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FF:1394-42H2

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Name:lung, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11133
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 stage30 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  SAMD00004674
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11133 CAGE DRX009043 DRR009917
Accession ID Mm9

Library idBAMCTSS
CNhs11133 DRZ001342 DRZ002725
Accession ID Mm10

Library idBAMCTSS
CNhs11133 DRZ012692 DRZ014075
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

CNhs11133

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0569
1001 0.244
1002 0.0331
1003 0.112
1004 0
1005 0.166
1006 0.0139
1007 0.0371
1008 0
1009 0.399
101 -0.132
1010 0
1011 -0.0958
1012 0.0598
1013 0.0242
1014 0.0174
1015 -0.155
1016 0.0634
1017 0
1018 0.0461
1019 0
102 0
1020 0
1021 0.0444
1022 0.157
1023 0
1024 0.608
1025 1.238
1026 0
1027 0
1028 0
1029 0.247
103 0.0913
1030 0.236
1031 0.29
1032 0.106
1033 0
1034 0.437
1035 0.0375
1036 -0.153
1037 0.00849
1038 0.481
1039 0.101
104 0
1040 0.527
1041 0.271



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: CNhs11133
Jaspar motif P-value
MA0002.2 0.429
MA0003.1 0.122
MA0004.1 0.0425
MA0006.1 0.0251
MA0007.1 0.92
MA0009.1 0.637
MA0014.1 0.684
MA0017.1 0.131
MA0018.2 2.40091e-4
MA0019.1 0.816
MA0024.1 2.83067e-5
MA0025.1 0.232
MA0027.1 0.336
MA0028.1 0.00816
MA0029.1 0.422
MA0030.1 0.0538
MA0031.1 2.3186e-4
MA0035.2 0.197
MA0038.1 0.82
MA0039.2 0.00134
MA0040.1 0.436
MA0041.1 0.333
MA0042.1 0.577
MA0043.1 0.0873
MA0046.1 8.42748e-8
MA0047.2 4.6797e-7
MA0048.1 0.887
MA0050.1 5.32429e-8
MA0051.1 3.98371e-5
MA0052.1 0.985
MA0055.1 0.829
MA0057.1 0.311
MA0058.1 0.0307
MA0059.1 0.0112
MA0060.1 4.38761e-7
MA0061.1 0.127
MA0062.2 0.0247
MA0065.2 0.559
MA0066.1 0.495
MA0067.1 0.903
MA0068.1 0.0996
MA0069.1 0.65
MA0070.1 0.804
MA0071.1 0.505
MA0072.1 0.423
MA0073.1 0.826
MA0074.1 0.558
MA0076.1 0.0038
MA0077.1 0.0413
MA0078.1 4.82441e-4
MA0079.2 0.0067
MA0080.2 6.1009e-8
MA0081.1 0.247
MA0083.1 0.159
MA0084.1 0.7
MA0087.1 0.959
MA0088.1 0.861
MA0090.1 0.0232
MA0091.1 0.773
MA0092.1 0.646
MA0093.1 0.0366
MA0099.2 0.841
MA0100.1 0.228
MA0101.1 0.178
MA0102.2 0.216
MA0103.1 0.821
MA0104.2 4.91083e-4
MA0105.1 0.876
MA0106.1 0.0288
MA0107.1 0.00519
MA0108.2 0.149
MA0111.1 0.523
MA0112.2 0.126
MA0113.1 0.133
MA0114.1 0.00868
MA0115.1 0.253
MA0116.1 0.705
MA0117.1 0.651
MA0119.1 0.0473
MA0122.1 0.27
MA0124.1 0.79
MA0125.1 0.103
MA0131.1 0.212
MA0135.1 0.831
MA0136.1 0.00591
MA0137.2 0.395
MA0138.2 0.507
MA0139.1 0.122
MA0140.1 0.644
MA0141.1 0.0146
MA0142.1 0.83
MA0143.1 0.239
MA0144.1 0.0989
MA0145.1 5.45955e-4
MA0146.1 0.22
MA0147.1 1.07828e-4
MA0148.1 9.93415e-6
MA0149.1 0.554
MA0150.1 0.264
MA0152.1 0.356
MA0153.1 1.04493e-5
MA0154.1 0.0207
MA0155.1 0.288
MA0156.1 3.23465e-4
MA0157.1 0.00121
MA0159.1 0.293
MA0160.1 0.054
MA0162.1 0.342
MA0163.1 0.461
MA0164.1 0.492
MA0258.1 0.606
MA0259.1 0.00327



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: CNhs11133
Novel motif P-value
1 0.925
10 0.529
100 0.459
101 0.56
102 0.422
103 0.368
104 0.639
105 0.413
106 4.94388e-4
107 0.0038
108 0.638
109 0.284
11 0.977
110 0.949
111 0.416
112 0.46
113 0.758
114 0.783
115 0.476
116 0.632
117 0.172
118 0.82
119 0.131
12 0.612
120 0.158
121 0.24
122 0.838
123 0.921
124 0.585
125 0.492
126 0.332
127 0.66
128 0.00271
129 0.187
13 0.00295
130 0.00362
131 0.0305
132 0.367
133 0.757
134 0.678
135 0.745
136 0.901
137 0.455
138 0.0462
139 0.987
14 0.283
140 0.951
141 0.391
142 0.194
143 0.364
144 0.984
145 0.187
146 0.626
147 0.738
148 0.189
149 0.0733
15 0.348
150 0.136
151 0.282
152 0.0161
153 0.455
154 0.245
155 0.773
156 0.00683
157 0.737
158 0.974
159 0.108
160 0.16
161 0.67
162 0.459
163 0.748
164 0.649
165 0.935
166 0.115
167 0.367
168 0.26
169 0.0187
17 0.467
18 0.0507
19 0.0628
2 0.104
20 0.503
21 0.578
22 0.0965
23 0.0358
24 0.241
25 0.124
26 0.0714
27 0.913
28 0.518
29 0.408
3 0.602
30 0.73
31 0.865
32 0.62
33 0.974
34 0.502
35 0.0661
36 0.813
37 0.0529
38 0.163
39 0.0757
4 0.818
40 0.623
41 0.291
42 0.647
43 0.162
44 0.301
45 0.118
46 0.911
47 0.941
48 0.898
49 0.263
5 0.806
50 0.338
51 0.665
52 0.031
53 0.483
54 0.743
55 0.941
56 0.508
57 0.838
58 0.838
59 0.143
6 0.996
60 0.0289
61 0.855
62 0.844
63 0.217
64 0.436
65 0.127
66 0.114
67 0.878
68 0.818
69 0.982
7 0.503
70 0.45
71 0.74
72 0.922
73 0.107
74 0.813
75 0.46
76 0.768
77 0.203
78 0.792
79 0.871
8 0.49
80 0.897
81 0.48
82 0.563
83 0.476
84 0.141
85 0.0754
86 0.922
87 0.114
88 0.46
89 0.996
9 0.174
90 0.617
91 0.365
92 0.255
93 0.44
94 0.34
95 0.641
96 0.828
97 0.428
98 0.745
99 0.211



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: CNhs11133


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)
0000310 (mouse neonate N30 sample)
0011489 (mouse lung- neonate N30 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)