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FF:822-18A4

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Name:lung, neonate N20
Species:Mouse (Mus musculus)
Library ID:CNhs11109
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 stage20 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  SAMD00004879
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11109 CAGE DRX009041 DRR009915
Accession ID Mm9

Library idBAMCTSS
CNhs11109 DRZ001340 DRZ002723
Accession ID Mm10

Library idBAMCTSS
CNhs11109 DRZ012690 DRZ014073
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

CNhs11109

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0.0659
100 0
1000 0.059
1001 0.253
1002 -0.0363
1003 0.193
1004 0
1005 0.2
1006 0.152
1007 0.0373
1008 0.0659
1009 0.441
101 -0.0759
1010 0
1011 -0.0788
1012 0.219
1013 0.0964
1014 0.0791
1015 -0.223
1016 0.0534
1017 0.0659
1018 0.174
1019 0
102 0
1020 0
1021 -0.0487
1022 0.261
1023 0.0659
1024 0.598
1025 1.222
1026 0
1027 0
1028 0
1029 0.395
103 0.113
1030 0.394
1031 0.279
1032 0.0744
1033 -5.948308e-4
1034 0.0874
1035 0.0659
1036 -0.0392
1037 0
1038 0.478
1039 0.163
104 0
1040 0.514
1041 0.297



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: CNhs11109
Jaspar motif P-value
MA0002.2 0.359
MA0003.1 0.0686
MA0004.1 0.152
MA0006.1 0.0648
MA0007.1 0.794
MA0009.1 0.362
MA0014.1 0.667
MA0017.1 0.193
MA0018.2 7.88765e-5
MA0019.1 0.932
MA0024.1 1.16491e-4
MA0025.1 0.275
MA0027.1 0.611
MA0028.1 0.00215
MA0029.1 0.566
MA0030.1 0.166
MA0031.1 0.0139
MA0035.2 0.159
MA0038.1 0.313
MA0039.2 0.0059
MA0040.1 0.714
MA0041.1 0.23
MA0042.1 0.471
MA0043.1 0.0193
MA0046.1 2.87509e-9
MA0047.2 9.58928e-6
MA0048.1 0.523
MA0050.1 4.28818e-6
MA0051.1 0.00381
MA0052.1 0.0129
MA0055.1 0.349
MA0057.1 0.109
MA0058.1 0.0548
MA0059.1 0.0522
MA0060.1 1.10758e-12
MA0061.1 0.0755
MA0062.2 6.5658e-4
MA0065.2 0.739
MA0066.1 0.974
MA0067.1 0.528
MA0068.1 0.795
MA0069.1 0.471
MA0070.1 0.806
MA0071.1 0.323
MA0072.1 0.193
MA0073.1 0.864
MA0074.1 0.459
MA0076.1 4.38208e-4
MA0077.1 0.014
MA0078.1 0.00803
MA0079.2 0.154
MA0080.2 2.32115e-8
MA0081.1 0.294
MA0083.1 0.00386
MA0084.1 0.795
MA0087.1 0.63
MA0088.1 0.997
MA0090.1 0.0363
MA0091.1 0.867
MA0092.1 0.388
MA0093.1 0.124
MA0099.2 0.834
MA0100.1 0.144
MA0101.1 0.365
MA0102.2 0.287
MA0103.1 0.569
MA0104.2 0.00726
MA0105.1 0.151
MA0106.1 0.0273
MA0107.1 0.0308
MA0108.2 0.347
MA0111.1 0.178
MA0112.2 0.00934
MA0113.1 0.573
MA0114.1 0.0663
MA0115.1 0.0717
MA0116.1 0.136
MA0117.1 0.498
MA0119.1 0.0356
MA0122.1 0.202
MA0124.1 0.179
MA0125.1 0.0644
MA0131.1 0.113
MA0135.1 0.491
MA0136.1 0.0337
MA0137.2 0.712
MA0138.2 0.719
MA0139.1 0.109
MA0140.1 0.883
MA0141.1 0.134
MA0142.1 0.779
MA0143.1 0.262
MA0144.1 0.224
MA0145.1 0.00205
MA0146.1 0.518
MA0147.1 0.00803
MA0148.1 3.20513e-4
MA0149.1 0.271
MA0150.1 0.677
MA0152.1 0.369
MA0153.1 1.49493e-6
MA0154.1 0.00316
MA0155.1 0.257
MA0156.1 0.0272
MA0157.1 0.0117
MA0159.1 0.748
MA0160.1 0.168
MA0162.1 0.127
MA0163.1 0.634
MA0164.1 0.602
MA0258.1 0.171
MA0259.1 0.0193



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: CNhs11109
Novel motif P-value
1 0.544
10 0.999
100 0.519
101 0.404
102 0.479
103 0.141
104 0.836
105 0.389
106 8.99126e-4
107 0.00384
108 0.969
109 0.258
11 0.879
110 0.678
111 0.729
112 0.227
113 0.876
114 0.386
115 0.654
116 0.956
117 0.211
118 0.893
119 0.056
12 0.694
120 0.314
121 0.315
122 0.681
123 0.616
124 0.418
125 0.625
126 0.205
127 0.109
128 0.00149
129 0.1
13 0.0398
130 0.012
131 0.154
132 0.395
133 0.73
134 0.937
135 0.528
136 0.256
137 0.248
138 0.0474
139 0.469
14 0.248
140 0.477
141 0.152
142 0.0556
143 0.717
144 0.966
145 0.18
146 0.813
147 0.767
148 0.47
149 0.0434
15 0.325
150 0.244
151 0.146
152 0.0451
153 0.446
154 0.32
155 0.572
156 0.0824
157 0.812
158 0.663
159 0.0228
160 0.0734
161 0.897
162 0.391
163 0.885
164 0.557
165 0.688
166 0.198
167 0.604
168 0.818
169 0.00745
17 0.252
18 0.258
19 0.0371
2 0.163
20 0.306
21 0.599
22 0.128
23 0.0165
24 0.317
25 0.359
26 0.0662
27 0.743
28 0.458
29 0.529
3 0.481
30 0.749
31 0.819
32 0.703
33 0.912
34 0.53
35 0.311
36 0.849
37 0.0468
38 0.242
39 0.153
4 0.619
40 0.701
41 0.454
42 0.499
43 0.13
44 0.448
45 0.157
46 0.586
47 0.602
48 0.902
49 0.232
5 0.441
50 0.398
51 0.434
52 0.0639
53 0.299
54 0.483
55 0.985
56 0.295
57 0.657
58 0.539
59 0.095
6 0.926
60 0.0413
61 0.869
62 0.509
63 0.154
64 0.72
65 0.142
66 0.0715
67 0.358
68 0.669
69 0.794
7 0.306
70 0.234
71 0.264
72 0.93
73 0.194
74 0.799
75 0.807
76 0.502
77 0.185
78 0.882
79 0.799
8 0.983
80 0.854
81 0.929
82 0.234
83 0.313
84 0.378
85 0.0325
86 0.885
87 0.0219
88 0.739
89 0.309
9 0.159
90 0.908
91 0.336
92 0.0722
93 0.444
94 0.853
95 0.685
96 0.378
97 0.66
98 0.856
99 0.24



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: CNhs11109


FANTOM5 (FF) ontology


Direct parent terms


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)
0000308 (mouse neonate N20 sample)
0011428 (mouse lung- neonate N20 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)