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FF:437-20E7

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Name:forelimb, embryo E15
Species:Mouse (Mus musculus)
Library ID:CNhs11007
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 stage15 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  SAMD00005428
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11007 CAGE DRX008967 DRR009841
Accession ID Mm9

Library idBAMCTSS
CNhs11007 DRZ001266 DRZ002649
Accession ID Mm10

Library idBAMCTSS
CNhs11007 DRZ012616 DRZ013999
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

CNhs11007

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.0196
1002 0.0533
1003 0.28
1004 0
1005 --0.0202
1006 --0.143
1007 0.161
1008 0
1009 0.135
101 0.0966
1010 0
1011 0.0924
1012 0
1013 --0.142
1014 0.621
1015 0.162
1016 0.304
1017 0.107
1018 0.578
1019 0
102 0
1020 0
1021 --0.0487
1022 --0.0704
1023 0
1024 0.0525
1025 0
1026 0
1027 0
1028 0
1029 0.539
103 0.508
1030 0
1031 0.388
1032 --0.0928
1033 0.0313
1034 0
1035 0
1036 0.16
1037 0
1038 0.0301
1039 --0.203
104 0
1040 0.211
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: CNhs11007

Jaspar motif P-value
MA0002.2 0.00714
MA0003.1 0.0129
MA0004.1 0.464
MA0006.1 0.483
MA0007.1 0.537
MA0009.1 0.747
MA0014.1 0.0754
MA0017.1 6.91858e-12
MA0018.2 0.00282
MA0019.1 0.0827
MA0024.1 0.00219
MA0025.1 0.0031
MA0027.1 0.393
MA0028.1 0.00838
MA0029.1 0.913
MA0030.1 0.0964
MA0031.1 0.00141
MA0035.2 3.55888e-8
MA0038.1 0.856
MA0039.2 0.00276
MA0040.1 0.145
MA0041.1 0.137
MA0042.1 0.268
MA0043.1 0.232
MA0046.1 5.81095e-23
MA0047.2 6.09246e-4
MA0048.1 0.0373
MA0050.1 0.00727
MA0051.1 5.86207e-5
MA0052.1 0.509
MA0055.1 0.882
MA0057.1 0.647
MA0058.1 0.261
MA0059.1 0.877
MA0060.1 0.913
MA0061.1 0.288
MA0062.2 8.13679e-7
MA0065.2 7.77485e-8
MA0066.1 0.199
MA0067.1 0.0352
MA0068.1 0.868
MA0069.1 0.941
MA0070.1 0.406
MA0071.1 6.44416e-5
MA0072.1 8.62813e-5
MA0073.1 0.645
MA0074.1 0.328
MA0076.1 0.00776
MA0077.1 0.934
MA0078.1 0.17
MA0079.2 0.309
MA0080.2 2.74538e-10
MA0081.1 0.0263
MA0083.1 0.485
MA0084.1 0.98
MA0087.1 0.475
MA0088.1 0.522
MA0090.1 0.266
MA0091.1 0.656
MA0092.1 0.636
MA0093.1 0.514
MA0099.2 0.0175
MA0100.1 0.361
MA0101.1 0.0831
MA0102.2 0.672
MA0103.1 0.00711
MA0104.2 0.489
MA0105.1 0.202
MA0106.1 0.206
MA0107.1 0.0779
MA0108.2 0.79
MA0111.1 0.4
MA0112.2 0.00779
MA0113.1 0.201
MA0114.1 1.79757e-10
MA0115.1 4.63698e-4
MA0116.1 0.1
MA0117.1 0.0183
MA0119.1 0.28
MA0122.1 0.646
MA0124.1 0.439
MA0125.1 0.838
MA0131.1 0.563
MA0135.1 0.175
MA0136.1 2.51351e-11
MA0137.2 0.0576
MA0138.2 2.79001e-5
MA0139.1 0.0419
MA0140.1 8.49481e-5
MA0141.1 3.45545e-8
MA0142.1 0.895
MA0143.1 0.518
MA0144.1 0.061
MA0145.1 0.14
MA0146.1 0.0562
MA0147.1 0.628
MA0148.1 0.00624
MA0149.1 0.00437
MA0150.1 2.60216e-6
MA0152.1 0.0175
MA0153.1 8.67678e-16
MA0154.1 0.0156
MA0155.1 0.828
MA0156.1 1.73348e-7
MA0157.1 0.2
MA0159.1 4.67319e-4
MA0160.1 3.31105e-8
MA0162.1 0.795
MA0163.1 0.569
MA0164.1 0.757
MA0258.1 0.0011
MA0259.1 0.828



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: CNhs11007

Novel motif P-value
1 0.187
10 0.849
100 0.625
101 0.851
102 0.397
103 0.183
104 0.379
105 0.74
106 0.126
107 0.772
108 0.713
109 0.0311
11 0.0847
110 0.559
111 0.0464
112 0.0921
113 0.696
114 0.0137
115 0.935
116 0.639
117 0.423
118 0.321
119 0.131
12 0.516
120 0.448
121 0.114
122 0.995
123 0.216
124 0.246
125 0.661
126 0.267
127 0.273
128 0.375
129 0.441
13 0.984
130 0.155
131 0.434
132 0.415
133 0.0707
134 0.835
135 0.831
136 0.0572
137 0.86
138 0.423
139 0.0405
14 0.349
140 0.644
141 0.737
142 0.303
143 0.55
144 0.282
145 0.517
146 0.217
147 0.256
148 0.361
149 0.333
15 0.0265
150 0.899
151 0.0101
152 0.104
153 0.581
154 0.415
155 0.814
156 0.479
157 0.763
158 0.466
159 0.305
160 0.243
161 0.434
162 0.891
163 0.121
164 0.383
165 0.0715
166 0.16
167 0.701
168 0.694
169 0.14
17 0.24
18 0.346
19 0.567
2 0.891
20 0.777
21 0.733
22 0.413
23 0.809
24 0.397
25 0.145
26 0.35
27 0.323
28 0.213
29 0.297
3 0.351
30 0.979
31 0.359
32 0.445
33 0.392
34 0.548
35 0.16
36 0.0983
37 0.103
38 0.246
39 0.649
4 0.769
40 0.0293
41 0.151
42 0.902
43 0.278
44 0.00959
45 0.245
46 0.774
47 0.159
48 0.0898
49 0.247
5 0.503
50 0.696
51 0.637
52 0.694
53 0.883
54 0.503
55 0.316
56 0.57
57 0.744
58 0.435
59 0.108
6 0.781
60 0.273
61 0.596
62 0.167
63 0.267
64 0.399
65 0.172
66 0.385
67 0.457
68 0.0345
69 0.602
7 0.51
70 0.0269
71 0.832
72 0.165
73 0.0382
74 0.903
75 0.0715
76 0.91
77 0.361
78 0.598
79 0.879
8 0.107
80 0.00389
81 0.376
82 0.166
83 0.556
84 0.38
85 0.0378
86 0.884
87 7.79746e-6
88 0.983
89 0.195
9 0.966
90 0.468
91 0.683
92 0.92
93 0.628
94 0.262
95 0.00882
96 0.698
97 0.839
98 0.295
99 0.547



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: CNhs11007


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)
0000298 (mouse embryonic day 15 sample)
0011351 (mouse forelimb- embryo E15 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)