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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00004839
 
|DRA_sample_Accession=CAGE@SAMD00004839
|accession_numbers=CAGE;DRX009124;DRR009998;DRZ001423;DRZ002806
+
|accession_numbers=CAGE;DRX009124;DRR009998;DRZ001423;DRZ002806;DRZ012773;DRZ014156
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002370,UBERON:0000479,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0004177,UBERON:0005057,UBERON:0002530,UBERON:0005058,UBERON:0010317,UBERON:0000153,UBERON:0002390,UBERON:0000949,UBERON:0002193,UBERON:0002405,UBERON:0009113
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002370,UBERON:0000479,UBERON:0004119,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000077,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002368,UBERON:0004177,UBERON:0005057,UBERON:0002530,UBERON:0005058,UBERON:0010317,UBERON:0000153,UBERON:0002390,UBERON:0000949,UBERON:0002193,UBERON:0002405,UBERON:0009113
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_cell_lineage_facet=

Latest revision as of 13:14, 10 August 2017


Name:thymus, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11125
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 stage25 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  SAMD00004839
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11125 CAGE DRX009124 DRR009998
Accession ID Mm9

Library idBAMCTSS
CNhs11125 DRZ001423 DRZ002806
Accession ID Mm10

Library idBAMCTSS
CNhs11125 DRZ012773 DRZ014156
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

CNhs11125

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0172
1001 0.0829
1002 --0.0696
1003 --0.145
1004 0
1005 0
1006 --0.143
1007 0.13
1008 0.0399
1009 --0.19
101 0.095
1010 0
1011 0
1012 0.544
1013 --0.14
1014 --0.0874
1015 0.0637
1016 --0.396
1017 0
1018 0.0657
1019 0
102 0.0764
1020 0.00393
1021 0.0399
1022 --0.261
1023 0
1024 --0.0134
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 0.359
103 --0.0787
1030 0.0399
1031 --0.84
1032 --0.447
1033 0.0349
1034 0
1035 0
1036 0.131
1037 0
1038 --0.337
1039 --0.238
104 0
1040 --0.106
1041 0.0399



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: CNhs11125

Jaspar motif P-value
MA0002.2 5.01606e-4
MA0003.1 0.304
MA0004.1 0.257
MA0006.1 0.93
MA0007.1 0.515
MA0009.1 0.561
MA0014.1 0.316
MA0017.1 0.919
MA0018.2 0.127
MA0019.1 0.47
MA0024.1 0.00256
MA0025.1 0.0115
MA0027.1 0.596
MA0028.1 1.52038e-5
MA0029.1 0.16
MA0030.1 0.888
MA0031.1 0.169
MA0035.2 0.478
MA0038.1 0.452
MA0039.2 0.276
MA0040.1 0.674
MA0041.1 0.248
MA0042.1 0.948
MA0043.1 0.162
MA0046.1 1.33716e-13
MA0047.2 0.586
MA0048.1 0.758
MA0050.1 3.84274e-7
MA0051.1 6.36405e-6
MA0052.1 2.29389e-4
MA0055.1 0.706
MA0057.1 0.751
MA0058.1 0.371
MA0059.1 0.015
MA0060.1 0.266
MA0061.1 5.78325e-5
MA0062.2 9.37552e-17
MA0065.2 0.648
MA0066.1 0.0133
MA0067.1 0.364
MA0068.1 0.535
MA0069.1 0.894
MA0070.1 0.522
MA0071.1 0.353
MA0072.1 5.26876e-6
MA0073.1 0.786
MA0074.1 0.924
MA0076.1 2.98315e-7
MA0077.1 0.113
MA0078.1 0.848
MA0079.2 0.0341
MA0080.2 1.38556e-13
MA0081.1 0.0213
MA0083.1 0.0339
MA0084.1 0.392
MA0087.1 0.392
MA0088.1 0.339
MA0090.1 0.0431
MA0091.1 0.0715
MA0092.1 0.946
MA0093.1 0.293
MA0099.2 0.141
MA0100.1 0.012
MA0101.1 3.52519e-4
MA0102.2 0.623
MA0103.1 2.26714e-4
MA0104.2 0.137
MA0105.1 6.20003e-8
MA0106.1 0.736
MA0107.1 4.09203e-4
MA0108.2 6.68755e-4
MA0111.1 0.227
MA0112.2 0.0188
MA0113.1 0.476
MA0114.1 0.424
MA0115.1 0.732
MA0116.1 0.00323
MA0117.1 0.759
MA0119.1 0.856
MA0122.1 0.989
MA0124.1 0.374
MA0125.1 0.36
MA0131.1 0.229
MA0135.1 0.138
MA0136.1 2.03243e-22
MA0137.2 0.061
MA0138.2 4.50413e-5
MA0139.1 0.28
MA0140.1 0.772
MA0141.1 0.565
MA0142.1 0.362
MA0143.1 0.326
MA0144.1 0.375
MA0145.1 0.453
MA0146.1 0.447
MA0147.1 0.0618
MA0148.1 0.538
MA0149.1 0.0375
MA0150.1 0.523
MA0152.1 0.977
MA0153.1 1.93508e-8
MA0154.1 0.114
MA0155.1 0.912
MA0156.1 9.4547e-26
MA0157.1 0.326
MA0159.1 0.135
MA0160.1 0.434
MA0162.1 0.662
MA0163.1 0.00503
MA0164.1 0.773
MA0258.1 0.0378
MA0259.1 0.62



