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FF:461-43C1

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Name:spleen, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs11035
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
tissuespleen
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  SAMD00005309
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11035 CAGE DRX009085 DRR009959
Accession ID Mm9

Library idBAMCTSS
CNhs11035 DRZ001384 DRZ002767
Accession ID Mm10

Library idBAMCTSS
CNhs11035 DRZ012734 DRZ014117
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

CNhs11035

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.00363
1001 --0.0631
1002 0.239
1003 0.0389
1004 0
1005 0.109
1006 --0.107
1007 0.0301
1008 0
1009 0.152
101 0.049
1010 0.209
1011 --0.00851
1012 0
1013 --0.0113
1014 0.209
1015 0.135
1016 0.187
1017 0.0815
1018 0.0815
1019 0
102 0
1020 0
1021 0
1022 --0.142
1023 0
1024 --0.00131
1025 0.247
1026 0
1027 0
1028 0
1029 --0.0945
103 0.259
1030 0
1031 0.329
1032 --0.0782
1033 0.015
1034 0.0301
1035 0
1036 0.123
1037 0
1038 0.0487
1039 --0.125
104 0
1040 0.202
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: CNhs11035

Jaspar motif P-value
MA0002.2 0.111
MA0003.1 0.174
MA0004.1 0.57
MA0006.1 0.0942
MA0007.1 0.892
MA0009.1 0.251
MA0014.1 0.811
MA0017.1 0.00213
MA0018.2 1.75304e-7
MA0019.1 0.165
MA0024.1 8.53203e-13
MA0025.1 0.00175
MA0027.1 0.00875
MA0028.1 0.499
MA0029.1 0.841
MA0030.1 0.222
MA0031.1 0.0174
MA0035.2 0.0104
MA0038.1 0.506
MA0039.2 0.0291
MA0040.1 0.442
MA0041.1 0.413
MA0042.1 0.48
MA0043.1 0.0115
MA0046.1 0.00524
MA0047.2 0.456
MA0048.1 0.0187
MA0050.1 0.115
MA0051.1 0.3
MA0052.1 1.33787e-5
MA0055.1 0.0236
MA0057.1 0.91
MA0058.1 0.587
MA0059.1 0.567
MA0060.1 7.32359e-4
MA0061.1 0.0174
MA0062.2 0.0236
MA0065.2 0.00318
MA0066.1 0.451
MA0067.1 0.0303
MA0068.1 0.241
MA0069.1 0.834
MA0070.1 0.819
MA0071.1 0.0489
MA0072.1 0.249
MA0073.1 0.997
MA0074.1 0.0838
MA0076.1 0.395
MA0077.1 0.64
MA0078.1 0.501
MA0079.2 0.031
MA0080.2 3.55221e-12
MA0081.1 0.00231
MA0083.1 0.26
MA0084.1 0.554
MA0087.1 0.178
MA0088.1 0.762
MA0090.1 0.575
MA0091.1 0.481
MA0092.1 0.56
MA0093.1 0.72
MA0099.2 0.00318
MA0100.1 0.469
MA0101.1 0.0825
MA0102.2 0.222
MA0103.1 2.75319e-5
MA0104.2 0.123
MA0105.1 0.0227
MA0106.1 0.123
MA0107.1 0.0837
MA0108.2 0.84
MA0111.1 0.939
MA0112.2 0.985
MA0113.1 0.25
MA0114.1 2.24783e-5
MA0115.1 2.99192e-4
MA0116.1 0.399
MA0117.1 0.0048
MA0119.1 0.241
MA0122.1 0.468
MA0124.1 0.328
MA0125.1 0.532
MA0131.1 0.884
MA0135.1 0.651
MA0136.1 6.67065e-12
MA0137.2 0.667
MA0138.2 0.00828
MA0139.1 0.14
MA0140.1 5.72709e-8
MA0141.1 0.00178
MA0142.1 0.876
MA0143.1 0.585
MA0144.1 0.81
MA0145.1 0.735
MA0146.1 0.234
MA0147.1 0.242
MA0148.1 0.611
MA0149.1 0.28
MA0150.1 0.0446
MA0152.1 0.572
MA0153.1 5.99419e-4
MA0154.1 0.00626
MA0155.1 0.0504
MA0156.1 1.14231e-12
MA0157.1 0.252
MA0159.1 0.0433
MA0160.1 0.0154
MA0162.1 0.321
MA0163.1 0.0108
MA0164.1 0.368
MA0258.1 0.216
MA0259.1 0.753



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: CNhs11035

Novel motif P-value
1 0.191
10 0.966
100 0.645
101 0.622
102 0.765
103 0.881
104 0.886
105 0.54
106 0.48
107 0.281
108 0.958
109 0.0826
11 0.751
110 0.69
111 0.206
112 0.461
113 0.971
114 0.078
115 0.322
116 0.242
117 0.854
118 0.967
119 0.382
12 0.223
120 0.432
121 0.918
122 0.864
123 0.0173
124 0.5
125 0.348
126 0.582
127 0.613
128 0.717
129 0.209
13 0.027
130 0.00615
131 0.909
132 0.399
133 0.103
134 0.187
135 0.319
136 0.0614
137 0.07
138 0.00642
139 0.0737
14 0.863
140 0.576
141 0.987
142 0.814
143 0.476
144 0.526
145 0.0526
146 0.822
147 0.289
148 0.122
149 0.434
15 0.731
150 0.0513
151 0.608
152 0.117
153 0.525
154 0.393
155 0.437
156 2.75692e-5
157 0.818
158 0.99
159 0.308
160 0.0431
161 0.0324
162 0.622
163 0.76
164 0.581
165 0.228
166 0.344
167 0.413
168 0.855
169 0.139
17 0.391
18 0.28
19 0.112
2 0.79
20 0.994
21 0.0841
22 0.242
23 0.259
24 0.00212
25 0.11
26 0.0188
27 0.962
28 0.231
29 0.928
3 0.916
30 0.638
31 0.545
32 0.307
33 0.177
34 0.381
35 0.0293
36 0.711
37 0.455
38 0.765
39 0.638
4 0.558
40 0.695
41 0.387
42 0.275
43 0.935
44 0.0657
45 0.722
46 0.692
47 0.406
48 0.608
49 0.295
5 0.507
50 0.0571
51 0.55
52 0.494
53 0.601
54 0.377
55 0.581
56 0.716
57 0.657
58 0.581
59 0.177
6 0.623
60 0.5
61 0.146
62 0.192
63 0.777
64 0.793
65 0.956
66 0.991
67 0.874
68 0.0547
69 0.944
7 0.543
70 0.00333
71 0.421
72 0.139
73 0.124
74 0.571
75 0.852
76 0.72
77 0.825
78 0.301
79 0.617
8 0.795
80 0.542
81 0.654
82 0.559
83 0.436
84 0.00312
85 0.233
86 0.921
87 0.617
88 0.767
89 0.499
9 0.244
90 0.257
91 0.761
92 0.441
93 0.91
94 0.717
95 0.12
96 0.35
97 0.909
98 0.477
99 0.186



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: CNhs11035


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)
0002106 (spleen)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002323 (body cavity)
0005177 (trunk region element)
0004177 (hemopoietic organ)
0005057 (immune organ)
0005172 (abdomen element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002390 (hematopoietic system)
0002417 (abdominal segment of trunk)
0002193 (hemolymphoid system)
0000916 (abdomen)
0002405 (immune system)

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)
0011360 (mouse spleen- 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:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)