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FF:1520-43B5

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Name:forelimb, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs11008
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 stage18 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  SAMD00005639
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11008 CAGE DRX008969 DRR009843
Accession ID Mm9

Library idBAMCTSS
CNhs11008 DRZ001268 DRZ002651
Accession ID Mm10

Library idBAMCTSS
CNhs11008 DRZ012618 DRZ014001
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

CNhs11008

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.00325
1001 0.0182
1002 0
1003 0.284
1004 0
1005 0
1006 --0.0587
1007 0.0367
1008 0
1009 0.159
101 0.0493
1010 0
1011 0
1012 0
1013 --0.0775
1014 0.518
1015 0.0133
1016 0.219
1017 0
1018 0.633
1019 0
102 0
1020 0
1021 --0.0487
1022 0
1023 0
1024 0.174
1025 0
1026 0
1027 0.0603
1028 0
1029 0.0612
103 0.74
1030 0
1031 0.409
1032 --0.0883
1033 0
1034 0
1035 0
1036 0.0998
1037 0
1038 0.0858
1039 --0.14
104 0
1040 0.187
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: CNhs11008

Jaspar motif P-value
MA0002.2 0.0882
MA0003.1 0.436
MA0004.1 0.186
MA0006.1 0.141
MA0007.1 0.468
MA0009.1 0.312
MA0014.1 0.424
MA0017.1 1.14219e-14
MA0018.2 0.00371
MA0019.1 0.25
MA0024.1 0.498
MA0025.1 0.135
MA0027.1 0.637
MA0028.1 1.05019e-5
MA0029.1 0.827
MA0030.1 0.386
MA0031.1 0.237
MA0035.2 6.54672e-7
MA0038.1 0.641
MA0039.2 0.0169
MA0040.1 0.577
MA0041.1 0.152
MA0042.1 0.265
MA0043.1 0.467
MA0046.1 3.67804e-23
MA0047.2 0.00999
MA0048.1 0.956
MA0050.1 0.0496
MA0051.1 0.00126
MA0052.1 4.24141e-4
MA0055.1 0.0645
MA0057.1 0.322
MA0058.1 0.0555
MA0059.1 0.0624
MA0060.1 0.411
MA0061.1 0.402
MA0062.2 1.27987e-9
MA0065.2 5.75691e-5
MA0066.1 0.47
MA0067.1 0.111
MA0068.1 0.387
MA0069.1 0.798
MA0070.1 0.909
MA0071.1 1.58942e-4
MA0072.1 0.0736
MA0073.1 0.761
MA0074.1 0.0515
MA0076.1 6.39201e-6
MA0077.1 0.413
MA0078.1 0.0342
MA0079.2 0.00909
MA0080.2 7.96946e-7
MA0081.1 0.00866
MA0083.1 0.293
MA0084.1 0.812
MA0087.1 0.412
MA0088.1 0.968
MA0090.1 0.0795
MA0091.1 0.894
MA0092.1 0.278
MA0093.1 0.205
MA0099.2 1.44464e-4
MA0100.1 0.0466
MA0101.1 0.123
MA0102.2 0.687
MA0103.1 0.0785
MA0104.2 0.0828
MA0105.1 0.809
MA0106.1 0.0357
MA0107.1 0.263
MA0108.2 4.60232e-20
MA0111.1 0.604
MA0112.2 0.308
MA0113.1 0.0359
MA0114.1 1.25486e-12
MA0115.1 4.21608e-7
MA0116.1 0.746
MA0117.1 0.184
MA0119.1 0.716
MA0122.1 0.605
MA0124.1 0.332
MA0125.1 0.0218
MA0131.1 0.963
MA0135.1 0.943
MA0136.1 5.21012e-8
MA0137.2 0.58
MA0138.2 0.076
MA0139.1 0.0993
MA0140.1 1.30915e-4
MA0141.1 3.74317e-10
MA0142.1 0.26
MA0143.1 0.218
MA0144.1 0.538
MA0145.1 0.0511
MA0146.1 0.911
MA0147.1 0.0659
MA0148.1 0.0169
MA0149.1 0.0286
MA0150.1 0.0103
MA0152.1 0.0101
MA0153.1 1.41139e-15
MA0154.1 0.835
MA0155.1 0.795
MA0156.1 5.08451e-5
MA0157.1 0.272
MA0159.1 1.63738e-4
MA0160.1 4.75909e-9
MA0162.1 0.923
MA0163.1 0.648
MA0164.1 0.323
MA0258.1 0.00952
MA0259.1 0.489



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: CNhs11008

Novel motif P-value
1 0.192
10 0.62
100 0.951
101 0.55
102 0.641
103 0.226
104 0.0656
105 0.591
106 0.444
107 0.143
108 0.734
109 0.279
11 0.126
110 0.714
111 0.0346
112 0.184
113 0.945
114 0.0654
115 0.587
116 0.867
117 0.0852
118 0.0359
119 0.379
12 0.485
120 0.554
121 0.0626
122 0.408
123 0.178
124 0.418
125 0.619
126 0.443
127 0.867
128 0.479
129 0.263
13 0.465
130 0.466
131 0.863
132 0.556
133 0.981
134 0.701
135 0.324
136 0.65
137 0.858
138 0.721
139 0.157
14 0.732
140 0.34
141 0.396
142 0.362
143 0.687
144 0.291
145 0.712
146 0.835
147 0.322
148 0.229
149 0.722
15 0.0168
150 0.906
151 0.282
152 0.0596
153 0.779
154 0.634
155 0.404
156 0.124
157 0.0176
158 0.144
159 0.257
160 0.0449
161 0.686
162 0.717
163 0.465
164 0.307
165 0.128
166 0.0442
167 0.0222
168 0.16
169 0.118
17 0.693
18 0.224
19 0.525
2 0.0994
20 0.176
21 0.426
22 0.444
23 0.126
24 0.915
25 0.274
26 0.0318
27 0.391
28 0.4
29 0.0482
3 0.205
30 0.0969
31 0.306
32 0.446
33 0.724
34 0.608
35 0.00174
36 0.0216
37 0.688
38 0.693
39 0.352
4 0.954
40 0.0627
41 0.0652
42 0.829
43 0.709
44 0.0466
45 0.391
46 0.727
47 0.312
48 0.127
49 0.0929
5 0.275
50 0.267
51 0.987
52 0.272
53 0.286
54 0.836
55 0.6
56 0.786
57 0.661
58 0.758
59 0.763
6 0.766
60 0.53
61 0.793
62 0.423
63 0.86
64 0.216
65 0.535
66 0.461
67 0.681
68 0.0195
69 0.682
7 0.835
70 0.137
71 0.867
72 0.562
73 0.722
74 0.836
75 0.29
76 0.0272
77 0.49
78 0.41
79 0.642
8 0.0785
80 0.0232
81 0.629
82 0.417
83 0.735
84 0.442
85 0.686
86 0.489
87 0.216
88 0.922
89 0.417
9 0.694
90 0.27
91 0.778
92 0.604
93 0.532
94 0.336
95 0.619
96 0.721
97 0.343
98 0.298
99 0.235



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: CNhs11008


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)
0000302 (mouse embryonic day 18 sample)
0011278 (mouse forelimb- embryo E18 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)


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