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FF:359-14H2

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Name:forelimb, embryo E12
Species:Mouse (Mus musculus)
Library ID:CNhs10600
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 stage12 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  SAMD00005383
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10600 CAGE DRX008964 DRR009838
Accession ID Mm9

Library idBAMCTSS
CNhs10600 DRZ001263 DRZ002646
Accession ID Mm10

Library idBAMCTSS
CNhs10600 DRZ012613 DRZ013996
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

CNhs10600

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0.0752
1000 0
1001 0
1002 0.0879
1003 0.0183
1004 0
1005 -0.0651
1006 -0.0491
1007 0.163
1008 0
1009 -0.0572
101 0.142
1010 0
1011 0.00517
1012 0
1013 -0.151
1014 0.152
1015 0.282
1016 0.556
1017 0
1018 0.0752
1019 0
102 0
1020 0
1021 0.139
1022 -0.0922
1023 0
1024 -0.0899
1025 0
1026 0
1027 0
1028 0
1029 0.182
103 0.00715
1030 0
1031 0.15
1032 -0.139
1033 0.0493
1034 0
1035 0
1036 0.0338
1037 0
1038 0.0625
1039 -0.216
104 0
1040 0.146
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: CNhs10600
Jaspar motif P-value
MA0002.2 7.30973e-4
MA0003.1 0.0599
MA0004.1 0.861
MA0006.1 0.379
MA0007.1 0.468
MA0009.1 0.296
MA0014.1 0.0947
MA0017.1 1.5345e-4
MA0018.2 0.509
MA0019.1 0.703
MA0024.1 5.90299e-5
MA0025.1 0.147
MA0027.1 0.24
MA0028.1 0.552
MA0029.1 0.925
MA0030.1 0.18
MA0031.1 0.0311
MA0035.2 5.06239e-4
MA0038.1 0.0168
MA0039.2 0.00984
MA0040.1 0.0287
MA0041.1 0.367
MA0042.1 0.46
MA0043.1 0.0264
MA0046.1 4.89279e-10
MA0047.2 0.013
MA0048.1 0.203
MA0050.1 2.75692e-5
MA0051.1 4.86594e-4
MA0052.1 0.392
MA0055.1 0.219
MA0057.1 0.0873
MA0058.1 0.767
MA0059.1 0.842
MA0060.1 4.66429e-14
MA0061.1 0.178
MA0062.2 0.903
MA0065.2 3.28993e-4
MA0066.1 0.146
MA0067.1 0.509
MA0068.1 0.63
MA0069.1 0.737
MA0070.1 0.935
MA0071.1 0.038
MA0072.1 0.0467
MA0073.1 0.554
MA0074.1 0.66
MA0076.1 0.354
MA0077.1 0.07
MA0078.1 0.898
MA0079.2 0.714
MA0080.2 3.99336e-10
MA0081.1 0.307
MA0083.1 0.843
MA0084.1 0.255
MA0087.1 0.879
MA0088.1 0.4
MA0090.1 0.944
MA0091.1 0.657
MA0092.1 0.611
MA0093.1 0.809
MA0099.2 4.28602e-5
MA0100.1 0.477
MA0101.1 0.533
MA0102.2 0.622
MA0103.1 0.00378
MA0104.2 0.585
MA0105.1 0.05
MA0106.1 0.203
MA0107.1 0.346
MA0108.2 0.905
MA0111.1 0.329
MA0112.2 5.14603e-6
MA0113.1 0.269
MA0114.1 0.0012
MA0115.1 0.174
MA0116.1 0.00279
MA0117.1 0.239
MA0119.1 0.0163
MA0122.1 0.932
MA0124.1 0.441
MA0125.1 0.244
MA0131.1 0.225
MA0135.1 0.821
MA0136.1 3.35915e-5
MA0137.2 0.328
MA0138.2 2.27713e-5
MA0139.1 0.0342
MA0140.1 0.0175
MA0141.1 0.00109
MA0142.1 0.903
MA0143.1 0.0181
MA0144.1 0.177
MA0145.1 0.0265
MA0146.1 0.371
MA0147.1 0.716
MA0148.1 4.36245e-4
MA0149.1 0.00508
MA0150.1 0.00185
MA0152.1 0.108
MA0153.1 9.16701e-11
MA0154.1 0.00171
MA0155.1 0.838
MA0156.1 0.0357
MA0157.1 0.126
MA0159.1 0.00145
MA0160.1 0.0142
MA0162.1 0.335
MA0163.1 0.0079
MA0164.1 0.831
MA0258.1 9.11974e-4
MA0259.1 0.65



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: CNhs10600
Novel motif P-value
1 0.0577
10 0.38
100 0.798
101 0.614
102 0.465
103 0.0369
104 0.942
105 0.292
106 0.008
107 0.115
108 0.736
109 0.0692
11 0.102
110 0.225
111 0.0364
112 0.0382
113 0.7
114 0.0128
115 0.337
116 0.458
117 0.305
118 0.842
119 0.0372
12 0.786
120 0.356
121 0.856
122 0.896
123 0.0554
124 0.143
125 0.784
126 0.405
127 0.113
128 0.0411
129 0.14
13 0.452
130 0.569
131 0.295
132 0.36
133 0.267
134 0.751
135 0.395
136 0.919
137 0.555
138 0.746
139 0.0076
14 0.36
140 0.0451
141 0.325
142 0.893
143 0.239
144 0.763
145 0.207
146 0.539
147 0.467
148 0.271
149 0.195
15 0.0729
150 0.529
151 0.0876
152 0.0817
153 0.114
154 0.973
155 0.801
156 0.612
157 0.793
158 0.771
159 0.933
160 0.69
161 0.386
162 0.825
163 0.081
164 0.161
165 0.205
166 0.309
167 0.871
168 0.359
169 0.00699
17 0.0543
18 0.278
19 0.137
2 0.712
20 0.718
21 0.893
22 0.273
23 0.113
24 0.595
25 0.46
26 0.34
27 0.373
28 0.354
29 0.373
3 0.166
30 0.777
31 0.324
32 0.174
33 0.651
34 0.632
35 0.317
36 0.119
37 0.0825
38 0.306
39 0.71
4 0.518
40 0.183
41 0.38
42 0.491
43 0.141
44 0.0051
45 0.533
46 0.307
47 0.0849
48 0.0991
49 0.124
5 0.142
50 0.991
51 0.528
52 0.272
53 0.506
54 0.382
55 0.35
56 0.314
57 0.502
58 0.274
59 0.0474
6 0.574
60 0.124
61 0.731
62 0.0732
63 0.128
64 0.35
65 0.1
66 0.559
67 0.996
68 0.0427
69 0.297
7 0.303
70 3.09702e-4
71 0.196
72 0.358
73 0.116
74 0.315
75 0.11
76 0.708
77 0.121
78 0.418
79 0.155
8 0.146
80 0.0997
81 0.322
82 0.0871
83 0.484
84 0.778
85 0.0204
86 0.66
87 0.126
88 0.781
89 0.131
9 0.577
90 0.11
91 0.397
92 0.0732
93 0.326
94 0.757
95 0.0943
96 0.187
97 0.969
98 0.22
99 0.52



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: CNhs10600


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)
0000295 (mouse embryonic day 12 sample)
0011322 (mouse forelimb- embryo E12 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)