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FF:824-19H1

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Name:spleen, neonate N20
Species:Mouse (Mus musculus)
Library ID:CNhs11112
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 stage20 days neonate
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  SAMD00005217
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11112 CAGE DRX009088 DRR009962
Accession ID Mm9

Library idBAMCTSS
CNhs11112 DRZ001387 DRZ002770
Accession ID Mm10

Library idBAMCTSS
CNhs11112 DRZ012737 DRZ014120
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

CNhs11112

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.00222
1002 --0.0921
1003 --0.0518
1004 0
1005 0.0556
1006 --0.143
1007 --0.00166
1008 0
1009 --0.134
101 0.133
1010 0
1011 0
1012 0.189
1013 --0.132
1014 --0.0317
1015 --0.162
1016 --0.324
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 --0.162
1023 0
1024 --0.0761
1025 0
1026 0
1027 0
1028 0
1029 0.138
103 --0.0447
1030 0.741
1031 --0.317
1032 --0.466
1033 0.00822
1034 0
1035 0
1036 0.25
1037 0
1038 --0.272
1039 --0.224
104 0
1040 --0.111
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: CNhs11112

Jaspar motif P-value
MA0002.2 0.00166
MA0003.1 0.496
MA0004.1 0.649
MA0006.1 0.38
MA0007.1 0.721
MA0009.1 0.406
MA0014.1 0.874
MA0017.1 0.252
MA0018.2 0.00832
MA0019.1 0.199
MA0024.1 4.57593e-6
MA0025.1 0.0565
MA0027.1 0.574
MA0028.1 0.0198
MA0029.1 0.829
MA0030.1 0.296
MA0031.1 0.593
MA0035.2 7.35339e-10
MA0038.1 0.11
MA0039.2 0.876
MA0040.1 0.617
MA0041.1 0.312
MA0042.1 0.969
MA0043.1 0.00276
MA0046.1 1.02928e-10
MA0047.2 0.912
MA0048.1 0.241
MA0050.1 1.02224e-10
MA0051.1 3.46315e-6
MA0052.1 4.63807e-6
MA0055.1 0.301
MA0057.1 0.816
MA0058.1 0.803
MA0059.1 0.145
MA0060.1 0.239
MA0061.1 8.72507e-4
MA0062.2 5.71053e-6
MA0065.2 0.314
MA0066.1 0.0829
MA0067.1 0.753
MA0068.1 0.736
MA0069.1 0.505
MA0070.1 0.226
MA0071.1 0.732
MA0072.1 0.633
MA0073.1 1
MA0074.1 0.735
MA0076.1 0.0402
MA0077.1 0.126
MA0078.1 0.719
MA0079.2 0.0259
MA0080.2 4.13609e-11
MA0081.1 0.0344
MA0083.1 0.0731
MA0084.1 0.228
MA0087.1 0.12
MA0088.1 0.111
MA0090.1 0.0473
MA0091.1 0.0543
MA0092.1 0.743
MA0093.1 0.729
MA0099.2 0.542
MA0100.1 0.069
MA0101.1 0.00311
MA0102.2 0.775
MA0103.1 0.881
MA0104.2 0.6
MA0105.1 5.73848e-6
MA0106.1 0.225
MA0107.1 0.00423
MA0108.2 5.93542e-4
MA0111.1 0.615
MA0112.2 0.00355
MA0113.1 0.5
MA0114.1 0.911
MA0115.1 0.669
MA0116.1 0.00123
MA0117.1 0.857
MA0119.1 0.235
MA0122.1 0.936
MA0124.1 0.844
MA0125.1 0.0529
MA0131.1 0.782
MA0135.1 0.0896
MA0136.1 2.41342e-13
MA0137.2 0.683
MA0138.2 0.00358
MA0139.1 0.231
MA0140.1 1.92838e-36
MA0141.1 0.492
MA0142.1 0.0778
MA0143.1 0.239
MA0144.1 0.734
MA0145.1 0.88
MA0146.1 0.313
MA0147.1 0.482
MA0148.1 0.551
MA0149.1 0.0523
MA0150.1 0.0682
MA0152.1 0.922
MA0153.1 2.30367e-7
MA0154.1 0.00404
MA0155.1 0.615
MA0156.1 2.51498e-11
MA0157.1 0.536
MA0159.1 0.151
MA0160.1 0.91
MA0162.1 0.261
MA0163.1 1.45769e-4
MA0164.1 0.381
MA0258.1 0.116
MA0259.1 0.909



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: CNhs11112

Novel motif P-value
1 0.0958
10 0.0174
100 0.738
101 0.767
102 0.716
103 0.01
104 0.918
105 0.548
106 0.289
107 0.657
108 0.342
109 0.111
11 0.225
110 0.0806
111 0.02
112 0.0337
113 0.898
114 0.396
115 0.559
116 0.951
117 5.90501e-4
118 0.0681
119 0.187
12 0.972
120 0.992
121 0.28
122 0.757
123 0.193
124 0.974
125 0.0198
126 0.194
127 0.38
128 0.288
129 0.114
13 0.00663
130 0.532
131 0.843
132 0.123
133 0.495
134 0.0981
135 0.983
136 0.931
137 0.0403
138 0.701
139 0.584
14 0.734
140 0.232
141 0.671
142 0.181
143 0.343
144 0.961
145 0.0144
146 0.948
147 0.88
148 0.172
149 0.423
15 0.0388
150 0.189
151 0.269
152 0.442
153 0.441
154 0.27
155 0.13
156 0.187
157 0.703
158 0.0386
159 0.126
160 0.608
161 0.091
162 0.704
163 0.579
164 0.0286
165 0.327
166 0.37
167 0.1
168 0.477
169 0.0536
17 0.472
18 0.209
19 0.414
2 0.261
20 0.0597
21 0.386
22 0.564
23 0.818
24 0.4
25 0.318
26 0.00187
27 0.758
28 0.19
29 0.0245
3 0.0527
30 0.329
31 0.889
32 0.667
33 0.27
34 0.945
35 0.47
36 0.0582
37 0.157
38 0.496
39 0.951
4 0.894
40 0.274
41 0.762
42 0.0747
43 0.109
44 0.474
45 0.706
46 0.147
47 0.169
48 0.237
49 0.051
5 0.0776
50 0.982
51 0.834
52 0.938
53 0.972
54 0.947
55 0.326
56 0.649
57 0.133
58 0.31
59 0.512
6 0.358
60 0.402
61 0.385
62 0.115
63 0.421
64 0.655
65 0.579
66 0.654
67 0.555
68 0.504
69 0.525
7 0.04
70 0.353
71 0.019
72 0.33
73 0.403
74 0.774
75 0.039
76 0.178
77 0.672
78 0.0261
79 0.957
8 0.0257
80 0.0284
81 0.436
82 0.569
83 0.462
84 0.16
85 0.323
86 0.584
87 0.772
88 0.587
89 0.652
9 0.46
90 0.0157
91 0.24
92 0.561
93 0.359
94 0.0593
95 0.17
96 0.0341
97 0.869
98 0.164
99 0.6



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: CNhs11112


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000308 (mouse neonate N20 sample)
0011430 (mouse spleen- neonate N20 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)