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FF:681-26C4

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Name:thymus, neonate N06
Species:Mouse (Mus musculus)
Library ID:CNhs11197
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 stage6 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  SAMD00005698
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11197 CAGE DRX009120 DRR009994
Accession ID Mm9

Library idBAMCTSS
CNhs11197 DRZ001419 DRZ002802
Accession ID Mm10

Library idBAMCTSS
CNhs11197 DRZ012769 DRZ014152
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
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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

CNhs11197

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 -0.0317
1001 0.0737
1002 -0.0373
1003 -0.0968
1004 0
1005 0.0104
1006 -0.111
1007 0.0592
1008 0
1009 -0.112
101 0.165
1010 0
1011 -0.00767
1012 0.418
1013 -0.102
1014 -0.0851
1015 0.082
1016 -0.338
1017 0
1018 0.115
1019 0
102 0.0418
1020 0
1021 0.0986
1022 -0.124
1023 0
1024 -0.0899
1025 0
1026 0
1027 0
1028 0
1029 0.46
103 -0.0319
1030 0.0418
1031 -0.547
1032 -0.465
1033 0.0472
1034 0
1035 0
1036 0.206
1037 0
1038 -0.372
1039 -0.177
104 0
1040 -0.121
1041 0.0418



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: CNhs11197
Jaspar motif P-value
MA0002.2 4.95602e-4
MA0003.1 0.379
MA0004.1 0.342
MA0006.1 0.92
MA0007.1 0.513
MA0009.1 0.269
MA0014.1 0.247
MA0017.1 0.619
MA0018.2 0.0691
MA0019.1 0.34
MA0024.1 2.37613e-5
MA0025.1 0.0137
MA0027.1 0.745
MA0028.1 1.22031e-6
MA0029.1 0.053
MA0030.1 0.741
MA0031.1 0.254
MA0035.2 0.37
MA0038.1 0.979
MA0039.2 0.316
MA0040.1 0.91
MA0041.1 0.32
MA0042.1 0.922
MA0043.1 0.228
MA0046.1 1.35651e-17
MA0047.2 0.481
MA0048.1 0.645
MA0050.1 2.97991e-6
MA0051.1 3.75859e-5
MA0052.1 0.00682
MA0055.1 0.909
MA0057.1 0.613
MA0058.1 0.496
MA0059.1 0.0179
MA0060.1 0.00416
MA0061.1 9.76286e-5
MA0062.2 2.59171e-17
MA0065.2 0.416
MA0066.1 0.0175
MA0067.1 0.578
MA0068.1 0.87
MA0069.1 0.896
MA0070.1 0.414
MA0071.1 0.423
MA0072.1 8.69775e-7
MA0073.1 0.783
MA0074.1 0.931
MA0076.1 3.92694e-9
MA0077.1 0.179
MA0078.1 0.549
MA0079.2 0.0372
MA0080.2 3.18617e-13
MA0081.1 0.024
MA0083.1 0.152
MA0084.1 0.536
MA0087.1 0.411
MA0088.1 0.177
MA0090.1 0.0677
MA0091.1 0.0482
MA0092.1 0.896
MA0093.1 0.382
MA0099.2 0.181
MA0100.1 0.00868
MA0101.1 2.49555e-4
MA0102.2 0.557
MA0103.1 1.5078e-4
MA0104.2 0.13
MA0105.1 1.10858e-7
MA0106.1 0.697
MA0107.1 3.34361e-4
MA0108.2 0.0286
MA0111.1 0.309
MA0112.2 0.0155
MA0113.1 0.734
MA0114.1 0.32
MA0115.1 0.419
MA0116.1 0.00253
MA0117.1 0.731
MA0119.1 0.897
MA0122.1 1
MA0124.1 0.264
MA0125.1 0.583
MA0131.1 0.061
MA0135.1 0.268
MA0136.1 1.43845e-22
MA0137.2 0.0293
MA0138.2 5.3102e-5
MA0139.1 0.175
MA0140.1 0.566
MA0141.1 0.321
MA0142.1 0.873
MA0143.1 0.235
MA0144.1 0.337
MA0145.1 0.391
MA0146.1 0.531
MA0147.1 0.0607
MA0148.1 0.573
MA0149.1 0.0459
MA0150.1 0.327
MA0152.1 0.908
MA0153.1 1.32055e-8
MA0154.1 0.0923
MA0155.1 0.801
MA0156.1 1.04672e-27
MA0157.1 0.365
MA0159.1 0.0891
MA0160.1 0.266
MA0162.1 0.39
MA0163.1 9.71296e-4
MA0164.1 0.886
MA0258.1 0.0794
MA0259.1 0.548



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: CNhs11197
Novel motif P-value
1 0.176
10 0.0128
100 0.681
101 0.881
102 0.521
103 0.205
104 0.843
105 0.862
106 0.82
107 0.758
108 0.266
109 0.22
11 0.128
110 0.0425
111 0.786
112 0.275
113 0.463
114 0.858
115 0.485
116 0.761
117 6.22329e-4
118 0.344
119 0.291
12 0.647
120 0.218
121 0.301
122 0.573
123 0.611
124 0.825
125 0.105
126 0.63
127 0.734
128 0.74
129 0.222
13 0.00812
130 0.212
131 0.585
132 0.538
133 0.803
134 0.54
135 0.272
136 0.479
137 0.307
138 0.582
139 0.58
14 0.708
140 0.812
141 0.972
142 0.575
143 0.251
144 0.142
145 0.16
146 0.732
147 0.26
148 0.402
149 0.659
15 0.167
150 0.39
151 0.265
152 0.087
153 0.174
154 0.107
155 0.102
156 0.0329
157 0.724
158 0.0941
159 0.0217
160 0.811
161 0.605
162 0.551
163 0.862
164 0.145
165 0.199
166 0.429
167 0.132
168 0.301
169 0.253
17 0.616
18 0.909
19 0.654
2 0.0852
20 0.298
21 0.388
22 0.836
23 0.73
24 0.098
25 0.22
26 0.0401
27 0.479
28 0.226
29 0.0531
3 0.147
30 0.12
31 0.495
32 0.0961
33 0.304
34 0.991
35 0.101
36 0.174
37 0.164
38 0.239
39 0.926
4 0.871
40 0.588
41 0.96
42 0.0207
43 0.538
44 0.881
45 0.7
46 0.0982
47 0.309
48 0.157
49 0.215
5 0.318
50 0.85
51 0.935
52 0.146
53 0.962
54 0.236
55 0.381
56 0.926
57 0.26
58 0.259
59 0.743
6 0.216
60 0.839
61 0.0592
62 0.117
63 0.678
64 0.77
65 0.586
66 0.567
67 0.921
68 0.271
69 0.438
7 0.104
70 0.523
71 0.0258
72 0.517
73 0.495
74 0.851
75 0.0353
76 0.0847
77 0.266
78 0.0969
79 0.687
8 0.521
80 0.102
81 0.998
82 0.793
83 0.795
84 0.138
85 0.496
86 0.226
87 0.139
88 0.322
89 0.421
9 0.247
90 0.0515
91 0.676
92 0.669
93 0.93
94 0.311
95 0.247
96 0.0368
97 0.529
98 0.677
99 0.482



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: CNhs11197


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)
0000312 (mouse neonate N6 sample)
0011401 (mouse thymus- neonate N06 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)