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FF:478-18C1

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Name:thymus, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs10581
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 stage17 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  SAMD00004685
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10581 CAGE DRX009116 DRR009990
Accession ID Mm9

Library idBAMCTSS
CNhs10581 DRZ001415 DRZ002798
Accession ID Mm10

Library idBAMCTSS
CNhs10581 DRZ012765 DRZ014148
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

CNhs10581

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.00829
1002 0.0389
1003 --0.0479
1004 0
1005 0
1006 --0.0762
1007 0.113
1008 0
1009 --0.0964
101 0.146
1010 0
1011 0.0288
1012 0.0715
1013 --0.128
1014 0.0478
1015 0.116
1016 --0.206
1017 0
1018 0.235
1019 0
102 0
1020 0
1021 0.0842
1022 --0.209
1023 0
1024 --0.00664
1025 0
1026 0
1027 --0.048
1028 0
1029 0.0719
103 0
1030 0
1031 --0.284
1032 --0.345
1033 0.0577
1034 0
1035 0.0715
1036 0.276
1037 0
1038 --0.15
1039 --0.134
104 0
1040 --0.0425
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: CNhs10581

Jaspar motif P-value
MA0002.2 9.40968e-5
MA0003.1 0.695
MA0004.1 0.307
MA0006.1 0.935
MA0007.1 0.215
MA0009.1 0.721
MA0014.1 0.202
MA0017.1 0.0087
MA0018.2 0.0509
MA0019.1 0.43
MA0024.1 1.76865e-10
MA0025.1 0.00136
MA0027.1 0.806
MA0028.1 1.8151e-8
MA0029.1 0.0442
MA0030.1 0.519
MA0031.1 0.472
MA0035.2 0.401
MA0038.1 0.162
MA0039.2 0.576
MA0040.1 0.666
MA0041.1 0.979
MA0042.1 0.864
MA0043.1 0.377
MA0046.1 2.64938e-18
MA0047.2 0.906
MA0048.1 0.43
MA0050.1 1.08625e-7
MA0051.1 5.6976e-7
MA0052.1 0.00451
MA0055.1 0.408
MA0057.1 0.547
MA0058.1 0.45
MA0059.1 0.029
MA0060.1 1.21326e-10
MA0061.1 2.34278e-7
MA0062.2 3.4721e-20
MA0065.2 0.597
MA0066.1 0.217
MA0067.1 0.904
MA0068.1 0.936
MA0069.1 0.908
MA0070.1 0.955
MA0071.1 0.803
MA0072.1 2.17557e-4
MA0073.1 0.709
MA0074.1 0.783
MA0076.1 4.64894e-11
MA0077.1 0.429
MA0078.1 0.692
MA0079.2 0.0666
MA0080.2 1.51319e-13
MA0081.1 0.00254
MA0083.1 0.105
MA0084.1 0.98
MA0087.1 0.571
MA0088.1 0.0572
MA0090.1 0.124
MA0091.1 0.166
MA0092.1 0.843
MA0093.1 0.332
MA0099.2 0.111
MA0100.1 0.00454
MA0101.1 6.17705e-7
MA0102.2 0.386
MA0103.1 6.24812e-5
MA0104.2 0.0317
MA0105.1 5.61405e-8
MA0106.1 0.55
MA0107.1 3.06282e-7
MA0108.2 0.0668
MA0111.1 0.914
MA0112.2 0.382
MA0113.1 0.746
MA0114.1 0.00306
MA0115.1 0.149
MA0116.1 0.00855
MA0117.1 0.375
MA0119.1 0.56
MA0122.1 0.899
MA0124.1 0.232
MA0125.1 0.722
MA0131.1 0.00537
MA0135.1 0.833
MA0136.1 3.26113e-26
MA0137.2 0.00711
MA0138.2 2.88543e-5
MA0139.1 0.224
MA0140.1 0.391
MA0141.1 0.00925
MA0142.1 0.658
MA0143.1 0.147
MA0144.1 0.246
MA0145.1 0.275
MA0146.1 0.289
MA0147.1 0.0125
MA0148.1 0.668
MA0149.1 0.308
MA0150.1 0.157
MA0152.1 0.958
MA0153.1 1.4306e-8
MA0154.1 0.223
MA0155.1 0.638
MA0156.1 7.68435e-31
MA0157.1 0.612
MA0159.1 0.429
MA0160.1 0.0687
MA0162.1 0.232
MA0163.1 4.86292e-4
MA0164.1 0.849
MA0258.1 0.782
MA0259.1 0.348



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: CNhs10581

Novel motif P-value
1 0.93
10 0.0341
100 0.9
101 0.897
102 0.499
103 0.363
104 0.693
105 0.741
106 0.815
107 0.46
108 0.37
109 0.315
11 0.187
110 0.0835
111 0.878
112 0.614
113 0.303
114 0.187
115 0.535
116 0.743
117 0.00403
118 0.197
119 0.485
12 0.329
120 0.336
121 0.246
122 0.795
123 0.608
124 0.556
125 0.174
126 0.958
127 0.78
128 0.907
129 0.368
13 0.0113
130 0.133
131 0.862
132 0.464
133 0.591
134 0.534
135 0.417
136 0.814
137 0.269
138 0.394
139 0.542
14 0.44
140 0.276
141 0.539
142 0.54
143 0.124
144 0.191
145 0.121
146 0.599
147 0.146
148 0.838
149 0.672
15 0.252
150 0.333
151 0.483
152 0.0893
153 0.417
154 0.434
155 0.318
156 0.605
157 0.399
158 0.38
159 0.213
160 0.949
161 0.63
162 0.159
163 0.867
164 0.226
165 0.384
166 0.211
167 0.859
168 0.42
169 0.673
17 0.839
18 0.876
19 0.305
2 0.0535
20 0.254
21 0.254
22 0.749
23 0.286
24 0.0365
25 0.251
26 0.0241
27 0.42
28 0.859
29 0.14
3 0.559
30 0.232
31 0.153
32 0.0217
33 0.571
34 0.459
35 0.531
36 0.343
37 0.715
38 0.322
39 0.528
4 0.992
40 0.261
41 0.875
42 0.0193
43 0.89
44 0.966
45 0.896
46 0.191
47 0.695
48 0.353
49 0.73
5 0.92
50 0.49
51 0.886
52 0.115
53 0.656
54 0.0846
55 0.695
56 0.844
57 0.898
58 0.299
59 0.913
6 0.251
60 0.519
61 0.0794
62 0.219
63 0.879
64 0.849
65 0.791
66 0.668
67 0.593
68 0.0854
69 0.991
7 0.144
70 0.969
71 0.0257
72 0.402
73 0.719
74 0.809
75 0.0989
76 0.109
77 0.163
78 0.231
79 0.702
8 0.923
80 0.0256
81 0.588
82 0.466
83 0.914
84 0.103
85 0.0725
86 0.487
87 0.72
88 0.15
89 0.356
9 0.301
90 0.472
91 0.328
92 0.0774
93 0.998
94 0.434
95 0.479
96 0.386
97 0.508
98 0.575
99 0.257



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: CNhs10581


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)
0000300 (mouse embryonic day 17 sample)
0011366 (mouse thymus- embryo E17 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)