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FF:1354-25G3

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Name:spleen, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11099
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 stage25 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  SAMD00004892
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11099 CAGE DRX009089 DRR009963
Accession ID Mm9

Library idBAMCTSS
CNhs11099 DRZ001388 DRZ002771
Accession ID Mm10

Library idBAMCTSS
CNhs11099 DRZ012738 DRZ014121
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

CNhs11099

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.00373
1002 -0.00929
1003 -0.0952
1004 0
1005 0.0895
1006 -0.143
1007 0.0757
1008 0
1009 -0.11
101 0.109
1010 0
1011 -0.018
1012 0.281
1013 -0.0543
1014 -0.0874
1015 -0.0823
1016 -0.333
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0895
1022 -0.171
1023 0
1024 -0.117
1025 0
1026 0
1027 0
1028 0
1029 0.105
103 -0.061
1030 0.842
1031 -0.345
1032 -0.324
1033 0.0971
1034 0
1035 0
1036 0.17
1037 0
1038 -0.277
1039 -0.185
104 0
1040 -0.121
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: CNhs11099
Jaspar motif P-value
MA0002.2 0.00606
MA0003.1 0.645
MA0004.1 0.723
MA0006.1 0.392
MA0007.1 0.812
MA0009.1 0.379
MA0014.1 0.624
MA0017.1 0.253
MA0018.2 0.0161
MA0019.1 0.258
MA0024.1 1.26292e-4
MA0025.1 0.126
MA0027.1 0.591
MA0028.1 0.0275
MA0029.1 0.741
MA0030.1 0.325
MA0031.1 0.929
MA0035.2 8.85354e-8
MA0038.1 0.094
MA0039.2 0.442
MA0040.1 0.687
MA0041.1 0.249
MA0042.1 0.825
MA0043.1 0.0049
MA0046.1 1.33357e-10
MA0047.2 0.945
MA0048.1 0.249
MA0050.1 2.32659e-13
MA0051.1 3.16512e-8
MA0052.1 4.80659e-5
MA0055.1 0.256
MA0057.1 0.671
MA0058.1 0.772
MA0059.1 0.175
MA0060.1 0.485
MA0061.1 2.44249e-4
MA0062.2 4.41613e-6
MA0065.2 0.222
MA0066.1 0.117
MA0067.1 0.917
MA0068.1 0.878
MA0069.1 0.754
MA0070.1 0.246
MA0071.1 0.727
MA0072.1 0.465
MA0073.1 0.804
MA0074.1 0.791
MA0076.1 0.0649
MA0077.1 0.103
MA0078.1 0.463
MA0079.2 0.0487
MA0080.2 7.98158e-12
MA0081.1 0.0235
MA0083.1 0.213
MA0084.1 0.406
MA0087.1 0.263
MA0088.1 0.169
MA0090.1 0.0474
MA0091.1 0.135
MA0092.1 0.79
MA0093.1 0.75
MA0099.2 0.636
MA0100.1 0.101
MA0101.1 5.6364e-4
MA0102.2 0.933
MA0103.1 0.999
MA0104.2 0.627
MA0105.1 6.56374e-7
MA0106.1 0.338
MA0107.1 6.24086e-4
MA0108.2 6.75158e-4
MA0111.1 0.581
MA0112.2 0.00191
MA0113.1 0.477
MA0114.1 0.81
MA0115.1 0.947
MA0116.1 0.00247
MA0117.1 0.772
MA0119.1 0.252
MA0122.1 0.708
MA0124.1 0.807
MA0125.1 0.0882
MA0131.1 0.913
MA0135.1 0.105
MA0136.1 2.72686e-14
MA0137.2 0.528
MA0138.2 0.0141
MA0139.1 0.175
MA0140.1 3.12822e-36
MA0141.1 0.517
MA0142.1 0.0302
MA0143.1 0.171
MA0144.1 0.73
MA0145.1 0.85
MA0146.1 0.226
MA0147.1 0.575
MA0148.1 0.728
MA0149.1 0.0287
MA0150.1 0.0491
MA0152.1 0.896
MA0153.1 1.82653e-6
MA0154.1 0.00235
MA0155.1 0.657
MA0156.1 3.68485e-12
MA0157.1 0.921
MA0159.1 0.0773
MA0160.1 0.944
MA0162.1 0.232
MA0163.1 1.00564e-4
MA0164.1 0.396
MA0258.1 0.0554
MA0259.1 0.971



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: CNhs11099
Novel motif P-value
1 0.0873
10 0.0265
100 0.858
101 0.947
102 0.583
103 0.0226
104 0.973
105 0.932
106 0.204
107 0.674
108 0.333
109 0.105
11 0.186
110 0.0717
111 0.0474
112 0.0297
113 0.727
114 0.449
115 0.522
116 0.839
117 7.74448e-4
118 0.0875
119 0.229
12 0.977
120 0.621
121 0.15
122 0.911
123 0.198
124 0.888
125 0.036
126 0.188
127 0.624
128 0.258
129 0.126
13 0.0109
130 0.34
131 0.815
132 0.137
133 0.391
134 0.0972
135 0.939
136 0.954
137 0.0308
138 0.891
139 0.563
14 0.64
140 0.382
141 0.487
142 0.0501
143 0.233
144 0.905
145 0.0344
146 0.971
147 0.783
148 0.0932
149 0.651
15 0.0407
150 0.199
151 0.25
152 0.829
153 0.357
154 0.384
155 0.101
156 0.76
157 0.989
158 0.0449
159 0.075
160 0.598
161 0.0604
162 0.95
163 0.299
164 0.023
165 0.202
166 0.552
167 0.0913
168 0.641
169 0.0277
17 0.349
18 0.193
19 0.355
2 0.262
20 0.052
21 0.338
22 0.539
23 0.954
24 0.267
25 0.268
26 0.00316
27 0.879
28 0.179
29 0.0333
3 0.0348
30 0.291
31 0.921
32 0.495
33 0.201
34 0.801
35 0.476
36 0.0419
37 0.138
38 0.49
39 0.894
4 0.936
40 0.204
41 0.757
42 0.0663
43 0.0766
44 0.609
45 0.738
46 0.148
47 0.181
48 0.21
49 0.0529
5 0.0932
50 0.997
51 0.828
52 0.905
53 0.892
54 0.886
55 0.307
56 0.506
57 0.128
58 0.332
59 0.352
6 0.547
60 0.368
61 0.277
62 0.134
63 0.403
64 0.623
65 0.417
66 0.708
67 0.535
68 0.21
69 0.357
7 0.0636
70 0.181
71 0.0255
72 0.211
73 0.29
74 0.759
75 0.0252
76 0.19
77 0.705
78 0.0247
79 0.797
8 0.0502
80 0.0458
81 0.391
82 0.669
83 0.336
84 0.0829
85 0.25
86 0.615
87 0.49
88 0.706
89 0.83
9 0.583
90 0.0256
91 0.18
92 0.676
93 0.478
94 0.0476
95 0.234
96 0.0146
97 0.885
98 0.154
99 0.676



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: CNhs11099


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)
0000309 (mouse neonate N25 sample)
0011491 (mouse spleen- neonate N25 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)