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FF:1273-19G4

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Name:thymus, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs10595
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 stage18 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  SAMD00004709
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10595 CAGE DRX009117 DRR009991
Accession ID Mm9

Library idBAMCTSS
CNhs10595 DRZ001416 DRZ002799
Accession ID Mm10

Library idBAMCTSS
CNhs10595 DRZ012766 DRZ014149
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

CNhs10595

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0
1002 0
1003 --0.063
1004 0
1005 0
1006 --0.064
1007 0.108
1008 0
1009 --0.111
101 0.128
1010 0
1011 0
1012 0.254
1013 --0.138
1014 0.109
1015 0.0493
1016 --0.262
1017 0
1018 0.0787
1019 0
102 0
1020 0
1021 0.145
1022 --0.17
1023 0
1024 --0.0112
1025 0
1026 0
1027 0
1028 0
1029 0.152
103 0
1030 0
1031 --0.331
1032 --0.328
1033 0.0787
1034 0
1035 0
1036 0.189
1037 0
1038 --0.22
1039 --0.196
104 0
1040 --0.0422
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: CNhs10595

Jaspar motif P-value
MA0002.2 9.71499e-5
MA0003.1 0.837
MA0004.1 0.464
MA0006.1 0.709
MA0007.1 0.295
MA0009.1 0.324
MA0014.1 0.195
MA0017.1 0.111
MA0018.2 0.0735
MA0019.1 0.754
MA0024.1 8.20631e-6
MA0025.1 0.00352
MA0027.1 0.888
MA0028.1 2.08695e-6
MA0029.1 0.0827
MA0030.1 0.466
MA0031.1 0.297
MA0035.2 0.815
MA0038.1 0.422
MA0039.2 0.503
MA0040.1 0.444
MA0041.1 0.8
MA0042.1 0.736
MA0043.1 0.343
MA0046.1 1.54099e-17
MA0047.2 0.716
MA0048.1 0.85
MA0050.1 3.76841e-6
MA0051.1 3.85684e-6
MA0052.1 0.122
MA0055.1 0.711
MA0057.1 0.615
MA0058.1 0.605
MA0059.1 0.0766
MA0060.1 1.32299e-6
MA0061.1 1.32032e-6
MA0062.2 4.81714e-19
MA0065.2 0.694
MA0066.1 0.041
MA0067.1 0.81
MA0068.1 0.521
MA0069.1 0.881
MA0070.1 0.535
MA0071.1 0.583
MA0072.1 3.30373e-7
MA0073.1 0.756
MA0074.1 0.859
MA0076.1 1.00861e-8
MA0077.1 0.323
MA0078.1 0.756
MA0079.2 0.0925
MA0080.2 8.96815e-14
MA0081.1 0.0145
MA0083.1 0.606
MA0084.1 0.526
MA0087.1 0.549
MA0088.1 0.137
MA0090.1 0.0681
MA0091.1 0.0619
MA0092.1 0.95
MA0093.1 0.511
MA0099.2 0.179
MA0100.1 0.00868
MA0101.1 6.64733e-6
MA0102.2 0.285
MA0103.1 2.74279e-5
MA0104.2 0.139
MA0105.1 8.7407e-9
MA0106.1 0.786
MA0107.1 5.2512e-6
MA0108.2 0.454
MA0111.1 0.383
MA0112.2 0.0593
MA0113.1 0.776
MA0114.1 0.0555
MA0115.1 0.354
MA0116.1 0.00142
MA0117.1 0.703
MA0119.1 0.996
MA0122.1 0.699
MA0124.1 0.397
MA0125.1 0.939
MA0131.1 0.0383
MA0135.1 0.355
MA0136.1 1.72414e-23
MA0137.2 0.0294
MA0138.2 2.1379e-4
MA0139.1 0.259
MA0140.1 0.817
MA0141.1 0.128
MA0142.1 0.775
MA0143.1 0.3
MA0144.1 0.333
MA0145.1 0.611
MA0146.1 0.408
MA0147.1 0.0673
MA0148.1 0.758
MA0149.1 0.242
MA0150.1 0.264
MA0152.1 0.953
MA0153.1 2.46036e-9
MA0154.1 0.0529
MA0155.1 0.549
MA0156.1 7.5479e-29
MA0157.1 0.518
MA0159.1 0.0751
MA0160.1 0.16
MA0162.1 0.223
MA0163.1 5.5199e-4
MA0164.1 0.624
MA0258.1 0.169
MA0259.1 0.707



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: CNhs10595

Novel motif P-value
1 0.493
10 0.0278
100 0.905
101 0.925
102 0.423
103 0.319
104 0.553
105 0.914
106 0.742
107 0.726
108 0.467
109 0.177
11 0.103
110 0.0887
111 0.945
112 0.302
113 0.202
114 0.758
115 0.466
116 0.727
117 0.00174
118 0.231
119 0.534
12 0.296
120 0.242
121 0.183
122 0.667
123 0.433
124 0.652
125 0.064
126 0.947
127 0.745
128 0.613
129 0.372
13 0.016
130 0.304
131 0.961
132 0.599
133 0.899
134 0.39
135 0.268
136 0.7
137 0.247
138 0.218
139 0.987
14 0.781
140 0.774
141 0.918
142 0.88
143 0.114
144 0.113
145 0.144
146 0.618
147 0.268
148 0.582
149 0.804
15 0.108
150 0.279
151 0.188
152 0.264
153 0.31
154 0.42
155 0.0811
156 0.523
157 0.628
158 0.141
159 0.0107
160 0.755
161 0.401
162 0.352
163 0.737
164 0.271
165 0.16
166 0.359
167 0.532
168 0.456
169 0.236
17 0.747
18 0.878
19 0.59
2 0.175
20 0.592
21 0.289
22 0.926
23 0.893
24 0.0666
25 0.258
26 0.036
27 0.258
28 0.248
29 0.0771
3 0.344
30 0.208
31 0.436
32 0.0793
33 0.532
34 0.511
35 0.158
36 0.283
37 0.261
38 0.276
39 0.614
4 0.727
40 0.417
41 0.834
42 0.0226
43 0.67
44 0.777
45 0.793
46 0.104
47 0.356
48 0.213
49 0.348
5 0.321
50 0.698
51 0.974
52 0.262
53 0.678
54 0.219
55 0.362
56 0.878
57 0.484
58 0.224
59 0.778
6 0.208
60 0.997
61 0.0888
62 0.0704
63 0.618
64 0.543
65 0.459
66 0.948
67 0.793
68 0.359
69 0.738
7 0.0872
70 0.695
71 0.0206
72 0.445
73 0.397
74 0.768
75 0.0483
76 0.279
77 0.543
78 0.0797
79 0.965
8 0.619
80 0.0417
81 0.897
82 0.655
83 0.964
84 0.322
85 0.418
86 0.144
87 0.303
88 0.243
89 0.406
9 0.246
90 0.154
91 0.575
92 0.311
93 0.862
94 0.361
95 0.326
96 0.141
97 0.466
98 0.423
99 0.44



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: CNhs10595


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)
0000302 (mouse embryonic day 18 sample)
0011516 (mouse thymus- embryo E18 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)