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FF:335-25E2

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Name:forelimb, embryo E11
Species:Mouse (Mus musculus)
Library ID:CNhs10596
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueforelimb
dev stage11 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  SAMD00005527
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10596 CAGE DRX008963 DRR009837
Accession ID Mm9

Library idBAMCTSS
CNhs10596 DRZ001262 DRZ002645
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs10596

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0496
1002 --0.0517
1003 --0.102
1004 0
1005 --0.0641
1006 --0.119
1007 0.118
1008 0
1009 --0.0572
101 0.149
1010 0
1011 0
1012 0
1013 --0.217
1014 0
1015 0.374
1016 0.493
1017 0
1018 0.0848
1019 0
102 0
1020 0
1021 0.0361
1022 --0.0855
1023 0
1024 --0.0905
1025 0
1026 0
1027 0
1028 0
1029 --0.0921
103 --0.0446
1030 0
1031 --0.0342
1032 --0.177
1033 0.053
1034 0
1035 0
1036 0.00662
1037 0
1038 --0.065
1039 --0.198
104 0
1040 0.00172
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: CNhs10596

Jaspar motif P-value
MA0002.2 0.0062
MA0003.1 0.0697
MA0004.1 0.422
MA0006.1 0.426
MA0007.1 0.568
MA0009.1 0.338
MA0014.1 0.103
MA0017.1 0.00201
MA0018.2 0.517
MA0019.1 0.745
MA0024.1 9.06651e-7
MA0025.1 0.305
MA0027.1 0.128
MA0028.1 0.0145
MA0029.1 0.878
MA0030.1 0.302
MA0031.1 0.077
MA0035.2 0.0867
MA0038.1 0.078
MA0039.2 0.00705
MA0040.1 0.485
MA0041.1 0.176
MA0042.1 0.992
MA0043.1 0.00836
MA0046.1 2.36024e-14
MA0047.2 0.0705
MA0048.1 0.0136
MA0050.1 6.50529e-8
MA0051.1 6.37755e-5
MA0052.1 0.00109
MA0055.1 0.0116
MA0057.1 0.169
MA0058.1 0.274
MA0059.1 0.236
MA0060.1 7.9107e-22
MA0061.1 0.199
MA0062.2 0.0288
MA0065.2 0.0124
MA0066.1 0.268
MA0067.1 0.293
MA0068.1 0.86
MA0069.1 0.724
MA0070.1 0.786
MA0071.1 0.232
MA0072.1 0.397
MA0073.1 0.953
MA0074.1 0.893
MA0076.1 0.00922
MA0077.1 0.00417
MA0078.1 0.0975
MA0079.2 0.736
MA0080.2 3.61812e-7
MA0081.1 0.552
MA0083.1 0.258
MA0084.1 0.617
MA0087.1 0.851
MA0088.1 0.704
MA0090.1 0.334
MA0091.1 0.971
MA0092.1 0.572
MA0093.1 0.397
MA0099.2 0.00188
MA0100.1 0.18
MA0101.1 0.835
MA0102.2 0.185
MA0103.1 0.0126
MA0104.2 0.0576
MA0105.1 0.107
MA0106.1 0.463
MA0107.1 0.639
MA0108.2 0.0712
MA0111.1 0.382
MA0112.2 6.67661e-4
MA0113.1 0.552
MA0114.1 0.0132
MA0115.1 0.802
MA0116.1 0.0153
MA0117.1 0.252
MA0119.1 0.00812
MA0122.1 0.872
MA0124.1 0.463
MA0125.1 0.0369
MA0131.1 0.128
MA0135.1 0.956
MA0136.1 0.212
MA0137.2 0.69
MA0138.2 3.43764e-5
MA0139.1 0.0372
MA0140.1 0.219
MA0141.1 0.0303
MA0142.1 0.678
MA0143.1 0.00104
MA0144.1 0.216
MA0145.1 0.0209
MA0146.1 0.968
MA0147.1 0.101
MA0148.1 5.97186e-4
MA0149.1 0.318
MA0150.1 0.00763
MA0152.1 0.974
MA0153.1 2.38509e-10
MA0154.1 0.00158
MA0155.1 0.873
MA0156.1 0.609
MA0157.1 0.211
MA0159.1 0.0167
MA0160.1 0.184
MA0162.1 0.534
MA0163.1 0.183
MA0164.1 0.53
MA0258.1 0.0131
MA0259.1 0.376



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: CNhs10596

Novel motif P-value
1 0.0994
10 0.818
100 0.534
101 0.517
102 0.691
103 0.0145
104 0.746
105 0.227
106 0.00707
107 0.0371
108 0.658
109 0.314
11 0.321
110 0.616
111 0.0612
112 0.0826
113 0.515
114 0.0782
115 0.245
116 0.868
117 0.45
118 0.771
119 0.0308
12 0.865
120 0.828
121 0.327
122 0.572
123 0.0383
124 0.248
125 0.695
126 0.793
127 0.0509
128 0.0592
129 0.206
13 0.887
130 0.735
131 0.189
132 0.311
133 0.778
134 0.862
135 0.219
136 0.479
137 0.363
138 0.739
139 0.0134
14 0.297
140 0.00542
141 0.164
142 0.238
143 0.986
144 0.98
145 0.391
146 0.664
147 0.383
148 0.547
149 0.186
15 0.146
150 0.729
151 0.144
152 0.151
153 0.0572
154 0.91
155 0.283
156 0.00253
157 0.52
158 0.868
159 0.15
160 0.739
161 0.656
162 0.72
163 0.0431
164 0.516
165 0.476
166 0.978
167 0.811
168 0.164
169 0.0799
17 0.076
18 0.586
19 0.0878
2 0.486
20 0.271
21 0.773
22 0.342
23 0.0211
24 0.815
25 0.572
26 0.626
27 0.374
28 0.403
29 0.776
3 0.298
30 0.661
31 0.423
32 0.214
33 0.8
34 0.676
35 0.367
36 0.53
37 0.193
38 0.33
39 0.791
4 0.638
40 0.592
41 0.883
42 0.742
43 0.179
44 0.151
45 0.445
46 0.463
47 0.138
48 0.241
49 0.165
5 0.139
50 0.943
51 0.446
52 0.19
53 0.347
54 0.279
55 0.61
56 0.366
57 0.716
58 0.225
59 0.0928
6 0.535
60 0.104
61 0.473
62 0.0841
63 0.2
64 0.488
65 0.155
66 0.281
67 0.542
68 0.401
69 0.248
7 0.369
70 0.00254
71 0.467
72 0.537
73 0.353
74 0.247
75 0.659
76 0.488
77 0.152
78 0.448
79 0.32
8 0.463
80 0.151
81 0.297
82 0.0285
83 0.49
84 0.894
85 0.0241
86 0.802
87 0.889
88 0.457
89 0.0652
9 0.407
90 0.0923
91 0.532
92 0.0256
93 0.512
94 0.77
95 0.563
96 0.262
97 0.875
98 0.379
99 0.644



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: CNhs10596


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)
0000294 (mouse embryonic day 11 sample)
0011314 (mouse forelimb- embryo E11 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)