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FF:430-45I2

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Name:thymus, embryo E15
Species:Mouse (Mus musculus)
Library ID:CNhs11005
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 stage15 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  SAMD00005419
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11005 CAGE DRX009114 DRR009988
Accession ID Mm9

Library idBAMCTSS
CNhs11005 DRZ001413 DRZ002796
Accession ID Mm10

Library idBAMCTSS
CNhs11005 DRZ012763 DRZ014146
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11005

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 -0.0142
1001 0
1002 0.189
1003 -0.0125
1004 0
1005 0
1006 -0.145
1007 0.0533
1008 0
1009 -0.0572
101 0.163
1010 0
1011 0.0706
1012 0.111
1013 -0.169
1014 0.284
1015 0.074
1016 -0.0682
1017 0
1018 0.46
1019 0
102 0
1020 0
1021 0.0395
1022 -0.143
1023 0
1024 0.0212
1025 0.0745
1026 0
1027 0.0425
1028 0
1029 0.0324
103 0.159
1030 0
1031 -9.683218e-5
1032 -0.141
1033 0
1034 0.0425
1035 0
1036 0.311
1037 0
1038 -0.216
1039 -0.0565
104 0
1040 -0.0397
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: CNhs11005
Jaspar motif P-value
MA0002.2 0.0119
MA0003.1 0.936
MA0004.1 0.681
MA0006.1 0.916
MA0007.1 0.43
MA0009.1 0.971
MA0014.1 0.526
MA0017.1 0.00124
MA0018.2 6.66521e-7
MA0019.1 0.782
MA0024.1 1.19813e-9
MA0025.1 1.35368e-4
MA0027.1 0.161
MA0028.1 4.49841e-5
MA0029.1 0.85
MA0030.1 0.0173
MA0031.1 0.00534
MA0035.2 0.182
MA0038.1 0.997
MA0039.2 0.598
MA0040.1 0.392
MA0041.1 0.0601
MA0042.1 0.289
MA0043.1 0.00957
MA0046.1 1.28915e-23
MA0047.2 0.00983
MA0048.1 0.0801
MA0050.1 1.05613e-4
MA0051.1 0.00404
MA0052.1 5.08832e-7
MA0055.1 0.0384
MA0057.1 0.605
MA0058.1 0.775
MA0059.1 0.00732
MA0060.1 0.00218
MA0061.1 1.79787e-6
MA0062.2 1.22171e-10
MA0065.2 0.15
MA0066.1 0.259
MA0067.1 0.0658
MA0068.1 0.377
MA0069.1 0.499
MA0070.1 0.784
MA0071.1 0.0056
MA0072.1 0.0544
MA0073.1 0.729
MA0074.1 0.949
MA0076.1 3.89133e-5
MA0077.1 0.144
MA0078.1 0.393
MA0079.2 0.169
MA0080.2 7.86969e-12
MA0081.1 0.0088
MA0083.1 0.0574
MA0084.1 0.853
MA0087.1 0.602
MA0088.1 0.0377
MA0090.1 0.127
MA0091.1 0.0927
MA0092.1 0.878
MA0093.1 0.731
MA0099.2 0.0342
MA0100.1 0.414
MA0101.1 8.16913e-7
MA0102.2 0.17
MA0103.1 0.0359
MA0104.2 0.0424
MA0105.1 1.11311e-7
MA0106.1 0.177
MA0107.1 2.33638e-7
MA0108.2 0.0341
MA0111.1 0.789
MA0112.2 0.0938
MA0113.1 0.657
MA0114.1 2.19525e-4
MA0115.1 0.0997
MA0116.1 0.00122
MA0117.1 0.176
MA0119.1 0.844
MA0122.1 0.873
MA0124.1 0.576
MA0125.1 0.543
MA0131.1 0.0764
MA0135.1 0.266
MA0136.1 5.50819e-15
MA0137.2 0.0114
MA0138.2 2.33684e-6
MA0139.1 0.0501
MA0140.1 0.344
MA0141.1 0.00294
MA0142.1 0.578
MA0143.1 0.669
MA0144.1 0.262
MA0145.1 0.551
MA0146.1 0.472
MA0147.1 0.00556
MA0148.1 0.0164
MA0149.1 0.566
MA0150.1 0.00957
MA0152.1 0.612
MA0153.1 5.7686e-8
MA0154.1 0.0231
MA0155.1 0.373
MA0156.1 9.99895e-19
MA0157.1 0.0539
MA0159.1 0.699
MA0160.1 0.00138
MA0162.1 0.113
MA0163.1 1.6284e-4
MA0164.1 0.848
MA0258.1 0.473
MA0259.1 0.351



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: CNhs11005
Novel motif P-value
1 0.91
10 0.0335
100 0.967
101 0.799
102 0.508
103 0.339
104 0.905
105 0.772
106 0.553
107 0.662
108 0.729
109 0.149
11 0.119
110 0.0755
111 0.551
112 0.271
113 0.49
114 0.207
115 0.881
116 0.391
117 0.0323
118 0.476
119 0.925
12 0.307
120 0.612
121 0.926
122 0.935
123 0.627
124 0.931
125 0.377
126 0.913
127 0.959
128 0.448
129 0.375
13 0.0077
130 0.197
131 0.776
132 0.399
133 0.177
134 0.242
135 0.283
136 0.787
137 0.00282
138 0.971
139 0.193
14 0.174
140 0.691
141 0.846
142 0.73
143 0.0896
144 0.654
145 0.0159
146 0.888
147 0.201
148 0.531
149 0.723
15 0.687
150 0.277
151 0.972
152 0.583
153 0.188
154 0.387
155 0.381
156 1.08945e-5
157 0.242
158 0.279
159 0.872
160 0.149
161 0.382
162 0.264
163 0.138
164 0.0972
165 0.554
166 0.691
167 0.361
168 0.165
169 0.344
17 0.71
18 0.842
19 0.716
2 0.387
20 0.388
21 0.0324
22 0.915
23 0.297
24 0.0732
25 0.542
26 0.00237
27 0.463
28 0.244
29 0.0559
3 0.384
30 0.335
31 0.231
32 0.423
33 0.88
34 0.744
35 0.717
36 0.457
37 0.211
38 0.193
39 0.939
4 0.911
40 0.28
41 0.344
42 0.0686
43 0.818
44 0.573
45 0.902
46 0.262
47 0.763
48 0.415
49 0.994
5 0.744
50 0.0345
51 0.82
52 0.545
53 0.54
54 0.111
55 0.784
56 0.806
57 0.436
58 0.275
59 0.167
6 0.271
60 0.663
61 0.0535
62 0.344
63 0.736
64 0.456
65 0.353
66 0.945
67 0.861
68 0.266
69 0.89
7 0.377
70 0.496
71 9.95694e-4
72 0.303
73 0.335
74 0.449
75 0.129
76 0.209
77 0.923
78 0.409
79 0.679
8 0.488
80 0.277
81 0.958
82 0.95
83 0.942
84 0.00566
85 0.104
86 0.555
87 0.368
88 0.175
89 0.471
9 0.752
90 0.503
91 0.497
92 0.213
93 0.657
94 0.442
95 0.327
96 0.346
97 0.303
98 0.412
99 0.753



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: CNhs11005


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)
0000298 (mouse embryonic day 15 sample)
0011346 (mouse thymus- embryo E15 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)