MA0006.1 0.0156
MA0007.1 0.0448
MA0009.1 0.943
MA0014.1 0.96
MA0017.1 2.74956e-4
MA0018.2 2.01189e-4
MA0019.1 0.72
MA0024.1 0.82
MA0025.1 0.527
MA0027.1 0.367
MA0028.1 1.31617e-5
MA0029.1 0.504
MA0030.1 0.138
MA0031.1 0.169
MA0035.2 8.85344e-4
MA0038.1 0.879
MA0039.2 0.092
MA0040.1 0.817
MA0041.1 0.285
MA0042.1 0.525
MA0043.1 0.0156
MA0046.1 8.70528e-11
MA0047.2 0.00174
MA0048.1 0.466
MA0050.1 0.0124
MA0051.1 0.148
MA0052.1 0.586
MA0055.1 0.923
MA0057.1 0.701
MA0058.1 6.52627e-4
MA0059.1 7.10455e-4
MA0060.1 2.62165e-5
MA0061.1 0.533
MA0062.2 3.99855e-7
MA0065.2 0.00145
MA0066.1 0.162
MA0067.1 0.31
MA0068.1 0.882
MA0069.1 0.612
MA0070.1 0.482
MA0071.1 0.00975
MA0072.1 0.0287
MA0073.1 0.598
MA0074.1 0.734
MA0076.1 1.22032e-6
MA0077.1 0.182
MA0078.1 0.00523
MA0079.2 0.13
MA0080.2 0.03
MA0081.1 0.749
MA0083.1 1.54819e-4
MA0084.1 0.412
MA0087.1 0.232
MA0088.1 0.125
MA0090.1 0.051
MA0091.1 0.928
MA0092.1 0.789
MA0093.1 0.00497
MA0099.2 0.0422
MA0100.1 0.155
MA0101.1 0.735
MA0102.2 0.905
MA0103.1 0.0109
MA0104.2 1.3983e-5
MA0105.1 0.482
MA0106.1 0.018
MA0107.1 0.0586
MA0108.2 0.392
MA0111.1 0.684
MA0112.2 0.725
MA0113.1 0.827
MA0114.1 1.78766e-7
MA0115.1 0.00637
MA0116.1 0.571
MA0117.1 0.152
MA0119.1 0.0843
MA0122.1 0.325
MA0124.1 0.283
MA0125.1 0.124
MA0131.1 0.341
MA0135.1 0.354
MA0136.1 0.211
MA0137.2 0.184
MA0138.2 0.0425
MA0139.1 0.557
MA0140.1 0.292
MA0141.1 2.00246e-6
MA0142.1 0.735
MA0143.1 0.845
MA0144.1 0.825
MA0145.1 0.001
MA0146.1 0.892
MA0147.1 1.36997e-6
MA0148.1 0.0178
MA0149.1 0.817
MA0150.1 0.00268
MA0152.1 0.0457
MA0153.1 1.67719e-6
MA0154.1 0.158
MA0155.1 0.135
MA0156.1 0.976
MA0157.1 0.163
MA0159.1 0.00445
MA0160.1 4.12779e-5
MA0162.1 0.102
MA0163.1 0.206
MA0164.1 0.493
MA0258.1 0.129
MA0259.1 0.0141



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: CNhs11111
Novel motif P-value
1 0.422
10 0.302
100 0.293
101 0.806
102 0.836
103 0.887
104 0.859
105 0.753
106 0.00179
107 2.12936e-4
108 0.765
109 0.16
11 0.227
110 0.423
111 0.213
112 0.911
113 0.732
114 0.138
115 0.462
116 0.892
117 0.0168
118 0.417
119 0.898
12 0.627
120 0.142
121 0.733
122 0.685
123 0.62
124 0.539
125 0.914
126 0.537
127 0.529
128 0.00916
129 0.341
13 0.172
130 0.0101
131 0.118
132 0.496
133 0.501
134 0.848
135 0.159
136 0.548
137 0.329
138 0.0347
139 0.211
14 0.899
140 0.659
141 0.72
142 0.457
143 0.646
144 0.511
145 0.479
146 0.709
147 0.654
148 0.687
149 0.268
15 0.875
150 0.0575
151 0.769
152 0.0916
153 0.575
154 0.0686
155 0.711
156 0.0228
157 0.931
158 0.864
159 0.0459
160 0.117
161 0.817
162 0.318
163 0.81
164 0.739
165 0.35
166 0.029
167 0.504
168 0.715
169 0.0627
17 0.663
18 0.0201
19 0.0691
2 0.265
20 0.54
21 0.673
22 0.329
23 0.214
24 0.853
25 0.0423
26 0.146
27 0.641
28 0.661
29 0.111
3 0.42
30 0.815
31 0.499
32 0.134
33 0.569
34 0.589
35 0.0247
36 0.599
37 0.483
38 0.591
39 0.0882
4 0.841
40 0.985
41 0.258
42 0.714
43 0.488
44 0.0956
45 0.308
46 0.679
47 0.481
48 0.331
49 0.866
5 0.612
50 0.27
51 0.898
52 0.0415
53 0.6
54 0.753
55 0.797
56 0.953
57 0.567
58 0.514
59 0.31
6 0.872
60 0.102
61 0.586
62 0.225
63 0.794
64 0.201
65 0.879
66 0.135
67 0.877
68 0.294
69 0.636
7 0.98
70 0.0921
71 0.654
72 0.259
73 0.974
74 0.996
75 0.0633
76 0.994
77 0.55
78 0.182
79 0.82
8 0.158
80 0.271
81 0.144
82 0.726
83 0.908
84 0.164
85 0.54
86 0.733
87 7.91034e-4
88 0.736
89 0.672
9 0.324
90 0.0776
91 0.241
92 0.457
93 0.487
94 0.369
95 0.29
96 0.377
97 0.803
98 0.433
99 0.255



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: CNhs11111


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)
0000313 (mouse neonate N7 sample)
0011408 (mouse lung- neonate N07 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)