Personal tools

FF:486-18I5

From FANTOM5_SSTAR

Jump to: navigation, search


Name:testis, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs11029
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 stage17 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  SAMD00005862
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11029 CAGE DRX009105 DRR009979
Accession ID Mm9

Library idBAMCTSS
CNhs11029 DRZ001404 DRZ002787
Accession ID Mm10

Library idBAMCTSS
CNhs11029 DRZ012754 DRZ014137
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

CNhs11029

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0631
1002 0.466
1003 0.0355
1004 0.0528
1005 --0.0571
1006 --0.00934
1007 0.00174
1008 0
1009 0.118
101 0.0493
1010 0
1011 0.0372
1012 0
1013 --0.157
1014 0.24
1015 0.203
1016 0.234
1017 0
1018 0
1019 0
102 0
1020 0.0528
1021 0
1022 --0.0712
1023 0
1024 --0.0371
1025 0.0528
1026 0.0528
1027 0
1028 0.0528
1029 0.0433
103 0.276
1030 0
1031 0.386
1032 0.0656
1033 0
1034 0
1035 0.0528
1036 --0.0276
1037 0
1038 --0.0113
1039 --0.067
104 0
1040 --0.0343
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: CNhs11029

Jaspar motif P-value
MA0002.2 0.0118
MA0003.1 0.619
MA0004.1 0.198
MA0006.1 0.116
MA0007.1 0.621
MA0009.1 0.393
MA0014.1 0.776
MA0017.1 0.00228
MA0018.2 0.802
MA0019.1 0.317
MA0024.1 3.34561e-6
MA0025.1 0.88
MA0027.1 0.505
MA0028.1 0.128
MA0029.1 0.847
MA0030.1 0.0155
MA0031.1 0.133
MA0035.2 0.948
MA0038.1 0.00273
MA0039.2 0.0346
MA0040.1 0.365
MA0041.1 0.355
MA0042.1 0.382
MA0043.1 0.473
MA0046.1 3.83305e-18
MA0047.2 0.032
MA0048.1 0.0388
MA0050.1 0.00889
MA0051.1 0.0144
MA0052.1 0.0143
MA0055.1 0.00255
MA0057.1 0.388
MA0058.1 0.0409
MA0059.1 0.118
MA0060.1 3.33786e-16
MA0061.1 0.158
MA0062.2 0.558
MA0065.2 0.0468
MA0066.1 0.0586
MA0067.1 0.996
MA0068.1 0.0288
MA0069.1 0.887
MA0070.1 0.175
MA0071.1 0.977
MA0072.1 0.25
MA0073.1 0.938
MA0074.1 0.809
MA0076.1 0.0616
MA0077.1 0.769
MA0078.1 0.0819
MA0079.2 0.189
MA0080.2 1.1574e-5
MA0081.1 0.366
MA0083.1 0.786
MA0084.1 0.919
MA0087.1 0.396
MA0088.1 0.837
MA0090.1 0.891
MA0091.1 0.462
MA0092.1 0.342
MA0093.1 0.112
MA0099.2 8.06631e-4
MA0100.1 0.558
MA0101.1 0.484
MA0102.2 0.792
MA0103.1 5.2849e-4
MA0104.2 0.00634
MA0105.1 0.00859
MA0106.1 0.904
MA0107.1 0.228
MA0108.2 0.3
MA0111.1 0.235
MA0112.2 0.00772
MA0113.1 0.439
MA0114.1 0.00277
MA0115.1 0.0612
MA0116.1 0.315
MA0117.1 0.161
MA0119.1 0.689
MA0122.1 0.867
MA0124.1 0.253
MA0125.1 0.799
MA0131.1 0.511
MA0135.1 0.887
MA0136.1 0.00443
MA0137.2 0.475
MA0138.2 0.00203
MA0139.1 0.82
MA0140.1 0.879
MA0141.1 0.0969
MA0142.1 0.0136
MA0143.1 0.746
MA0144.1 0.263
MA0145.1 0.0254
MA0146.1 0.492
MA0147.1 0.0165
MA0148.1 0.0023
MA0149.1 0.185
MA0150.1 0.00104
MA0152.1 0.187
MA0153.1 1.2141e-12
MA0154.1 0.0497
MA0155.1 0.94
MA0156.1 0.204
MA0157.1 0.106
MA0159.1 1.15939e-4
MA0160.1 0.689
MA0162.1 0.153
MA0163.1 0.819
MA0164.1 0.577
MA0258.1 0.00192
MA0259.1 0.0338



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: CNhs11029

Novel motif P-value
1 0.199
10 0.43
100 0.51
101 0.545
102 0.789
103 0.586
104 0.899
105 0.499
106 4.20138e-4
107 0.00813
108 0.645
109 0.978
11 0.393
110 0.883
111 0.394
112 0.587
113 0.258
114 0.0501
115 0.722
116 0.725
117 0.934
118 0.914
119 0.138
12 0.452
120 0.521
121 0.801
122 0.831
123 0.277
124 0.131
125 0.041
126 0.992
127 0.109
128 1.89609e-4
129 0.141
13 0.923
130 0.372
131 0.746
132 0.772
133 0.845
134 0.457
135 0.54
136 0.0463
137 0.844
138 0.373
139 0.163
14 0.0928
140 0.339
141 0.304
142 0.84
143 0.199
144 0.0962
145 0.929
146 0.317
147 0.806
148 0.0911
149 0.39
15 0.101
150 0.953
151 0.0568
152 0.577
153 0.285
154 0.873
155 0.684
156 0.00471
157 0.428
158 0.124
159 0.0223
160 0.691
161 0.619
162 0.573
163 0.0248
164 0.989
165 0.0615
166 0.736
167 0.284
168 0.658
169 0.916
17 0.153
18 0.182
19 0.596
2 0.454
20 0.664
21 0.477
22 0.781
23 0.107
24 0.892
25 0.391
26 0.821
27 0.277
28 0.248
29 0.45
3 0.229
30 0.851
31 0.176
32 0.539
33 0.293
34 0.896
35 0.0494
36 0.474
37 0.228
38 0.718
39 0.911
4 0.878
40 0.911
41 0.0952
42 0.566
43 0.244
44 0.443
45 0.354
46 0.137
47 0.534
48 0.443
49 0.134
5 0.0565
50 0.767
51 0.794
52 0.116
53 0.86
54 0.355
55 0.276
56 0.302
57 0.758
58 0.325
59 0.602
6 0.814
60 0.0327
61 0.876
62 0.135
63 0.248
64 0.863
65 0.338
66 0.297
67 0.484
68 8.8302e-4
69 0.573
7 0.449
70 0.0143
71 0.231
72 0.811
73 0.466
74 0.928
75 0.459
76 0.797
77 0.414
78 0.281
79 0.926
8 0.253
80 0.077
81 0.331
82 0.46
83 0.528
84 0.187
85 0.00554
86 0.0997
87 0.277
88 0.92
89 0.021
9 0.851
90 0.178
91 0.601
92 0.161
93 0.441
94 0.224
95 0.489
96 0.422
97 0.806
98 0.126
99 0.737



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: CNhs11029


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)
0000300 (mouse embryonic day 17 sample)
0011372 (mouse testis- embryo E17 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)