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FF:38-12B5

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Name:thymus, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10471
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 stageadult
sexmale
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  SAMD00005500
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10471 CAGE DRX009112 DRR009986
Accession ID Mm9

Library idBAMCTSS
CNhs10471 DRZ001411 DRZ002794
Accession ID Mm10

Library idBAMCTSS
CNhs10471 DRZ012761 DRZ014144
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

CNhs10471

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.012
1001 --0.0356
1002 0.00855
1003 --0.0966
1004 0
1005 0
1006 --0.143
1007 0.0224
1008 0
1009 --0.0807
101 0.0634
1010 0
1011 0.0117
1012 0.29
1013 --0.0487
1014 --0.0874
1015 --0.066
1016 --0.379
1017 0
1018 0.119
1019 0
102 0
1020 0
1021 0
1022 --0.102
1023 0
1024 --0.0899
1025 0
1026 0
1027 --0.048
1028 0
1029 0.107
103 --0.0829
1030 0
1031 --0.627
1032 --0.389
1033 0.044
1034 0
1035 0
1036 0.0968
1037 0
1038 --0.418
1039 --0.21
104 0
1040 --0.121
1041 0.119



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: CNhs10471

Jaspar motif P-value
MA0002.2 1.42537e-7
MA0003.1 0.982
MA0004.1 0.425
MA0006.1 0.478
MA0007.1 0.412
MA0009.1 0.337
MA0014.1 0.233
MA0017.1 0.797
MA0018.2 0.142
MA0019.1 0.629
MA0024.1 0.0422
MA0025.1 0.162
MA0027.1 0.396
MA0028.1 0.00114
MA0029.1 0.109
MA0030.1 0.998
MA0031.1 0.0366
MA0035.2 0.537
MA0038.1 0.617
MA0039.2 0.566
MA0040.1 0.396
MA0041.1 0.824
MA0042.1 0.491
MA0043.1 0.115
MA0046.1 1.58767e-15
MA0047.2 0.356
MA0048.1 0.135
MA0050.1 5.55893e-10
MA0051.1 3.62711e-8
MA0052.1 0.00247
MA0055.1 0.0428
MA0057.1 0.642
MA0058.1 0.652
MA0059.1 0.185
MA0060.1 0.723
MA0061.1 3.57043e-6
MA0062.2 8.66102e-16
MA0065.2 0.516
MA0066.1 0.00851
MA0067.1 0.418
MA0068.1 0.729
MA0069.1 0.594
MA0070.1 0.605
MA0071.1 0.535
MA0072.1 9.1781e-6
MA0073.1 0.847
MA0074.1 0.989
MA0076.1 9.33152e-5
MA0077.1 0.148
MA0078.1 0.944
MA0079.2 0.0546
MA0080.2 1.18603e-14
MA0081.1 0.0114
MA0083.1 0.369
MA0084.1 0.434
MA0087.1 0.163
MA0088.1 0.344
MA0090.1 0.0792
MA0091.1 0.0547
MA0092.1 0.986
MA0093.1 0.461
MA0099.2 0.235
MA0100.1 0.0334
MA0101.1 4.1492e-4
MA0102.2 0.633
MA0103.1 5.53107e-5
MA0104.2 0.382
MA0105.1 3.0784e-9
MA0106.1 0.971
MA0107.1 9.46151e-5
MA0108.2 0.0238
MA0111.1 0.17
MA0112.2 0.00705
MA0113.1 0.698
MA0114.1 0.349
MA0115.1 0.488
MA0116.1 0.00293
MA0117.1 0.996
MA0119.1 0.893
MA0122.1 0.699
MA0124.1 0.351
MA0125.1 0.368
MA0131.1 0.519
MA0135.1 0.809
MA0136.1 6.54962e-24
MA0137.2 0.108
MA0138.2 0.00112
MA0139.1 0.125
MA0140.1 0.491
MA0141.1 0.278
MA0142.1 0.0613
MA0143.1 0.42
MA0144.1 0.365
MA0145.1 0.859
MA0146.1 0.176
MA0147.1 0.262
MA0148.1 0.356
MA0149.1 0.0799
MA0150.1 0.889
MA0152.1 0.697
MA0153.1 7.65464e-10
MA0154.1 0.037
MA0155.1 0.911
MA0156.1 3.80457e-25
MA0157.1 0.129
MA0159.1 0.0845
MA0160.1 0.43
MA0162.1 0.33
MA0163.1 0.00309
MA0164.1 0.859
MA0258.1 0.0481
MA0259.1 0.801



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: CNhs10471

Novel motif P-value
1 0.27
10 0.0332
100 0.976
101 0.528
102 0.554
103 0.185
104 0.692
105 0.988
106 0.538
107 0.994
108 0.454
109 0.24
11 0.102
110 0.102
111 0.654
112 0.13
113 0.0839
114 0.466
115 0.608
116 0.813
117 0.00122
118 0.184
119 0.0891
12 0.468
120 0.0898
121 0.106
122 0.852
123 0.423
124 0.371
125 0.134
126 0.951
127 0.788
128 0.277
129 0.202
13 0.0553
130 0.457
131 0.93
132 0.723
133 0.935
134 0.553
135 0.343
136 0.803
137 0.332
138 0.504
139 0.374
14 0.882
140 0.444
141 0.633
142 0.956
143 0.0714
144 0.162
145 0.143
146 0.531
147 0.596
148 0.317
149 0.632
15 0.0659
150 0.467
151 0.031
152 0.21
153 0.188
154 0.335
155 0.0926
156 0.209
157 0.879
158 0.124
159 0.0191
160 0.63
161 0.263
162 0.27
163 0.661
164 0.176
165 0.0632
166 0.325
167 0.289
168 0.357
169 0.0483
17 0.485
18 0.75
19 0.817
2 0.404
20 0.947
21 0.593
22 0.725
23 0.551
24 0.0913
25 0.142
26 0.0717
27 0.136
28 0.129
29 0.213
3 0.181
30 0.335
31 0.924
32 0.155
33 0.506
34 0.83
35 0.0883
36 0.252
37 0.146
38 0.232
39 0.716
4 0.981
40 0.453
41 0.817
42 0.0385
43 0.336
44 0.693
45 0.666
46 0.116
47 0.218
48 0.156
49 0.221
5 0.178
50 0.849
51 0.895
52 0.48
53 0.823
54 0.491
55 0.14
56 0.546
57 0.501
58 0.19
59 0.769
6 0.171
60 0.669
61 0.131
62 0.0458
63 0.436
64 0.629
65 0.27
66 0.608
67 0.959
68 0.644
69 0.767
7 0.0733
70 0.133
71 0.055
72 0.435
73 0.336
74 0.966
75 0.029
76 0.291
77 0.515
78 0.0993
79 0.813
8 0.383
80 0.032
81 0.844
82 0.299
83 0.65
84 0.594
85 0.732
86 0.106
87 0.892
88 0.331
89 0.718
9 0.221
90 0.171
91 0.916
92 0.871
93 0.387
94 0.305
95 0.693
96 0.0645
97 0.656
98 0.372
99 0.545



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: CNhs10471


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)
0007023 (adult 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)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011329 (mouse thymus- adult 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)