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FF:748-24E4

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Name:thymus, neonate N10
Species:Mouse (Mus musculus)
Library ID:CNhs11194
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 stage10 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  SAMD00005475
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11194 CAGE DRX009122 DRR009996
Accession ID Mm9

Library idBAMCTSS
CNhs11194 DRZ001421 DRZ002804
Accession ID Mm10

Library idBAMCTSS
CNhs11194 DRZ012771 DRZ014154
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

CNhs11194

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.129
1002 --0.0259
1003 --0.112
1004 0
1005 0
1006 --0.172
1007 0.0849
1008 0.0417
1009 --0.12
101 0.112
1010 0
1011 0.0798
1012 0.547
1013 --0.163
1014 --0.0874
1015 0.0751
1016 --0.459
1017 0
1018 0
1019 0
102 0.0417
1020 0
1021 0.177
1022 --0.22
1023 0
1024 --0.0529
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 0.527
103 --0.0678
1030 0.0417
1031 --0.684
1032 --0.521
1033 0.0419
1034 0
1035 0
1036 0.142
1037 0
1038 --0.36
1039 --0.166
104 0
1040 --0.121
1041 0



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: CNhs11194

Jaspar motif P-value
MA0002.2 0.0108
MA0003.1 0.255
MA0004.1 0.338
MA0006.1 0.989
MA0007.1 0.515
MA0009.1 0.458
MA0014.1 0.297
MA0017.1 0.903
MA0018.2 0.0318
MA0019.1 0.367
MA0024.1 3.83111e-4
MA0025.1 0.00824
MA0027.1 0.724
MA0028.1 1.77824e-5
MA0029.1 0.152
MA0030.1 0.648
MA0031.1 0.276
MA0035.2 0.424
MA0038.1 0.414
MA0039.2 0.17
MA0040.1 0.915
MA0041.1 0.246
MA0042.1 0.94
MA0043.1 0.0731
MA0046.1 1.08319e-14
MA0047.2 0.455
MA0048.1 0.556
MA0050.1 1.49803e-5
MA0051.1 4.46721e-5
MA0052.1 3.58696e-4
MA0055.1 0.945
MA0057.1 0.749
MA0058.1 0.514
MA0059.1 0.0153
MA0060.1 0.386
MA0061.1 3.50978e-4
MA0062.2 2.89415e-14
MA0065.2 0.367
MA0066.1 0.0091
MA0067.1 0.599
MA0068.1 0.965
MA0069.1 0.769
MA0070.1 0.436
MA0071.1 0.254
MA0072.1 7.94811e-6
MA0073.1 0.776
MA0074.1 0.974
MA0076.1 1.35018e-6
MA0077.1 0.187
MA0078.1 0.889
MA0079.2 0.0252
MA0080.2 1.08083e-12
MA0081.1 0.0458
MA0083.1 0.0269
MA0084.1 0.479
MA0087.1 0.403
MA0088.1 0.324
MA0090.1 0.0646
MA0091.1 0.0407
MA0092.1 0.842
MA0093.1 0.385
MA0099.2 0.136
MA0100.1 0.0174
MA0101.1 8.15918e-4
MA0102.2 0.462
MA0103.1 2.92081e-4
MA0104.2 0.126
MA0105.1 3.00991e-7
MA0106.1 0.653
MA0107.1 0.00144
MA0108.2 6.81634e-4
MA0111.1 0.248
MA0112.2 0.0106
MA0113.1 0.682
MA0114.1 0.627
MA0115.1 0.84
MA0116.1 0.00157
MA0117.1 0.778
MA0119.1 0.964
MA0122.1 0.906
MA0124.1 0.363
MA0125.1 0.442
MA0131.1 0.155
MA0135.1 0.128
MA0136.1 9.91674e-20
MA0137.2 0.0971
MA0138.2 2.5952e-5
MA0139.1 0.197
MA0140.1 0.768
MA0141.1 0.807
MA0142.1 0.655
MA0143.1 0.392
MA0144.1 0.515
MA0145.1 0.342
MA0146.1 0.526
MA0147.1 0.0579
MA0148.1 0.52
MA0149.1 0.0218
MA0150.1 0.504
MA0152.1 0.795
MA0153.1 2.05904e-8
MA0154.1 0.112
MA0155.1 0.975
MA0156.1 1.79994e-21
MA0157.1 0.43
MA0159.1 0.108
MA0160.1 0.495
MA0162.1 0.551
MA0163.1 0.0015
MA0164.1 0.788
MA0258.1 0.0428
MA0259.1 0.615



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: CNhs11194

Novel motif P-value
1 0.141
10 0.0104
100 0.591
101 0.808
102 0.573
103 0.123
104 0.869
105 0.72
106 0.703
107 0.978
108 0.251
109 0.27
11 0.115
110 0.052
111 0.656
112 0.157
113 0.46
114 0.495
115 0.452
116 0.861
117 5.36424e-4
118 0.2
119 0.189
12 0.622
120 0.368
121 0.483
122 0.674
123 0.617
124 0.842
125 0.0675
126 0.533
127 0.688
128 0.527
129 0.12
13 0.0146
130 0.334
131 0.431
132 0.811
133 0.874
134 0.553
135 0.352
136 0.271
137 0.49
138 0.618
139 0.28
14 0.796
140 0.99
141 0.86
142 0.467
143 0.33
144 0.201
145 0.093
146 0.867
147 0.413
148 0.202
149 0.628
15 0.114
150 0.341
151 0.256
152 0.0568
153 0.182
154 0.0626
155 0.0955
156 0.00347
157 0.747
158 0.0529
159 0.0178
160 0.966
161 0.277
162 0.599
163 0.951
164 0.121
165 0.451
166 0.375
167 0.123
168 0.289
169 0.462
17 0.527
18 0.699
19 0.747
2 0.0737
20 0.207
21 0.558
22 0.884
23 0.931
24 0.251
25 0.228
26 0.0287
27 0.629
28 0.201
29 0.03
3 0.116
30 0.102
31 0.606
32 0.211
33 0.389
34 0.963
35 0.0461
36 0.113
37 0.215
38 0.232
39 0.984
4 0.779
40 0.535
41 0.975
42 0.0336
43 0.352
44 0.839
45 0.666
46 0.107
47 0.336
48 0.2
49 0.107
5 0.307
50 0.801
51 0.904
52 0.191
53 0.81
54 0.304
55 0.465
56 0.818
57 0.16
58 0.235
59 0.628
6 0.223
60 0.914
61 0.067
62 0.102
63 0.567
64 0.69
65 0.478
66 0.544
67 0.765
68 0.467
69 0.518
7 0.141
70 0.293
71 0.0276
72 0.592
73 0.533
74 0.777
75 0.0205
76 0.0332
77 0.261
78 0.136
79 0.716
8 0.268
80 0.132
81 0.998
82 0.742
83 0.911
84 0.129
85 0.854
86 0.283
87 0.0359
88 0.304
89 0.514
9 0.361
90 0.0308
91 0.881
92 0.978
93 0.832
94 0.268
95 0.383
96 0.0104
97 0.516
98 0.471
99 0.477



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: CNhs11194


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)
0000305 (mouse neonate N10 sample)
0011413 (mouse thymus- neonate N10 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)