Personal tools

FF:389-23F5

From FANTOM5_SSTAR

Jump to: navigation, search


Name:testis, embryo E13
Species:Mouse (Mus musculus)
Library ID:CNhs11031
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
tissuetestis
dev stage13 days embryo
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  SAMD00005814
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11031 CAGE DRX009102 DRR009976
Accession ID Mm9

Library idBAMCTSS
CNhs11031 DRZ001401 DRZ002784
Accession ID Mm10

Library idBAMCTSS
CNhs11031 DRZ012751 DRZ014134
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11031

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 -0.0366
1002 0.276
1003 -0.122
1004 0
1005 -0.0389
1006 -0.104
1007 0.133
1008 0
1009 -0.0572
101 0.136
1010 0
1011 -0.0261
1012 0
1013 -0.188
1014 0.114
1015 0.231
1016 0.262
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 -0.0271
1023 0
1024 -0.0899
1025 0
1026 0
1027 0
1028 0
1029 -0.0543
103 0.0354
1030 0
1031 0.244
1032 -0.121
1033 0
1034 0
1035 0.0605
1036 -0.0157
1037 0
1038 0.0143
1039 -0.0649
104 0
1040 0.0401
1041 0



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: CNhs11031
Jaspar motif P-value
MA0002.2 0.0017
MA0003.1 0.953
MA0004.1 0.497
MA0006.1 0.39
MA0007.1 0.453
MA0009.1 0.876
MA0014.1 0.727
MA0017.1 0.00776
MA0018.2 0.725
MA0019.1 0.353
MA0024.1 7.40215e-7
MA0025.1 0.582
MA0027.1 0.239
MA0028.1 0.0067
MA0029.1 0.867
MA0030.1 0.183
MA0031.1 0.13
MA0035.2 0.69
MA0038.1 0.0557
MA0039.2 0.528
MA0040.1 0.339
MA0041.1 0.358
MA0042.1 0.516
MA0043.1 0.354
MA0046.1 5.99726e-25
MA0047.2 0.0562
MA0048.1 0.0237
MA0050.1 8.17823e-4
MA0051.1 0.00184
MA0052.1 2.60087e-4
MA0055.1 0.009
MA0057.1 0.185
MA0058.1 0.294
MA0059.1 0.464
MA0060.1 5.09244e-13
MA0061.1 0.104
MA0062.2 0.0173
MA0065.2 0.0101
MA0066.1 0.0481
MA0067.1 0.69
MA0068.1 0.0279
MA0069.1 0.607
MA0070.1 0.582
MA0071.1 0.846
MA0072.1 0.366
MA0073.1 0.87
MA0074.1 0.918
MA0076.1 0.00488
MA0077.1 0.303
MA0078.1 0.661
MA0079.2 0.253
MA0080.2 1.02789e-5
MA0081.1 0.99
MA0083.1 0.223
MA0084.1 0.898
MA0087.1 0.584
MA0088.1 0.999
MA0090.1 0.79
MA0091.1 0.718
MA0092.1 0.38
MA0093.1 0.434
MA0099.2 1.03301e-4
MA0100.1 0.335
MA0101.1 0.791
MA0102.2 0.426
MA0103.1 0.00125
MA0104.2 0.188
MA0105.1 2.14407e-4
MA0106.1 0.339
MA0107.1 0.341
MA0108.2 6.38784e-4
MA0111.1 0.202
MA0112.2 2.20059e-4
MA0113.1 0.982
MA0114.1 0.007
MA0115.1 0.343
MA0116.1 0.019
MA0117.1 0.164
MA0119.1 0.32
MA0122.1 0.92
MA0124.1 0.072
MA0125.1 0.341
MA0131.1 0.217
MA0135.1 0.832
MA0136.1 0.105
MA0137.2 0.467
MA0138.2 4.30425e-4
MA0139.1 0.356
MA0140.1 0.576
MA0141.1 0.229
MA0142.1 0.242
MA0143.1 0.0894
MA0144.1 0.322
MA0145.1 0.00674
MA0146.1 0.407
MA0147.1 0.23
MA0148.1 0.00632
MA0149.1 0.099
MA0150.1 0.00933
MA0152.1 0.578
MA0153.1 2.64433e-15
MA0154.1 0.0109
MA0155.1 0.629
MA0156.1 0.908
MA0157.1 0.147
MA0159.1 0.00204
MA0160.1 0.685
MA0162.1 0.132
MA0163.1 0.0792
MA0164.1 0.799
MA0258.1 0.00126
MA0259.1 0.24



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: CNhs11031
Novel motif P-value
1 0.107
10 0.331
100 0.705
101 0.404
102 0.637
103 0.181
104 0.841
105 0.159
106 0.00395
107 0.048
108 0.675
109 0.399
11 0.28
110 0.649
111 0.336
112 0.396
113 0.436
114 0.0973
115 0.579
116 0.426
117 0.943
118 0.68
119 0.217
12 0.642
120 0.529
121 0.403
122 0.655
123 0.168
124 0.253
125 0.0327
126 0.805
127 0.118
128 0.00317
129 0.0274
13 0.945
130 0.377
131 0.541
132 0.157
133 0.823
134 0.454
135 0.976
136 0.101
137 0.632
138 0.871
139 0.0446
14 0.145
140 0.371
141 0.0447
142 0.934
143 0.077
144 0.124
145 0.918
146 0.561
147 0.508
148 0.141
149 0.165
15 0.146
150 0.832
151 0.0613
152 0.343
153 0.526
154 0.871
155 0.599
156 2.03758e-4
157 0.608
158 0.394
159 0.027
160 0.902
161 0.759
162 0.623
163 0.0915
164 0.905
165 0.15
166 0.891
167 0.437
168 0.201
169 0.286
17 0.0964
18 0.171
19 0.756
2 0.515
20 0.378
21 0.806
22 0.674
23 0.0452
24 0.896
25 0.37
26 0.735
27 0.238
28 0.388
29 0.873
3 0.319
30 0.678
31 0.136
32 0.154
33 0.816
34 0.833
35 0.0972
36 0.206
37 0.223
38 0.629
39 0.866
4 0.681
40 0.494
41 0.152
42 0.625
43 0.209
44 0.275
45 0.462
46 0.17
47 0.357
48 0.367
49 0.128
5 0.114
50 0.987
51 0.754
52 0.219
53 0.65
54 0.389
55 0.689
56 0.241
57 0.649
58 0.251
59 0.154
6 0.827
60 0.0742
61 0.512
62 0.0922
63 0.164
64 0.708
65 0.167
66 0.582
67 0.679
68 2.93841e-4
69 0.808
7 0.442
70 0.00356
71 0.254
72 0.545
73 0.411
74 0.494
75 0.529
76 0.452
77 0.309
78 0.528
79 0.713
8 0.258
80 0.151
81 0.219
82 0.528
83 0.499
84 0.154
85 0.0106
86 0.315
87 0.523
88 0.427
89 0.0727
9 0.844
90 0.126
91 0.316
92 0.105
93 0.561
94 0.322
95 0.757
96 0.285
97 0.831
98 0.0811
99 0.818



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: CNhs11031


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)
0000922 (embryo)
0000473 (testis)
0000991 (gonad)
0000479 (tissue)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003135 (male reproductive organ)
0003133 (reproductive organ)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0003101 (male organism)
0000079 (male reproductive system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000293 (mouse embryonic day 13 sample)
0011332 (mouse testis- embryo E13 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:0009117 (indifferent gonad)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0005564 (gonad primordium)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)