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FF:1393-42G2

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Name:thymus, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11132
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 stage30 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  SAMD00006007
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11132 CAGE DRX009125 DRR009999
Accession ID Mm9

Library idBAMCTSS
CNhs11132 DRZ001424 DRZ002807
Accession ID Mm10

Library idBAMCTSS
CNhs11132 DRZ012774 DRZ014157
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

CNhs11132

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 -0.0115
1001 0.0738
1002 -0.0837
1003 -0.116
1004 0
1005 0.048
1006 -0.143
1007 0.159
1008 0
1009 -0.19
101 0.03
1010 0
1011 0.023
1012 0.567
1013 0.0207
1014 -0.0874
1015 -0.0323
1016 -0.379
1017 0
1018 0.167
1019 0
102 0.131
1020 0
1021 0
1022 -0.224
1023 0
1024 -0.103
1025 -0.0611
1026 0
1027 0
1028 0
1029 0.39
103 -0.0788
1030 0.048
1031 -0.757
1032 -0.429
1033 0.104
1034 0
1035 0
1036 0.0803
1037 0
1038 -0.301
1039 -0.0378
104 0
1040 -0.121
1041 0.048



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: CNhs11132
Jaspar motif P-value
MA0002.2 1.82127e-4
MA0003.1 0.439
MA0004.1 0.309
MA0006.1 0.697
MA0007.1 0.353
MA0009.1 0.45
MA0014.1 0.395
MA0017.1 0.817
MA0018.2 0.0994
MA0019.1 0.492
MA0024.1 0.0569
MA0025.1 0.0144
MA0027.1 0.662
MA0028.1 3.64475e-6
MA0029.1 0.205
MA0030.1 0.768
MA0031.1 0.0349
MA0035.2 0.44
MA0038.1 0.274
MA0039.2 0.454
MA0040.1 0.513
MA0041.1 0.325
MA0042.1 0.905
MA0043.1 0.147
MA0046.1 4.57227e-14
MA0047.2 0.361
MA0048.1 0.814
MA0050.1 1.09854e-7
MA0051.1 2.09528e-6
MA0052.1 2.02474e-4
MA0055.1 0.282
MA0057.1 0.747
MA0058.1 0.395
MA0059.1 0.039
MA0060.1 0.598
MA0061.1 1.07682e-4
MA0062.2 2.91989e-19
MA0065.2 0.695
MA0066.1 0.0125
MA0067.1 0.308
MA0068.1 0.523
MA0069.1 0.954
MA0070.1 0.6
MA0071.1 0.397
MA0072.1 3.88486e-6
MA0073.1 0.752
MA0074.1 0.914
MA0076.1 2.45594e-8
MA0077.1 0.0701
MA0078.1 0.628
MA0079.2 0.0546
MA0080.2 7.0926e-14
MA0081.1 0.0241
MA0083.1 0.0555
MA0084.1 0.545
MA0087.1 0.344
MA0088.1 0.429
MA0090.1 0.0397
MA0091.1 0.0722
MA0092.1 0.957
MA0093.1 0.308
MA0099.2 0.12
MA0100.1 0.0308
MA0101.1 6.5061e-4
MA0102.2 0.494
MA0103.1 3.52092e-5
MA0104.2 0.315
MA0105.1 3.37347e-8
MA0106.1 0.901
MA0107.1 6.2943e-4
MA0108.2 5.44483e-4
MA0111.1 0.259
MA0112.2 0.0128
MA0113.1 0.517
MA0114.1 0.321
MA0115.1 0.691
MA0116.1 0.004
MA0117.1 0.858
MA0119.1 0.966
MA0122.1 0.952
MA0124.1 0.395
MA0125.1 0.401
MA0131.1 0.307
MA0135.1 0.201
MA0136.1 6.94065e-24
MA0137.2 0.1
MA0138.2 2.53715e-4
MA0139.1 0.179
MA0140.1 0.756
MA0141.1 0.384
MA0142.1 0.41
MA0143.1 0.288
MA0144.1 0.422
MA0145.1 0.679
MA0146.1 0.323
MA0147.1 0.192
MA0148.1 0.429
MA0149.1 0.0299
MA0150.1 0.411
MA0152.1 0.939
MA0153.1 1.3443e-8
MA0154.1 0.115
MA0155.1 0.934
MA0156.1 4.22736e-27
MA0157.1 0.135
MA0159.1 0.122
MA0160.1 0.297
MA0162.1 0.701
MA0163.1 0.00413
MA0164.1 0.9
MA0258.1 0.045
MA0259.1 0.889



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: CNhs11132
Novel motif P-value
1 0.157
10 0.024
100 0.77
101 0.699
102 0.508
103 0.222
104 0.942
105 0.829
106 0.717
107 0.892
108 0.211
109 0.319
11 0.124
110 0.0836
111 0.744
112 0.15
113 0.33
114 0.386
115 0.448
116 0.984
117 4.70776e-4
118 0.154
119 0.234
12 0.672
120 0.218
121 0.433
122 0.978
123 0.412
124 0.683
125 0.152
126 0.556
127 0.84
128 0.533
129 0.184
13 0.0359
130 0.312
131 0.603
132 0.847
133 0.989
134 0.696
135 0.393
136 0.341
137 0.48
138 0.773
139 0.248
14 0.949
140 0.992
141 0.62
142 0.487
143 0.225
144 0.153
145 0.147
146 0.709
147 0.402
148 0.227
149 0.883
15 0.0829
150 0.471
151 0.0864
152 0.204
153 0.153
154 0.0962
155 0.0745
156 0.136
157 0.732
158 0.0841
159 0.0554
160 0.877
161 0.403
162 0.697
163 0.879
164 0.175
165 0.298
166 0.341
167 0.156
168 0.242
169 0.198
17 0.605
18 0.756
19 0.709
2 0.094
20 0.311
21 0.596
22 0.996
23 0.842
24 0.164
25 0.22
26 0.0564
27 0.314
28 0.113
29 0.117
3 0.103
30 0.161
31 0.6
32 0.131
33 0.479
34 0.883
35 0.0679
36 0.158
37 0.116
38 0.195
39 0.73
4 0.773
40 0.672
41 0.88
42 0.0272
43 0.405
44 0.887
45 0.85
46 0.129
47 0.394
48 0.216
49 0.131
5 0.224
50 0.714
51 0.832
52 0.152
53 0.995
54 0.41
55 0.444
56 0.652
57 0.302
58 0.182
59 0.721
6 0.2
60 0.985
61 0.0625
62 0.0797
63 0.672
64 0.832
65 0.405
66 0.436
67 0.787
68 0.622
69 0.38
7 0.136
70 0.198
71 0.0782
72 0.539
73 0.259
74 0.784
75 0.0111
76 0.0548
77 0.224
78 0.175
79 0.876
8 0.64
80 0.0769
81 0.87
82 0.605
83 0.761
84 0.137
85 0.929
86 0.129
87 0.143
88 0.415
89 0.371
9 0.268
90 0.0345
91 0.831
92 0.968
93 0.8
94 0.324
95 0.436
96 0.0166
97 0.546
98 0.602
99 0.435



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: CNhs11132


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)
0000310 (mouse neonate N30 sample)
0011497 (mouse thymus- neonate N30 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)