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FF:402-44I4

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Name:thymus, embryo E14
Species:Mouse (Mus musculus)
Library ID:CNhs11041
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 stage14 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  SAMD00005455
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11041 CAGE DRX009113 DRR009987
Accession ID Mm9

Library idBAMCTSS
CNhs11041 DRZ001412 DRZ002795
Accession ID Mm10

Library idBAMCTSS
CNhs11041 DRZ012762 DRZ014145
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

CNhs11041

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 -0.0749
1002 0.215
1003 -0.105
1004 0
1005 0
1006 -0.143
1007 0.0425
1008 0
1009 -0.112
101 0.122
1010 0
1011 0.00849
1012 0
1013 -0.191
1014 0.163
1015 0.187
1016 0.13
1017 0
1018 0.584
1019 0
102 0
1020 0
1021 0.148
1022 -0.303
1023 0
1024 0.00826
1025 0.0492
1026 0
1027 0
1028 0
1029 -0.0989
103 0.148
1030 0
1031 0.22
1032 -0.0964
1033 0
1034 0
1035 0
1036 0.147
1037 0
1038 -0.275
1039 -0.136
104 0
1040 -0.0407
1041 0



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: CNhs11041
Jaspar motif P-value
MA0002.2 0.11
MA0003.1 0.791
MA0004.1 0.907
MA0006.1 0.907
MA0007.1 0.635
MA0009.1 0.364
MA0014.1 0.65
MA0017.1 6.90554e-4
MA0018.2 0.00633
MA0019.1 0.506
MA0024.1 4.80313e-13
MA0025.1 0.00581
MA0027.1 0.0149
MA0028.1 4.73825e-5
MA0029.1 0.906
MA0030.1 0.0178
MA0031.1 0.00881
MA0035.2 0.86
MA0038.1 0.672
MA0039.2 0.713
MA0040.1 0.357
MA0041.1 0.157
MA0042.1 0.371
MA0043.1 0.204
MA0046.1 3.9621e-18
MA0047.2 4.77842e-4
MA0048.1 0.00253
MA0050.1 0.0457
MA0051.1 0.354
MA0052.1 5.11058e-8
MA0055.1 8.02599e-6
MA0057.1 0.706
MA0058.1 0.743
MA0059.1 0.017
MA0060.1 8.12152e-9
MA0061.1 1.03842e-4
MA0062.2 8.43065e-10
MA0065.2 0.0391
MA0066.1 0.732
MA0067.1 0.225
MA0068.1 0.17
MA0069.1 0.233
MA0070.1 0.919
MA0071.1 0.00108
MA0072.1 0.00252
MA0073.1 0.936
MA0074.1 0.539
MA0076.1 6.51296e-5
MA0077.1 0.835
MA0078.1 0.994
MA0079.2 0.918
MA0080.2 8.64602e-10
MA0081.1 0.00265
MA0083.1 0.347
MA0084.1 0.782
MA0087.1 0.333
MA0088.1 0.0759
MA0090.1 0.58
MA0091.1 0.599
MA0092.1 0.891
MA0093.1 0.957
MA0099.2 0.138
MA0100.1 0.636
MA0101.1 3.03044e-5
MA0102.2 0.167
MA0103.1 0.87
MA0104.2 0.0918
MA0105.1 1.0466e-4
MA0106.1 0.265
MA0107.1 1.09412e-4
MA0108.2 0.604
MA0111.1 0.908
MA0112.2 0.846
MA0113.1 0.935
MA0114.1 3.67061e-5
MA0115.1 0.0309
MA0116.1 0.00855
MA0117.1 0.02
MA0119.1 0.33
MA0122.1 0.975
MA0124.1 0.403
MA0125.1 0.354
MA0131.1 0.0737
MA0135.1 0.231
MA0136.1 2.75251e-13
MA0137.2 0.0574
MA0138.2 1.77516e-6
MA0139.1 0.16
MA0140.1 0.723
MA0141.1 2.7823e-4
MA0142.1 0.623
MA0143.1 0.777
MA0144.1 0.458
MA0145.1 0.522
MA0146.1 0.376
MA0147.1 0.0122
MA0148.1 6.66331e-4
MA0149.1 0.473
MA0150.1 0.00396
MA0152.1 0.194
MA0153.1 7.38999e-5
MA0154.1 0.0821
MA0155.1 0.378
MA0156.1 4.12348e-13
MA0157.1 0.102
MA0159.1 0.772
MA0160.1 0.00339
MA0162.1 0.0878
MA0163.1 0.00213
MA0164.1 0.956
MA0258.1 0.889
MA0259.1 0.34



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: CNhs11041
Novel motif P-value
1 0.247
10 0.278
100 0.806
101 0.437
102 0.349
103 0.965
104 0.609
105 0.427
106 0.708
107 0.47
108 0.705
109 0.232
11 0.301
110 0.201
111 0.584
112 0.912
113 0.221
114 0.0238
115 0.702
116 0.359
117 0.108
118 0.913
119 0.449
12 0.541
120 0.675
121 0.849
122 0.899
123 0.5
124 0.889
125 0.964
126 0.795
127 0.344
128 0.916
129 0.45
13 0.0369
130 0.341
131 0.993
132 0.214
133 0.375
134 0.216
135 0.781
136 0.21
137 0.0341
138 0.987
139 0.00162
14 0.111
140 0.173
141 0.787
142 0.338
143 0.153
144 0.631
145 0.271
146 0.823
147 0.141
148 0.286
149 0.738
15 0.597
150 0.403
151 0.746
152 0.984
153 0.4
154 0.546
155 0.659
156 1.39665e-7
157 0.198
158 0.107
159 0.13
160 0.413
161 0.223
162 0.423
163 0.0496
164 0.17
165 0.827
166 0.26
167 0.72
168 0.113
169 0.674
17 0.367
18 0.385
19 0.769
2 0.366
20 0.426
21 0.0125
22 0.914
23 0.19
24 0.0432
25 0.192
26 0.0268
27 0.996
28 0.0608
29 0.161
3 0.9
30 0.831
31 0.197
32 0.313
33 0.457
34 0.331
35 0.226
36 0.428
37 0.617
38 0.572
39 0.828
4 0.891
40 0.058
41 0.507
42 0.23
43 0.339
44 0.777
45 0.753
46 0.981
47 0.446
48 0.909
49 0.225
5 0.193
50 0.0189
51 0.674
52 0.78
53 0.868
54 0.147
55 0.745
56 0.723
57 0.756
58 0.92
59 0.0586
6 0.594
60 0.288
61 0.258
62 0.732
63 0.934
64 0.555
65 0.663
66 0.333
67 0.512
68 0.193
69 0.629
7 0.706
70 0.484
71 0.0382
72 0.247
73 0.284
74 0.536
75 0.256
76 0.311
77 0.904
78 0.845
79 0.753
8 0.805
80 0.552
81 0.401
82 0.392
83 0.972
84 0.0177
85 0.0423
86 0.616
87 0.114
88 0.261
89 0.212
9 0.884
90 0.402
91 0.659
92 0.0873
93 0.579
94 0.831
95 0.091
96 0.798
97 0.495
98 0.655
99 0.55



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: CNhs11041


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)
0000296 (mouse embryonic day 14 sample)
0011336 (mouse thymus- embryo E14 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)