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FF:1541-43F8

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Name:thymus, neonate N02
Species:Mouse (Mus musculus)
Library ID:CNhs11181
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 stage2 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  SAMD00004748
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11181 CAGE DRX009118 DRR009992
Accession ID Mm9

Library idBAMCTSS
CNhs11181 DRZ001417 DRZ002800
Accession ID Mm10

Library idBAMCTSS
CNhs11181 DRZ012767 DRZ014150
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

CNhs11181

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.0133
1002 -4.923381e-4
1003 --0.0929
1004 0
1005 0
1006 --0.0934
1007 0.102
1008 0.0493
1009 --0.109
101 0.134
1010 0
1011 0.0433
1012 0.429
1013 --0.12
1014 --0.0851
1015 0.121
1016 --0.276
1017 0
1018 0.134
1019 0
102 0.0493
1020 0
1021 0.218
1022 --0.249
1023 0
1024 0.00111
1025 --0.0611
1026 0
1027 0
1028 0
1029 0.252
103 --0.0402
1030 0
1031 --0.529
1032 --0.39
1033 0.0493
1034 0
1035 0
1036 0.161
1037 0
1038 --0.419
1039 --0.225
104 0
1040 --0.121
1041 0.0493



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: CNhs11181

Jaspar motif P-value
MA0002.2 0.00351
MA0003.1 0.358
MA0004.1 0.339
MA0006.1 0.971
MA0007.1 0.475
MA0009.1 0.37
MA0014.1 0.168
MA0017.1 0.568
MA0018.2 0.0268
MA0019.1 0.44
MA0024.1 1.1952e-5
MA0025.1 0.00169
MA0027.1 0.553
MA0028.1 4.20465e-6
MA0029.1 0.171
MA0030.1 0.528
MA0031.1 0.441
MA0035.2 0.378
MA0038.1 0.666
MA0039.2 0.234
MA0040.1 0.703
MA0041.1 0.247
MA0042.1 0.92
MA0043.1 0.0624
MA0046.1 6.31016e-17
MA0047.2 0.666
MA0048.1 0.442
MA0050.1 7.33911e-7
MA0051.1 8.38286e-6
MA0052.1 0.00211
MA0055.1 0.955
MA0057.1 0.679
MA0058.1 0.564
MA0059.1 0.0112
MA0060.1 0.0272
MA0061.1 1.75287e-5
MA0062.2 1.45774e-16
MA0065.2 0.595
MA0066.1 0.01
MA0067.1 0.687
MA0068.1 0.591
MA0069.1 0.96
MA0070.1 0.381
MA0071.1 0.406
MA0072.1 8.76734e-6
MA0073.1 0.813
MA0074.1 0.893
MA0076.1 2.2603e-7
MA0077.1 0.123
MA0078.1 0.835
MA0079.2 0.0302
MA0080.2 2.69867e-13
MA0081.1 0.0202
MA0083.1 0.111
MA0084.1 0.422
MA0087.1 0.391
MA0088.1 0.427
MA0090.1 0.0909
MA0091.1 0.0341
MA0092.1 0.871
MA0093.1 0.39
MA0099.2 0.139
MA0100.1 0.0148
MA0101.1 2.76991e-5
MA0102.2 0.422
MA0103.1 9.25475e-5
MA0104.2 0.0944
MA0105.1 4.66804e-8
MA0106.1 0.75
MA0107.1 5.01618e-5
MA0108.2 0.00501
MA0111.1 0.206
MA0112.2 0.0123
MA0113.1 0.655
MA0114.1 0.247
MA0115.1 0.551
MA0116.1 0.00299
MA0117.1 0.589
MA0119.1 0.797
MA0122.1 0.987
MA0124.1 0.33
MA0125.1 0.548
MA0131.1 0.0874
MA0135.1 0.262
MA0136.1 1.71989e-21
MA0137.2 0.0646
MA0138.2 3.92394e-6
MA0139.1 0.195
MA0140.1 0.498
MA0141.1 0.357
MA0142.1 0.712
MA0143.1 0.272
MA0144.1 0.249
MA0145.1 0.45
MA0146.1 0.411
MA0147.1 0.0345
MA0148.1 0.582
MA0149.1 0.0418
MA0150.1 0.335
MA0152.1 0.762
MA0153.1 2.13701e-8
MA0154.1 0.131
MA0155.1 0.799
MA0156.1 5.86625e-25
MA0157.1 0.458
MA0159.1 0.101
MA0160.1 0.242
MA0162.1 0.421
MA0163.1 1.96536e-4
MA0164.1 0.717
MA0258.1 0.0315
MA0259.1 0.678



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: CNhs11181

Novel motif P-value
1 0.23
10 0.0104
100 0.766
101 1
102 0.48
103 0.188
104 0.906
105 0.894
106 0.676
107 0.951
108 0.236
109 0.3
11 0.121
110 0.0464
111 0.671
112 0.141
113 0.392
114 0.942
115 0.446
116 0.732
117 9.46648e-4
118 0.172
119 0.328
12 0.65
120 0.185
121 0.423
122 0.64
123 0.675
124 0.78
125 0.119
126 0.579
127 0.975
128 0.604
129 0.199
13 0.0124
130 0.193
131 0.549
132 0.7
133 0.66
134 0.484
135 0.44
136 0.571
137 0.34
138 0.766
139 0.556
14 0.685
140 0.794
141 0.977
142 0.705
143 0.161
144 0.171
145 0.0566
146 0.889
147 0.291
148 0.378
149 0.836
15 0.103
150 0.306
151 0.278
152 0.0793
153 0.221
154 0.0751
155 0.146
156 0.00315
157 0.384
158 0.164
159 0.0697
160 0.926
161 0.315
162 0.632
163 0.759
164 0.118
165 0.273
166 0.305
167 0.145
168 0.353
169 0.331
17 0.665
18 0.743
19 0.673
2 0.0685
20 0.216
21 0.365
22 0.947
23 0.843
24 0.147
25 0.235
26 0.0169
27 0.528
28 0.276
29 0.0446
3 0.153
30 0.11
31 0.458
32 0.117
33 0.358
34 0.914
35 0.0987
36 0.158
37 0.257
38 0.229
39 0.983
4 0.813
40 0.503
41 0.988
42 0.0329
43 0.47
44 0.849
45 0.83
46 0.102
47 0.434
48 0.227
49 0.185
5 0.345
50 0.922
51 0.877
52 0.198
53 0.837
54 0.329
55 0.345
56 0.923
57 0.226
58 0.249
59 0.836
6 0.251
60 0.964
61 0.0523
62 0.095
63 0.538
64 0.747
65 0.51
66 0.593
67 0.647
68 0.257
69 0.472
7 0.123
70 0.373
71 0.0228
72 0.519
73 0.514
74 0.833
75 0.0382
76 0.0296
77 0.249
78 0.0733
79 0.719
8 0.34
80 0.0912
81 0.967
82 0.873
83 0.788
84 0.0774
85 0.592
86 0.341
87 0.21
88 0.291
89 0.356
9 0.33
90 0.0364
91 0.804
92 0.64
93 0.969
94 0.245
95 0.361
96 0.063
97 0.47
98 0.346
99 0.331



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: CNhs11181


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000307 (mouse neonate N2 sample)
0011280 (mouse thymus- neonate N02 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)