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FF:456-26C5

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Name:thymus, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs11002
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
tissuethymus
dev stage16 days embryo
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  SAMD00005771
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11002 CAGE DRX009115 DRR009989
Accession ID Mm9

Library idBAMCTSS
CNhs11002 DRZ001414 DRZ002797
Accession ID Mm10

Library idBAMCTSS
CNhs11002 DRZ012764 DRZ014147
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

CNhs11002

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 -1.32877e-4
1001 -9.4797e-4
1002 0.0539
1003 --0.00528
1004 0
1005 0
1006 --0.143
1007 0.09
1008 0
1009 --0.0997
101 0.223
1010 0
1011 0.00955
1012 0.182
1013 --0.157
1014 0.13
1015 0.0739
1016 --0.141
1017 0
1018 0.342
1019 0
102 0
1020 0
1021 0.00436
1022 --0.262
1023 0
1024 --0.0865
1025 0
1026 0
1027 0
1028 0
1029 0.0698
103 0
1030 0
1031 --0.27
1032 --0.335
1033 0
1034 0
1035 0.053
1036 0.317
1037 0
1038 --0.276
1039 --0.0919
104 0
1040 --0.0609
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: CNhs11002

Jaspar motif P-value
MA0002.2 0.00194
MA0003.1 0.678
MA0004.1 0.281
MA0006.1 0.759
MA0007.1 0.15
MA0009.1 0.654
MA0014.1 0.171
MA0017.1 0.175
MA0018.2 7.37814e-4
MA0019.1 0.479
MA0024.1 4.44543e-8
MA0025.1 6.83001e-4
MA0027.1 0.566
MA0028.1 1.17125e-5
MA0029.1 0.341
MA0030.1 0.0253
MA0031.1 0.132
MA0035.2 0.448
MA0038.1 0.923
MA0039.2 0.245
MA0040.1 0.607
MA0041.1 0.0653
MA0042.1 0.524
MA0043.1 0.0173
MA0046.1 5.36164e-22
MA0047.2 0.132
MA0048.1 0.228
MA0050.1 1.88685e-7
MA0051.1 3.94405e-6
MA0052.1 6.45087e-5
MA0055.1 0.225
MA0057.1 0.541
MA0058.1 0.409
MA0059.1 0.00158
MA0060.1 0.0477
MA0061.1 1.90658e-5
MA0062.2 5.7297e-13
MA0065.2 0.764
MA0066.1 0.0736
MA0067.1 0.476
MA0068.1 0.812
MA0069.1 0.996
MA0070.1 0.404
MA0071.1 0.563
MA0072.1 0.478
MA0073.1 0.794
MA0074.1 0.906
MA0076.1 1.93733e-6
MA0077.1 0.0607
MA0078.1 0.657
MA0079.2 0.0526
MA0080.2 1.34809e-11
MA0081.1 0.0144
MA0083.1 0.0153
MA0084.1 0.325
MA0087.1 0.286
MA0088.1 0.0466
MA0090.1 0.087
MA0091.1 0.0212
MA0092.1 0.888
MA0093.1 0.35
MA0099.2 0.203
MA0100.1 0.0477
MA0101.1 8.17379e-6
MA0102.2 0.199
MA0103.1 0.00168
MA0104.2 0.0199
MA0105.1 6.55772e-8
MA0106.1 0.384
MA0107.1 1.43107e-5
MA0108.2 0.00407
MA0111.1 0.637
MA0112.2 0.0139
MA0113.1 0.983
MA0114.1 0.121
MA0115.1 0.701
MA0116.1 0.00124
MA0117.1 0.568
MA0119.1 0.795
MA0122.1 0.992
MA0124.1 0.734
MA0125.1 0.69
MA0131.1 0.0759
MA0135.1 0.102
MA0136.1 1.81381e-17
MA0137.2 0.0184
MA0138.2 1.42568e-4
MA0139.1 0.067
MA0140.1 0.608
MA0141.1 0.358
MA0142.1 0.484
MA0143.1 0.285
MA0144.1 0.37
MA0145.1 0.324
MA0146.1 0.634
MA0147.1 0.00386
MA0148.1 0.22
MA0149.1 0.246
MA0150.1 0.531
MA0152.1 0.661
MA0153.1 4.3964e-8
MA0154.1 0.0555
MA0155.1 0.635
MA0156.1 2.52861e-20
MA0157.1 0.331
MA0159.1 0.0877
MA0160.1 0.273
MA0162.1 0.154
MA0163.1 2.4804e-5
MA0164.1 0.937
MA0258.1 0.123
MA0259.1 0.266



