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FF:2104-43C7

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Name:thymus, neonate N03
Species:Mouse (Mus musculus)
Library ID:CNhs11137
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuethymus
dev stage3 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  DRS008982
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11137 CAGE DRX009119 DRR009993
Accession ID Mm9

Library idBAMCTSS
CNhs11137 DRZ001418 DRZ002801
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs11137

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0154
1001 0.0201
1002 0.0354
1003 --0.0553
1004 0
1005 0
1006 --0.0828
1007 0.06
1008 0
1009 --0.13
101 0.144
1010 0
1011 0
1012 0.345
1013 --0.153
1014 --0.0851
1015 0.0974
1016 --0.267
1017 0
1018 0.0598
1019 0
102 0.0598
1020 0
1021 0
1022 --0.173
1023 0
1024 --0.0899
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 0.295
103 --0.025
1030 0
1031 --0.473
1032 --0.341
1033 --0.00432
1034 0
1035 0
1036 0.216
1037 0
1038 --0.414
1039 --0.186
104 0
1040 --0.0865
1041 0.0598



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: CNhs11137

Jaspar motif P-value
MA0002.2 0.00319
MA0003.1 0.286
MA0004.1 0.346
MA0006.1 0.929
MA0007.1 0.474
MA0009.1 0.543
MA0014.1 0.167
MA0017.1 0.801
MA0018.2 0.022
MA0019.1 0.424
MA0024.1 1.59965e-5
MA0025.1 0.00261
MA0027.1 0.701
MA0028.1 1.41051e-5
MA0029.1 0.14
MA0030.1 0.526
MA0031.1 0.421
MA0035.2 0.415
MA0038.1 0.794
MA0039.2 0.207
MA0040.1 0.971
MA0041.1 0.24
MA0042.1 0.737
MA0043.1 0.061
MA0046.1 9.59915e-17
MA0047.2 0.8
MA0048.1 0.613
MA0050.1 4.96881e-6
MA0051.1 5.00418e-5
MA0052.1 0.0131
MA0055.1 0.918
MA0057.1 0.701
MA0058.1 0.502
MA0059.1 0.00741
MA0060.1 0.0464
MA0061.1 4.27295e-5
MA0062.2 3.0166e-15
MA0065.2 0.501
MA0066.1 0.00692
MA0067.1 0.844
MA0068.1 0.491
MA0069.1 0.797
MA0070.1 0.444
MA0071.1 0.367
MA0072.1 1.42994e-5
MA0073.1 0.824
MA0074.1 0.895
MA0076.1 7.19693e-7
MA0077.1 0.146
MA0078.1 0.674
MA0079.2 0.0293
MA0080.2 5.79634e-13
MA0081.1 0.0261
MA0083.1 0.215
MA0084.1 0.351
MA0087.1 0.318
MA0088.1 0.258
MA0090.1 0.0411
MA0091.1 0.0317
MA0092.1 0.912
MA0093.1 0.398
MA0099.2 0.123
MA0100.1 0.0136
MA0101.1 9.0462e-5
MA0102.2 0.356
MA0103.1 3.91685e-4
MA0104.2 0.0826
MA0105.1 1.26197e-8
MA0106.1 0.727
MA0107.1 1.41736e-4
MA0108.2 0.0102
MA0111.1 0.326
MA0112.2 0.0107
MA0113.1 0.565
MA0114.1 0.372
MA0115.1 0.712
MA0116.1 0.00111
MA0117.1 0.619
MA0119.1 0.861
MA0122.1 0.921
MA0124.1 0.382
MA0125.1 0.51
MA0131.1 0.1
MA0135.1 0.196
MA0136.1 5.33999e-22
MA0137.2 0.0524
MA0138.2 8.57689e-6
MA0139.1 0.162
MA0140.1 0.745
MA0141.1 0.52
MA0142.1 0.607
MA0143.1 0.373
MA0144.1 0.405
MA0145.1 0.323
MA0146.1 0.531
MA0147.1 0.036
MA0148.1 0.757
MA0149.1 0.0584
MA0150.1 0.405
MA0152.1 0.813
MA0153.1 1.65081e-8
MA0154.1 0.11
MA0155.1 0.795
MA0156.1 2.41597e-24
MA0157.1 0.53
MA0159.1 0.132
MA0160.1 0.332
MA0162.1 0.422
MA0163.1 7.49012e-4
MA0164.1 0.729
MA0258.1 0.0316
MA0259.1 0.589



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: CNhs11137

Novel motif P-value
1 0.198
10 0.0106
100 0.643
101 0.997
102 0.48
103 0.191
104 0.775
105 0.957
106 0.697
107 0.975
108 0.302
109 0.287
11 0.105
110 0.0454
111 0.582
112 0.207
113 0.376
114 0.685
115 0.413
116 0.672
117 8.58091e-4
118 0.247
119 0.262
12 0.619
120 0.192
121 0.439
122 0.659
123 0.837
124 0.699
125 0.104
126 0.429
127 0.993
128 0.548
129 0.127
13 0.014
130 0.332
131 0.56
132 0.699
133 0.625
134 0.325
135 0.421
136 0.309
137 0.303
138 0.723
139 0.41
14 0.76
140 0.87
141 0.907
142 0.644
143 0.215
144 0.194
145 0.062
146 0.716
147 0.368
148 0.256
149 0.73
15 0.144
150 0.365
151 0.2
152 0.0736
153 0.224
154 0.0472
155 0.248
156 0.0236
157 0.45
158 0.129
159 0.0545
160 0.848
161 0.479
162 0.458
163 0.706
164 0.144
165 0.293
166 0.546
167 0.114
168 0.474
169 0.31
17 0.607
18 0.821
19 0.851
2 0.0848
20 0.267
21 0.42
22 0.882
23 0.899
24 0.169
25 0.235
26 0.0294
27 0.553
28 0.259
29 0.0397
3 0.123
30 0.153
31 0.449
32 0.123
33 0.419
34 0.951
35 0.0986
36 0.11
37 0.183
38 0.257
39 0.975
4 0.913
40 0.479
41 0.903
42 0.0243
43 0.397
44 0.811
45 0.751
46 0.11
47 0.323
48 0.202
49 0.171
5 0.29
50 0.975
51 0.947
52 0.225
53 0.987
54 0.268
55 0.301
56 0.725
57 0.19
58 0.244
59 0.844
6 0.233
60 0.917
61 0.0455
62 0.0824
63 0.511
64 0.627
65 0.499
66 0.607
67 0.685
68 0.348
69 0.513
7 0.106
70 0.38
71 0.0212
72 0.44
73 0.527
74 0.818
75 0.0259
76 0.0433
77 0.281
78 0.108
79 0.8
8 0.327
80 0.125
81 0.902
82 0.794
83 0.799
84 0.0438
85 0.82
86 0.265
87 0.125
88 0.294
89 0.472
9 0.262
90 0.0592
91 0.897
92 0.979
93 0.757
94 0.195
95 0.498
96 0.011
97 0.502
98 0.611
99 0.457



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: CNhs11137


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)
0000311 (mouse neonate N3 sample)
0011304 (mouse thymus- neonate N03 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)