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FF:384-1E2

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Name:forelimb, embryo E13
Species:Mouse (Mus musculus)
Library ID:CNhs10589
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
tissueforelimb
dev stage13 days embryo
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  SAMD00005279
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10589 CAGE DRX008965 DRR009839
Accession ID Mm9

Library idBAMCTSS
CNhs10589 DRZ001264 DRZ002647
Accession ID Mm10

Library idBAMCTSS
CNhs10589 DRZ012614 DRZ013997
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

CNhs10589

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 -0.0234
1002 0.0584
1003 0.208
1004 0
1005 -0.0389
1006 -0.0825
1007 0.114
1008 0
1009 -0.006
101 0.103
1010 0
1011 0.0498
1012 0
1013 -0.188
1014 0.218
1015 0.253
1016 0.46
1017 0
1018 0.231
1019 0
102 0
1020 0
1021 0
1022 0
1023 0
1024 0
1025 0
1026 0.102
1027 0.07
1028 0
1029 0.173
103 0.131
1030 0
1031 0.231
1032 -0.184
1033 0.11
1034 0
1035 0
1036 0.177
1037 0
1038 0.044
1039 -0.194
104 0
1040 0.153
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: CNhs10589
Jaspar motif P-value
MA0002.2 3.08786e-4
MA0003.1 0.134
MA0004.1 0.969
MA0006.1 0.386
MA0007.1 0.244
MA0009.1 0.281
MA0014.1 0.0905
MA0017.1 6.1793e-7
MA0018.2 0.557
MA0019.1 0.663
MA0024.1 8.35905e-4
MA0025.1 0.104
MA0027.1 0.0991
MA0028.1 0.575
MA0029.1 0.967
MA0030.1 0.155
MA0031.1 0.0607
MA0035.2 1.51197e-4
MA0038.1 0.0395
MA0039.2 0.0449
MA0040.1 0.116
MA0041.1 0.404
MA0042.1 0.31
MA0043.1 0.0373
MA0046.1 5.05515e-19
MA0047.2 0.00352
MA0048.1 0.365
MA0050.1 8.43025e-4
MA0051.1 0.00143
MA0052.1 0.92
MA0055.1 0.283
MA0057.1 0.14
MA0058.1 0.97
MA0059.1 0.598
MA0060.1 1.84008e-11
MA0061.1 0.156
MA0062.2 0.97
MA0065.2 7.0341e-5
MA0066.1 0.0786
MA0067.1 0.45
MA0068.1 0.348
MA0069.1 0.393
MA0070.1 0.77
MA0071.1 0.0304
MA0072.1 0.0242
MA0073.1 0.794
MA0074.1 0.379
MA0076.1 0.321
MA0077.1 0.0699
MA0078.1 0.657
MA0079.2 0.419
MA0080.2 5.49812e-9
MA0081.1 0.453
MA0083.1 0.629
MA0084.1 0.363
MA0087.1 0.972
MA0088.1 0.378
MA0090.1 0.793
MA0091.1 0.358
MA0092.1 0.577
MA0093.1 0.955
MA0099.2 4.92672e-4
MA0100.1 0.756
MA0101.1 0.512
MA0102.2 0.691
MA0103.1 0.00265
MA0104.2 0.919
MA0105.1 0.00896
MA0106.1 0.359
MA0107.1 0.306
MA0108.2 0.646
MA0111.1 0.21
MA0112.2 1.66366e-6
MA0113.1 0.244
MA0114.1 7.72762e-5
MA0115.1 0.00981
MA0116.1 0.00125
MA0117.1 0.268
MA0119.1 0.0381
MA0122.1 0.593
MA0124.1 0.316
MA0125.1 0.094
MA0131.1 0.303
MA0135.1 0.285
MA0136.1 5.5606e-5
MA0137.2 0.375
MA0138.2 3.79914e-5
MA0139.1 0.0153
MA0140.1 8.7027e-4
MA0141.1 3.66811e-4
MA0142.1 0.603
MA0143.1 0.12
MA0144.1 0.228
MA0145.1 0.0422
MA0146.1 0.302
MA0147.1 0.95
MA0148.1 8.71767e-5
MA0149.1 0.00403
MA0150.1 6.32051e-4
MA0152.1 0.104
MA0153.1 2.99867e-17
MA0154.1 5.04855e-4
MA0155.1 0.788
MA0156.1 0.0977
MA0157.1 0.281
MA0159.1 0.00151
MA0160.1 0.00433
MA0162.1 0.31
MA0163.1 0.00234
MA0164.1 0.96
MA0258.1 3.01546e-4
MA0259.1 0.699



