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FF:640-42C6

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Name:lung, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11224
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 stage0 day 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  SAMD00004963
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11224 CAGE DRX009037 DRR009911
Accession ID Mm9

Library idBAMCTSS
CNhs11224 DRZ001336 DRZ002719
Accession ID Mm10

Library idBAMCTSS
CNhs11224 DRZ012686 DRZ014069
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 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

CNhs11224

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.00159
1001 0.15
1002 0.092
1003 0.065
1004 0
1005 0.143
1006 0
1007 0.157
1008 0
1009 0.395
101 --0.0995
1010 0
1011 --0.0976
1012 0.0926
1013 0.0846
1014 0.203
1015 --0.0993
1016 0.36
1017 0
1018 0.251
1019 0
102 0
1020 0
1021 0
1022 0.139
1023 0
1024 0.594
1025 1.122
1026 0
1027 0
1028 0.0774
1029 0.424
103 0.198
1030 0
1031 0.433
1032 0.0236
1033 0
1034 0.164
1035 0.0774
1036 --0.151
1037 0
1038 0.42
1039 --0.0351
104 0
1040 0.491
1041 0



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: CNhs11224

Jaspar motif P-value
MA0002.2 0.101
MA0003.1 0.319
MA0004.1 0.0398
MA0006.1 0.0401
MA0007.1 0.809
MA0009.1 0.807
MA0014.1 0.916
MA0017.1 4.4892e-4
MA0018.2 0.00905
MA0019.1 0.701
MA0024.1 3.20136e-4
MA0025.1 0.726
MA0027.1 0.442
MA0028.1 3.07922e-4
MA0029.1 0.952
MA0030.1 0.0302
MA0031.1 2.95792e-4
MA0035.2 0.338
MA0038.1 0.523
MA0039.2 0.0771
MA0040.1 0.8
MA0041.1 0.304
MA0042.1 0.654
MA0043.1 0.533
MA0046.1 7.94682e-4
MA0047.2 4.78816e-8
MA0048.1 0.486
MA0050.1 0.181
MA0051.1 0.165
MA0052.1 0.458
MA0055.1 0.198
MA0057.1 0.727
MA0058.1 0.00647
MA0059.1 2.10902e-4
MA0060.1 4.65224e-6
MA0061.1 0.544
MA0062.2 4.03486e-5
MA0065.2 0.0106
MA0066.1 0.0677
MA0067.1 0.78
MA0068.1 0.544
MA0069.1 0.484
MA0070.1 0.521
MA0071.1 0.0261
MA0072.1 0.133
MA0073.1 0.574
MA0074.1 0.755
MA0076.1 2.43981e-4
MA0077.1 0.545
MA0078.1 0.0302
MA0079.2 0.0164
MA0080.2 0.7
MA0081.1 0.797
MA0083.1 2.33364e-4
MA0084.1 0.515
MA0087.1 0.465
MA0088.1 0.0412
MA0090.1 0.00879
MA0091.1 0.39
MA0092.1 0.836
MA0093.1 0.0393
MA0099.2 0.695
MA0100.1 0.314
MA0101.1 0.974
MA0102.2 0.156
MA0103.1 0.746
MA0104.2 9.46635e-5
MA0105.1 0.0172
MA0106.1 0.157
MA0107.1 0.169
MA0108.2 0.0246
MA0111.1 0.77
MA0112.2 0.131
MA0113.1 0.357
MA0114.1 7.62592e-6
MA0115.1 0.0694
MA0116.1 0.0159
MA0117.1 0.259
MA0119.1 0.386
MA0122.1 0.49
MA0124.1 0.128
MA0125.1 0.522
MA0131.1 0.29
MA0135.1 0.708
MA0136.1 0.0111
MA0137.2 0.43
MA0138.2 0.239
MA0139.1 0.391
MA0140.1 0.976
MA0141.1 8.72131e-5
MA0142.1 0.031
MA0143.1 0.103
MA0144.1 0.61
MA0145.1 0.0189
MA0146.1 0.312
MA0147.1 1.59698e-5
MA0148.1 4.07844e-6
MA0149.1 0.733
MA0150.1 0.00399
MA0152.1 0.362
MA0153.1 3.68861e-4
MA0154.1 0.92
MA0155.1 0.349
MA0156.1 0.441
MA0157.1 0.0395
MA0159.1 0.0214
MA0160.1 0.00239
MA0162.1 0.768
MA0163.1 0.00704
MA0164.1 0.501
MA0258.1 0.129
MA0259.1 0.0444



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: CNhs11224

Novel motif P-value
1 0.258
10 0.0558
100 0.309
101 0.62
102 0.279
103 0.466
104 0.942
105 0.785
106 0.0123
107 0.00392
108 0.997
109 0.462
11 0.209
110 0.294
111 0.274
112 0.512
113 0.539
114 0.669
115 0.445
116 0.395
117 0.0575
118 0.893
119 0.906
12 0.632
120 0.171
121 0.567
122 0.96
123 0.862
124 0.784
125 0.99
126 0.458
127 0.252
128 0.0395
129 1
13 0.154
130 0.148
131 0.221
132 0.258
133 0.808
134 0.922
135 0.887
136 0.214
137 0.648
138 0.0139
139 0.274
14 0.992
140 0.323
141 0.336
142 0.595
143 0.158
144 0.703
145 0.211
146 0.752
147 0.257
148 0.583
149 0.409
15 0.536
150 0.117
151 0.455
152 0.0117
153 0.517
154 0.579
155 0.99
156 0.656
157 0.785
158 0.363
159 0.0495
160 0.593
161 0.75
162 0.394
163 0.289
164 0.743
165 0.336
166 0.431
167 0.163
168 0.391
169 0.445
17 0.938
18 0.00693
19 0.365
2 0.31
20 0.841
21 0.632
22 0.266
23 0.281
24 0.644
25 0.0183
26 0.695
27 0.255
28 0.995
29 0.0557
3 0.503
30 0.676
31 0.498
32 0.341
33 0.757
34 0.951
35 0.00429
36 0.313
37 0.387
38 0.928
39 0.0816
4 0.402
40 0.868
41 0.352
42 0.572
43 0.966
44 0.146
45 0.296
46 0.323
47 0.16
48 0.169
49 0.589
5 0.508
50 0.279
51 0.886
52 0.0467
53 0.944
54 0.935
55 0.598
56 0.888
57 0.242
58 0.424
59 0.513
6 0.468
60 0.101
61 0.817
62 0.151
63 0.878
64 0.107
65 0.987
66 0.117
67 0.884
68 0.436
69 0.799
7 0.895
70 0.404
71 0.109
72 0.157
73 0.196
74 0.566
75 0.0745
76 0.957
77 0.273
78 0.559
79 0.832
8 0.114
80 0.317
81 0.00889
82 0.424
83 0.408
84 0.594
85 0.914
86 0.984
87 0.00499
88 0.841
89 0.361
9 0.354
90 0.00225
91 0.386
92 0.775
93 0.782
94 0.031
95 0.539
96 0.159
97 0.553
98 0.28
99 0.807



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: CNhs11224


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)
0000304 (mouse neonate N0 sample)
0011394 (mouse lung- neonate N00 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)


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