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: CNhs11002

Novel motif P-value
1 0.269
10 0.0108
100 0.652
101 0.807
102 0.636
103 0.157
104 0.867
105 0.91
106 0.488
107 0.729
108 0.383
109 0.125
11 0.0583
110 0.039
111 0.284
112 0.148
113 0.659
114 0.663
115 0.911
116 0.493
117 0.00289
118 0.202
119 0.437
12 0.375
120 0.556
121 0.626
122 0.813
123 0.349
124 0.333
125 0.0889
126 0.75
127 0.873
128 0.674
129 0.304
13 0.01
130 0.203
131 0.976
132 0.493
133 0.217
134 0.55
135 0.49
136 0.888
137 0.0314
138 0.639
139 0.827
14 0.287
140 0.539
141 0.933
142 0.672
143 0.098
144 0.604
145 0.0202
146 0.985
147 0.297
148 0.725
149 0.728
15 0.153
150 0.246
151 0.502
152 0.246
153 0.187
154 0.202
155 0.293
156 0.00898
157 0.414
158 0.442
159 0.185
160 0.282
161 0.218
162 0.306
163 0.668
164 0.0387
165 0.0852
166 0.3
167 0.115
168 0.179
169 0.213
17 0.709
18 0.523
19 0.958
2 0.265
20 0.217
21 0.11
22 0.987
23 0.437
24 0.116
25 0.421
26 0.00319
27 0.355
28 0.951
29 0.0253
3 0.127
30 0.157
31 0.374
32 0.126
33 0.584
34 0.861
35 0.332
36 0.245
37 0.258
38 0.23
39 0.999
4 0.992
40 0.398
41 0.835
42 0.0304
43 0.503
44 0.487
45 0.85
46 0.06
47 0.349
48 0.134
49 0.313
5 0.575
50 0.54
51 0.927
52 0.307
53 0.776
54 0.324
55 0.806
56 0.935
57 0.166
58 0.195
59 0.523
6 0.266
60 0.935
61 0.0495
62 0.0927
63 0.546
64 0.434
65 0.399
66 0.8
67 0.938
68 0.313
69 0.835
7 0.124
70 0.138
71 0.0024
72 0.415
73 0.39
74 0.76
75 0.0434
76 0.0929
77 0.662
78 0.0922
79 0.928
8 0.106
80 0.105
81 0.826
82 0.703
83 0.768
84 0.0219
85 0.504
86 0.379
87 0.214
88 0.158
89 0.594
9 0.414
90 0.185
91 0.734
92 0.47
93 0.972
94 0.163
95 0.311
96 0.103
97 0.421
98 0.323
99 0.479



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: CNhs11002


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)
0000922 (embryo)
0002370 (thymus)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0004177 (hemopoietic organ)
0005057 (immune organ)
0002530 (gland)
0005058 (hemolymphoid system gland)
0010317 (germ layer / neural crest derived structure)
0000153 (anterior region of body)
0002390 (hematopoietic system)
0000949 (endocrine system)
0002193 (hemolymphoid system)
0002405 (immune system)
0009113 (thymic region)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000299 (mouse embryonic day 16 sample)
0011355 (mouse thymus- embryo E16 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:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)