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: CNhs10589
Novel motif P-value
1 0.0587
10 0.274
100 0.994
101 0.622
102 0.407
103 0.0387
104 0.651
105 0.393
106 0.00826
107 0.0852
108 0.822
109 0.0786
11 0.0918
110 0.204
111 0.0135
112 0.0199
113 0.679
114 0.0114
115 0.426
116 0.568
117 0.21
118 0.502
119 0.0406
12 0.671
120 0.42
121 0.897
122 0.96
123 0.104
124 0.272
125 0.255
126 0.349
127 0.128
128 0.0406
129 0.169
13 0.336
130 0.412
131 0.385
132 0.57
133 0.274
134 0.657
135 0.614
136 0.954
137 0.536
138 0.826
139 0.00656
14 0.327
140 0.0301
141 0.242
142 0.488
143 0.363
144 0.64
145 0.205
146 0.531
147 0.503
148 0.224
149 0.32
15 0.0653
150 0.422
151 0.0872
152 0.157
153 0.157
154 0.801
155 0.488
156 0.00194
157 0.548
158 0.388
159 0.598
160 0.652
161 0.343
162 0.935
163 0.116
164 0.157
165 0.138
166 0.458
167 0.736
168 0.569
169 0.00461
17 0.0579
18 0.241
19 0.135
2 0.944
20 0.977
21 0.904
22 0.312
23 0.227
24 0.648
25 0.371
26 0.333
27 0.488
28 0.344
29 0.295
3 0.15
30 0.969
31 0.294
32 0.2
33 0.596
34 0.676
35 0.146
36 0.0677
37 0.0631
38 0.375
39 0.765
4 0.476
40 0.213
41 0.251
42 0.461
43 0.121
44 0.0166
45 0.548
46 0.246
47 0.114
48 0.115
49 0.0966
5 0.119
50 0.844
51 0.607
52 0.315
53 0.68
54 0.361
55 0.315
56 0.334
57 0.507
58 0.276
59 0.0828
6 0.515
60 0.107
61 0.9
62 0.0703
63 0.192
64 0.37
65 0.156
66 0.623
67 0.69
68 0.00586
69 0.315
7 0.269
70 6.60004e-4
71 0.157
72 0.488
73 0.134
74 0.365
75 0.0446
76 0.829
77 0.126
78 0.366
79 0.31
8 0.07
80 0.138
81 0.346
82 0.0783
83 0.143
84 0.78
85 0.0115
86 0.72
87 0.292
88 0.869
89 0.174
9 0.626
90 0.0616
91 0.353
92 0.0868
93 0.734
94 0.661
95 0.114
96 0.15
97 0.733
98 0.139
99 0.541



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: CNhs10589


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)
0002102 (forelimb)
0000479 (tissue)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)
0004708 (paired limb/fin)
0002101 (limb)
0004710 (pectoral appendage)
0010317 (germ layer / neural crest derived structure)
0010707 (appendage girdle complex)
0000153 (anterior region of body)
0010708 (pectoral complex)

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)
0011331 (mouse forelimb- 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:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0005417 (forelimb bud)
UBERON:0005733 (limb field)
UBERON:0005732 (limb/fin field)
UBERON:0005729 (forelimb/pectoral fin field)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)