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FF:820-7A2

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Name:thymus, neonate N20
Species:Mouse (Mus musculus)
Library ID:CNhs11186
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 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  SAMD00004712
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11186 CAGE DRX009123 DRR009997
Accession ID Mm9

Library idBAMCTSS
CNhs11186 DRZ001422 DRZ002805
Accession ID Mm10

Library idBAMCTSS
CNhs11186 DRZ012772 DRZ014155
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

CNhs11186

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 0.0981
1002 --0.0537
1003 --0.0838
1004 0
1005 0.143
1006 --0.14
1007 0.0617
1008 0.111
1009 --0.0886
101 0.0894
1010 0
1011 0.0404
1012 0.536
1013 --0.157
1014 --0.0874
1015 0.0156
1016 --0.483
1017 0
1018 0.0773
1019 0
102 0.0773
1020 0
1021 0.0286
1022 --0.27
1023 0
1024 --0.135
1025 --0.0611
1026 0
1027 0
1028 0
1029 0.356
103 --0.0788
1030 0.0404
1031 --0.738
1032 --0.469
1033 0.0449
1034 0
1035 0
1036 0.0906
1037 0
1038 --0.257
1039 --0.177
104 0
1040 --0.0865
1041 0.0404



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: CNhs11186

Jaspar motif P-value
MA0002.2 4.92799e-4
MA0003.1 0.428
MA0004.1 0.392
MA0006.1 0.794
MA0007.1 0.519
MA0009.1 0.454
MA0014.1 0.233
MA0017.1 0.921
MA0018.2 0.0523
MA0019.1 0.642
MA0024.1 0.00468
MA0025.1 0.0102
MA0027.1 0.645
MA0028.1 1.60227e-4
MA0029.1 0.143
MA0030.1 0.701
MA0031.1 0.273
MA0035.2 0.37
MA0038.1 0.626
MA0039.2 0.22
MA0040.1 0.997
MA0041.1 0.241
MA0042.1 0.944
MA0043.1 0.083
MA0046.1 2.59624e-14
MA0047.2 0.702
MA0048.1 0.886
MA0050.1 8.11051e-8
MA0051.1 3.05998e-6
MA0052.1 6.21576e-4
MA0055.1 0.405
MA0057.1 0.73
MA0058.1 0.664
MA0059.1 0.0588
MA0060.1 0.695
MA0061.1 1.17116e-5
MA0062.2 1.19128e-14
MA0065.2 0.45
MA0066.1 0.00798
MA0067.1 0.507
MA0068.1 0.961
MA0069.1 0.834
MA0070.1 0.423
MA0071.1 0.456
MA0072.1 4.61998e-5
MA0073.1 0.772
MA0074.1 0.882
MA0076.1 1.47848e-5
MA0077.1 0.168
MA0078.1 0.74
MA0079.2 0.0323
MA0080.2 1.16205e-13
MA0081.1 0.0263
MA0083.1 0.066
MA0084.1 0.347
MA0087.1 0.374
MA0088.1 0.487
MA0090.1 0.0355
MA0091.1 0.0571
MA0092.1 0.963
MA0093.1 0.464
MA0099.2 0.218
MA0100.1 0.024
MA0101.1 1.06221e-4
MA0102.2 0.833
MA0103.1 9.83106e-5
MA0104.2 0.213
MA0105.1 9.89957e-9
MA0106.1 0.666
MA0107.1 6.34631e-5
MA0108.2 0.0112
MA0111.1 0.283
MA0112.2 0.0074
MA0113.1 0.697
MA0114.1 0.442
MA0115.1 0.659
MA0116.1 0.00437
MA0117.1 0.81
MA0119.1 0.968
MA0122.1 0.845
MA0124.1 0.414
MA0125.1 0.228
MA0131.1 0.267
MA0135.1 0.167
MA0136.1 1.45624e-21
MA0137.2 0.103
MA0138.2 6.43836e-5
MA0139.1 0.2
MA0140.1 0.511
MA0141.1 0.54
MA0142.1 0.436
MA0143.1 0.326
MA0144.1 0.497
MA0145.1 0.459
MA0146.1 0.428
MA0147.1 0.109
MA0148.1 0.53
MA0149.1 0.0582
MA0150.1 0.593
MA0152.1 0.914
MA0153.1 4.33631e-9
MA0154.1 0.0616
MA0155.1 0.976
MA0156.1 3.11567e-23
MA0157.1 0.484
MA0159.1 0.102
MA0160.1 0.511
MA0162.1 0.532
MA0163.1 0.00334
MA0164.1 0.665
MA0258.1 0.0245
MA0259.1 0.831



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: CNhs11186

Novel motif P-value
1 0.167
10 0.012
100 0.827
101 0.663
102 0.56
103 0.181
104 0.8
105 0.754
106 0.601
107 0.958
108 0.303
109 0.371
11 0.139
110 0.0612
111 0.767
112 0.131
113 0.255
114 0.52
115 0.517
116 0.794
117 2.96113e-4
118 0.15
119 0.255
12 0.591
120 0.24
121 0.448
122 0.914
123 0.617
124 0.813
125 0.104
126 0.555
127 0.683
128 0.367
129 0.187
13 0.0319
130 0.465
131 0.516
132 0.82
133 0.761
134 0.601
135 0.537
136 0.372
137 0.279
138 0.734
139 0.214
14 0.84
140 0.931
141 0.784
142 0.672
143 0.271
144 0.147
145 0.0845
146 0.833
147 0.406
148 0.265
149 0.885
15 0.0884
150 0.298
151 0.127
152 0.107
153 0.186
154 0.0985
155 0.111
156 0.635
157 0.824
158 0.0566
159 0.0137
160 0.934
161 0.313
162 0.566
163 0.98
164 0.15
165 0.222
166 0.386
167 0.109
168 0.248
169 0.302
17 0.492
18 0.683
19 0.65
2 0.106
20 0.297
21 0.517
22 0.979
23 0.883
24 0.253
25 0.22
26 0.0371
27 0.41
28 0.145
29 0.0592
3 0.118
30 0.194
31 0.714
32 0.183
33 0.557
34 0.955
35 0.0443
36 0.204
37 0.232
38 0.325
39 0.819
4 0.95
40 0.662
41 0.989
42 0.0287
43 0.381
44 0.697
45 0.841
46 0.105
47 0.372
48 0.257
49 0.128
5 0.193
50 0.876
51 0.828
52 0.284
53 0.938
54 0.396
55 0.347
56 0.654
57 0.216
58 0.193
59 0.799
6 0.278
60 0.824
61 0.0435
62 0.0648
63 0.445
64 0.815
65 0.497
66 0.513
67 0.754
68 0.646
69 0.535
7 0.147
70 0.238
71 0.0348
72 0.495
73 0.434
74 0.846
75 0.0197
76 0.055
77 0.288
78 0.12
79 0.744
8 0.327
80 0.0937
81 0.947
82 0.757
83 0.939
84 0.246
85 0.989
86 0.177
87 0.13
88 0.282
89 0.612
9 0.302
90 0.0283
91 0.96
92 0.851
93 0.94
94 0.236
95 0.49
96 0.0169
97 0.505
98 0.546
99 0.397



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: CNhs11186


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)
0000308 (mouse neonate N20 sample)
0011426 (mouse thymus- 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:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)