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FF:399-16E2

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Name:eyeball, embryo E14
Species:Mouse (Mus musculus)
Library ID:CNhs10521
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
tissueeyeball
dev stage14 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  SAMD00005492
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10521 CAGE DRX008956 DRR009830
Accession ID Mm9

Library idBAMCTSS
CNhs10521 DRZ001255 DRZ002638
Accession ID Mm10

Library idBAMCTSS
CNhs10521 DRZ012605 DRZ013988
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

CNhs10521

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.0536
10 0
100 0.0899
1000 -0.0355
1001 -0.0749
1002 0.208
1003 -0.121
1004 0.503
1005 -0.169
1006 0.0161
1007 0.0466
1008 0
1009 -0.0572
101 0.0814
1010 0
1011 -0.0358
1012 0
1013 -0.147
1014 0.283
1015 0.322
1016 0.207
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.116
1022 -0.0842
1023 0
1024 0
1025 -0.0611
1026 0
1027 0.486
1028 0
1029 -0.129
103 0.0605
1030 0
1031 0.209
1032 -0.0175
1033 0.0466
1034 0
1035 0
1036 0.1
1037 0
1038 -0.122
1039 -0.121
104 0
1040 -0.0678
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: CNhs10521
Jaspar motif P-value
MA0002.2 9.20287e-4
MA0003.1 0.452
MA0004.1 0.857
MA0006.1 0.313
MA0007.1 0.319
MA0009.1 0.254
MA0014.1 0.463
MA0017.1 3.6258e-6
MA0018.2 0.0197
MA0019.1 0.981
MA0024.1 8.99982e-4
MA0025.1 0.622
MA0027.1 0.132
MA0028.1 0.305
MA0029.1 0.99
MA0030.1 0.178
MA0031.1 0.0546
MA0035.2 0.0726
MA0038.1 0.00411
MA0039.2 0.465
MA0040.1 0.201
MA0041.1 0.135
MA0042.1 0.756
MA0043.1 0.00611
MA0046.1 1.10616e-18
MA0047.2 0.00133
MA0048.1 0.934
MA0050.1 1.34247e-6
MA0051.1 2.05267e-4
MA0052.1 0.315
MA0055.1 0.241
MA0057.1 0.107
MA0058.1 0.934
MA0059.1 0.983
MA0060.1 1.6461e-20
MA0061.1 0.0366
MA0062.2 0.629
MA0065.2 5.52949e-6
MA0066.1 0.168
MA0067.1 0.901
MA0068.1 0.102
MA0069.1 0.0587
MA0070.1 0.137
MA0071.1 0.623
MA0072.1 0.583
MA0073.1 0.952
MA0074.1 0.433
MA0076.1 0.094
MA0077.1 4.98087e-4
MA0078.1 0.105
MA0079.2 0.629
MA0080.2 3.64073e-11
MA0081.1 0.198
MA0083.1 0.493
MA0084.1 0.107
MA0087.1 0.124
MA0088.1 0.659
MA0090.1 0.91
MA0091.1 0.421
MA0092.1 0.383
MA0093.1 0.898
MA0099.2 6.51738e-4
MA0100.1 0.861
MA0101.1 0.21
MA0102.2 0.156
MA0103.1 0.00287
MA0104.2 0.487
MA0105.1 0.00242
MA0106.1 0.267
MA0107.1 0.0679
MA0108.2 8.71863e-6
MA0111.1 0.408
MA0112.2 3.02324e-6
MA0113.1 0.332
MA0114.1 3.53403e-5
MA0115.1 0.0104
MA0116.1 0.0107
MA0117.1 0.598
MA0119.1 0.00217
MA0122.1 0.855
MA0124.1 0.747
MA0125.1 0.0294
MA0131.1 0.546
MA0135.1 0.0276
MA0136.1 5.09481e-6
MA0137.2 0.177
MA0138.2 0.113
MA0139.1 0.0835
MA0140.1 0.00979
MA0141.1 0.00589
MA0142.1 0.139
MA0143.1 0.00335
MA0144.1 0.0962
MA0145.1 0.0288
MA0146.1 0.177
MA0147.1 0.712
MA0148.1 3.08044e-5
MA0149.1 0.0553
MA0150.1 0.14
MA0152.1 0.961
MA0153.1 8.69294e-16
MA0154.1 8.84398e-4
MA0155.1 0.664
MA0156.1 0.0132
MA0157.1 0.0776
MA0159.1 0.0261
MA0160.1 0.0498
MA0162.1 0.684
MA0163.1 7.86216e-4
MA0164.1 0.831
MA0258.1 0.00166
MA0259.1 0.687



