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FF:1517-43C4

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Name:forelimb, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs10598
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 stage17 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  SAMD00005953
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10598 CAGE DRX008968 DRR009842
Accession ID Mm9

Library idBAMCTSS
CNhs10598 DRZ001267 DRZ002650
Accession ID Mm10

Library idBAMCTSS
CNhs10598 DRZ012617 DRZ014000
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
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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

CNhs10598

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0943
1001 0.0995
1002 0.0351
1003 0.417
1004 0
1005 0
1006 -0.0559
1007 0.101
1008 0
1009 0.204
101 0.0481
1010 0
1011 0.134
1012 0
1013 -0.0754
1014 0.403
1015 0.0869
1016 0.224
1017 0.13
1018 0.49
1019 0
102 0
1020 0
1021 0
1022 0
1023 0
1024 0.11
1025 0
1026 0
1027 0
1028 0
1029 0.28
103 0.694
1030 0
1031 0.365
1032 0.0199
1033 0.0484
1034 0
1035 0
1036 0.159
1037 0
1038 0.00596
1039 -0.119
104 0
1040 0.229
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: CNhs10598
Jaspar motif P-value
MA0002.2 0.133
MA0003.1 0.342
MA0004.1 0.297
MA0006.1 0.237
MA0007.1 0.547
MA0009.1 0.896
MA0014.1 0.202
MA0017.1 1.04364e-13
MA0018.2 0.0106
MA0019.1 0.245
MA0024.1 0.36
MA0025.1 0.17
MA0027.1 0.0979
MA0028.1 2.67237e-5
MA0029.1 0.824
MA0030.1 0.27
MA0031.1 0.0899
MA0035.2 5.59515e-5
MA0038.1 0.141
MA0039.2 0.101
MA0040.1 0.074
MA0041.1 0.0527
MA0042.1 0.233
MA0043.1 0.797
MA0046.1 1.14943e-17
MA0047.2 0.0057
MA0048.1 0.253
MA0050.1 1.95109e-5
MA0051.1 8.54274e-5
MA0052.1 2.69838e-14
MA0055.1 0.0149
MA0057.1 0.662
MA0058.1 0.138
MA0059.1 0.0189
MA0060.1 0.206
MA0061.1 0.552
MA0062.2 9.18134e-9
MA0065.2 3.11823e-4
MA0066.1 0.504
MA0067.1 0.202
MA0068.1 0.271
MA0069.1 0.707
MA0070.1 0.983
MA0071.1 3.59908e-4
MA0072.1 0.0221
MA0073.1 0.649
MA0074.1 0.235
MA0076.1 3.82286e-5
MA0077.1 0.946
MA0078.1 0.231
MA0079.2 0.0264
MA0080.2 2.22637e-6
MA0081.1 0.0714
MA0083.1 0.0175
MA0084.1 0.656
MA0087.1 0.561
MA0088.1 0.838
MA0090.1 0.0649
MA0091.1 0.689
MA0092.1 0.66
MA0093.1 0.334
MA0099.2 0.00355
MA0100.1 0.0809
MA0101.1 0.313
MA0102.2 0.739
MA0103.1 0.0594
MA0104.2 0.0743
MA0105.1 0.637
MA0106.1 0.335
MA0107.1 0.437
MA0108.2 3.45931e-23
MA0111.1 0.296
MA0112.2 0.181
MA0113.1 0.0616
MA0114.1 3.03472e-11
MA0115.1 2.62546e-5
MA0116.1 0.116
MA0117.1 0.184
MA0119.1 0.411
MA0122.1 0.761
MA0124.1 0.198
MA0125.1 0.00673
MA0131.1 0.849
MA0135.1 0.209
MA0136.1 9.2969e-8
MA0137.2 0.125
MA0138.2 0.137
MA0139.1 0.0155
MA0140.1 8.69891e-4
MA0141.1 2.16858e-9
MA0142.1 0.15
MA0143.1 0.4
MA0144.1 0.295
MA0145.1 0.0608
MA0146.1 0.75
MA0147.1 0.0403
MA0148.1 0.00228
MA0149.1 0.0029
MA0150.1 0.00819
MA0152.1 0.0169
MA0153.1 3.33566e-12
MA0154.1 0.385
MA0155.1 0.62
MA0156.1 5.59956e-6
MA0157.1 0.922
MA0159.1 7.31249e-4
MA0160.1 5.00689e-6
MA0162.1 0.963
MA0163.1 0.18
MA0164.1 0.722
MA0258.1 0.0131
MA0259.1 0.404



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: CNhs10598
Novel motif P-value
1 0.164
10 0.226
100 0.987
101 0.567
102 0.652
103 0.0875
104 0.285
105 0.869
106 0.99
107 0.319
108 0.874
109 0.379
11 0.0714
110 0.461
111 0.0607
112 0.0584
113 0.873
114 0.0867
115 0.649
116 0.713
117 0.0696
118 0.0741
119 0.192
12 0.524
120 0.448
121 0.309
122 0.469
123 0.478
124 0.494
125 0.082
126 0.43
127 0.754
128 0.716
129 0.411
13 0.821
130 0.426
131 0.594
132 0.732
133 0.438
134 0.306
135 0.629
136 0.564
137 0.919
138 0.782
139 0.155
14 0.976
140 0.626
141 0.585
142 0.636
143 0.178
144 0.141
145 0.268
146 0.987
147 0.198
148 0.383
149 0.719
15 0.00867
150 0.852
151 0.149
152 0.0414
153 0.721
154 0.575
155 0.543
156 1.48154e-5
157 0.255
158 0.328
159 1
160 0.203
161 0.407
162 0.964
163 0.426
164 0.0977
165 0.179
166 0.118
167 0.0904
168 0.162
169 0.0715
17 0.974
18 0.15
19 0.726
2 0.184
20 0.14
21 0.966
22 0.465
23 0.489
24 0.957
25 0.286
26 0.236
27 0.389
28 0.483
29 0.042
3 0.182
30 0.0807
31 0.323
32 0.625
33 0.285
34 0.46
35 0.00555
36 0.0153
37 0.737
38 0.453
39 0.804
4 0.893
40 0.0471
41 0.508
42 0.7
43 0.313
44 0.0797
45 0.192
46 0.84
47 0.304
48 0.128
49 0.0471
5 0.374
50 0.284
51 0.754
52 0.329
53 0.553
54 0.847
55 0.529
56 0.803
57 0.553
58 0.753
59 0.7
6 0.781
60 0.647
61 0.78
62 0.351
63 0.916
64 0.19
65 0.339
66 0.991
67 0.682
68 0.00461
69 0.988
7 0.956
70 0.146
71 0.543
72 0.459
73 0.819
74 0.7
75 0.134
76 0.0234
77 0.79
78 0.5
79 0.425
8 0.04
80 0.0485
81 0.724
82 0.447
83 0.384
84 0.82
85 0.497
86 0.529
87 0.113
88 0.934
89 0.7
9 0.582
90 0.0345
91 0.801
92 0.553
93 0.294
94 0.384
95 0.245
96 0.858
97 0.992
98 0.272
99 0.673



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: CNhs10598


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)
0000300 (mouse embryonic day 17 sample)
0011277 (mouse forelimb- 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: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)