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: CNhs11125

Novel motif P-value
1 0.158
10 0.0175
100 0.769
101 0.834
102 0.487
103 0.213
104 0.828
105 0.857
106 0.768
107 0.813
108 0.246
109 0.34
11 0.114
110 0.0801
111 0.664
112 0.144
113 0.361
114 0.46
115 0.581
116 0.952
117 3.71898e-4
118 0.187
119 0.204
12 0.646
120 0.135
121 0.367
122 0.937
123 0.524
124 0.837
125 0.0772
126 0.475
127 0.754
128 0.469
129 0.15
13 0.0277
130 0.387
131 0.413
132 0.769
133 0.898
134 0.613
135 0.457
136 0.313
137 0.405
138 0.684
139 0.194
14 0.883
140 0.91
141 0.779
142 0.338
143 0.223
144 0.195
145 0.0963
146 0.815
147 0.434
148 0.23
149 0.901
15 0.0945
150 0.365
151 0.193
152 0.0849
153 0.21
154 0.088
155 0.106
156 0.158
157 0.691
158 0.0769
159 0.0477
160 0.875
161 0.277
162 0.653
163 0.934
164 0.117
165 0.24
166 0.427
167 0.125
168 0.327
169 0.4
17 0.53
18 0.724
19 0.657
2 0.067
20 0.204
21 0.553
22 0.903
23 0.979
24 0.225
25 0.232
26 0.0373
27 0.522
28 0.176
29 0.0717
3 0.12
30 0.138
31 0.604
32 0.141
33 0.534
34 0.87
35 0.0438
36 0.161
37 0.17
38 0.244
39 0.804
4 0.901
40 0.608
41 0.948
42 0.0365
43 0.404
44 0.751
45 0.74
46 0.101
47 0.337
48 0.184
49 0.121
5 0.197
50 0.757
51 0.941
52 0.166
53 0.917
54 0.347
55 0.418
56 0.739
57 0.221
58 0.247
59 0.698
6 0.301
60 0.95
61 0.0438
62 0.11
63 0.566
64 0.69
65 0.462
66 0.443
67 0.873
68 0.588
69 0.69
7 0.163
70 0.232
71 0.0347
72 0.5
73 0.442
74 0.995
75 0.0173
76 0.0346
77 0.294
78 0.0971
79 0.621
8 0.372
80 0.14
81 0.922
82 0.816
83 0.753
84 0.132
85 0.829
86 0.22
87 0.124
88 0.311
89 0.517
9 0.311
90 0.0317
91 0.914
92 0.898
93 0.698
94 0.199
95 0.38
96 0.0125
97 0.513
98 0.632
99 0.357



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: CNhs11125


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)
0000309 (mouse neonate N25 sample)
0011496 (mouse thymus- neonate N25 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)