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: CNhs10521
Novel motif P-value
1 0.0588
10 0.107
100 0.817
101 0.59
102 0.583
103 0.0532
104 0.983
105 0.358
106 0.00725
107 0.0499
108 0.844
109 0.14
11 0.106
110 0.081
111 6.61576e-4
112 0.0147
113 0.705
114 0.0188
115 0.887
116 0.51
117 0.131
118 0.495
119 0.0451
12 0.541
120 0.41
121 0.797
122 0.945
123 0.754
124 0.455
125 0.115
126 0.329
127 0.0711
128 0.0378
129 0.169
13 0.0202
130 0.756
131 0.903
132 0.296
133 0.0723
134 0.921
135 0.0532
136 0.728
137 0.411
138 0.4
139 0.00759
14 0.547
140 0.00977
141 0.0636
142 0.418
143 0.59
144 0.986
145 0.0996
146 0.577
147 0.395
148 0.109
149 0.214
15 0.0829
150 0.472
151 0.221
152 0.0741
153 0.461
154 0.362
155 0.478
156 4.20124e-4
157 0.811
158 0.209
159 0.00926
160 0.311
161 0.475
162 0.695
163 0.51
164 0.0272
165 0.108
166 0.751
167 0.249
168 0.652
169 0.00106
17 0.0232
18 0.689
19 0.12
2 0.482
20 0.957
21 0.831
22 0.224
23 0.069
24 0.563
25 0.673
26 0.0487
27 0.457
28 0.298
29 0.22
3 0.101
30 0.766
31 0.568
32 0.12
33 0.656
34 0.938
35 0.417
36 0.313
37 0.046
38 0.36
39 0.355
4 0.485
40 0.618
41 0.981
42 0.325
43 0.112
44 0.157
45 0.482
46 0.122
47 0.139
48 0.129
49 0.12
5 0.0846
50 0.889
51 0.564
52 0.201
53 0.69
54 0.56
55 0.806
56 0.315
57 0.429
58 0.283
59 0.0833
6 0.563
60 0.0305
61 0.574
62 0.0794
63 0.107
64 0.589
65 0.138
66 0.226
67 0.729
68 0.039
69 0.562
7 0.135
70 0.0178
71 0.062
72 0.547
73 0.0959
74 0.346
75 0.0386
76 0.69
77 0.165
78 0.15
79 0.155
8 0.122
80 0.2
81 0.416
82 0.00982
83 0.895
84 0.702
85 0.00811
86 0.187
87 0.252
88 0.826
89 0.164
9 0.341
90 0.077
91 0.428
92 0.0591
93 0.0958
94 0.375
95 0.2
96 0.32
97 0.735
98 0.363
99 0.693



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: CNhs10521


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)
0000970 (eye)
0000019 (camera-type eye)
0000033 (head)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0000047 (simple eye)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0001032 (sensory system)
0010317 (germ layer / neural crest derived structure)
0004088 (ocular region)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002104 (visual system)
0004456 (entire sense organ system)
0001456 (face)

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)
0000296 (mouse embryonic day 14 sample)
0011335 (mouse eyeball- embryo E14 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:0006601 (presumptive ectoderm)
UBERON:0003056 (pre-chordal neural plate)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)