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FF:426-16C9

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Name:eyeball, embryo E15
Species:Mouse (Mus musculus)
Library ID:CNhs10593
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 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  SAMD00004677
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10593 CAGE DRX008957 DRR009831
Accession ID Mm9

Library idBAMCTSS
CNhs10593 DRZ001256 DRZ002639
Accession ID Mm10

Library idBAMCTSS
CNhs10593 DRZ012606 DRZ013989
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

CNhs10593

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.0719
10 0
100 0.0719
1000 0
1001 -0.0303
1002 0.269
1003 -0.0539
1004 0.497
1005 -0.0389
1006 0.0416
1007 0.00775
1008 0
1009 0.0584
101 0.0713
1010 0
1011 0.0204
1012 0
1013 -0.147
1014 0.279
1015 0.224
1016 0.3
1017 0
1018 0.0719
1019 0
102 0
1020 0
1021 0.0719
1022 -0.0704
1023 0
1024 -0.0322
1025 0
1026 0
1027 0.41
1028 0
1029 -0.0424
103 0.16
1030 0
1031 0.271
1032 -7.9209e-4
1033 0.0584
1034 0
1035 0
1036 0.0278
1037 0
1038 -0.0217
1039 -0.176
104 0
1040 0.0117
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: CNhs10593
Jaspar motif P-value
MA0002.2 6.74939e-5
MA0003.1 0.354
MA0004.1 0.623
MA0006.1 0.323
MA0007.1 0.276
MA0009.1 0.27
MA0014.1 0.188
MA0017.1 2.62133e-7
MA0018.2 0.0773
MA0019.1 0.641
MA0024.1 0.00207
MA0025.1 0.229
MA0027.1 0.462
MA0028.1 0.928
MA0029.1 0.913
MA0030.1 0.363
MA0031.1 0.0886
MA0035.2 0.0185
MA0038.1 9.04169e-4
MA0039.2 0.355
MA0040.1 0.0926
MA0041.1 0.166
MA0042.1 0.441
MA0043.1 0.12
MA0046.1 6.16473e-19
MA0047.2 7.44076e-4
MA0048.1 0.612
MA0050.1 1.0849e-7
MA0051.1 1.57441e-4
MA0052.1 0.69
MA0055.1 0.914
MA0057.1 0.131
MA0058.1 0.657
MA0059.1 0.332
MA0060.1 7.22073e-17
MA0061.1 0.0564
MA0062.2 0.298
MA0065.2 1.23956e-6
MA0066.1 0.079
MA0067.1 0.903
MA0068.1 0.25
MA0069.1 0.0602
MA0070.1 0.307
MA0071.1 0.265
MA0072.1 0.686
MA0073.1 0.922
MA0074.1 0.228
MA0076.1 0.51
MA0077.1 0.00171
MA0078.1 0.318
MA0079.2 0.374
MA0080.2 9.35648e-12
MA0081.1 0.228
MA0083.1 0.948
MA0084.1 0.0642
MA0087.1 0.0678
MA0088.1 0.313
MA0090.1 0.789
MA0091.1 0.4
MA0092.1 0.333
MA0093.1 0.658
MA0099.2 0.00219
MA0100.1 0.998
MA0101.1 0.151
MA0102.2 0.417
MA0103.1 0.00367
MA0104.2 0.901
MA0105.1 0.00406
MA0106.1 0.166
MA0107.1 0.0951
MA0108.2 1.99412e-7
MA0111.1 0.491
MA0112.2 1.20505e-5
MA0113.1 0.218
MA0114.1 6.00225e-6
MA0115.1 3.92795e-4
MA0116.1 0.00833
MA0117.1 0.673
MA0119.1 0.00977
MA0122.1 0.826
MA0124.1 0.41
MA0125.1 0.0023
MA0131.1 0.566
MA0135.1 0.0256
MA0136.1 1.5578e-8
MA0137.2 0.0445
MA0138.2 0.179
MA0139.1 0.0575
MA0140.1 0.00213
MA0141.1 1.90697e-4
MA0142.1 0.119
MA0143.1 0.0081
MA0144.1 0.0612
MA0145.1 0.0566
MA0146.1 0.154
MA0147.1 0.863
MA0148.1 3.33905e-5
MA0149.1 0.00296
MA0150.1 0.123
MA0152.1 0.989
MA0153.1 2.12946e-18
MA0154.1 0.00277
MA0155.1 0.741
MA0156.1 0.0026
MA0157.1 0.0944
MA0159.1 0.00594
MA0160.1 0.0205
MA0162.1 0.597
MA0163.1 3.24484e-4
MA0164.1 0.95
MA0258.1 0.00145
MA0259.1 0.919



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: CNhs10593
Novel motif P-value
1 0.0631
10 0.0639
100 0.978
101 0.755
102 0.667
103 0.0262
104 0.775
105 0.323
106 0.0168
107 0.0902
108 0.893
109 0.0323
11 0.0435
110 0.0598
111 3.85463e-4
112 0.00918
113 0.896
114 0.019
115 0.881
116 0.52
117 0.0396
118 0.444
119 0.0402
12 0.708
120 0.384
121 0.766
122 0.893
123 0.913
124 0.534
125 0.0338
126 0.231
127 0.0801
128 0.0652
129 0.331
13 0.0111
130 0.758
131 0.729
132 0.272
133 0.253
134 0.672
135 0.301
136 0.503
137 0.69
138 0.577
139 0.00677
14 0.699
140 0.0631
141 0.0528
142 0.68
143 0.512
144 0.872
145 0.0834
146 0.544
147 0.563
148 0.0931
149 0.232
15 0.0622
150 0.344
151 0.25
152 0.0726
153 0.338
154 0.467
155 0.31
156 4.9982e-4
157 0.857
158 0.189
159 0.0228
160 0.377
161 0.248
162 0.761
163 0.517
164 0.00997
165 0.0768
166 0.794
167 0.177
168 0.702
169 0.00113
17 0.0285
18 0.557
19 0.175
2 0.744
20 0.66
21 0.646
22 0.244
23 0.204
24 0.318
25 0.567
26 0.0311
27 0.505
28 0.373
29 0.157
3 0.0551
30 0.924
31 0.545
32 0.196
33 0.387
34 0.96
35 0.36
36 0.158
37 0.0242
38 0.23
39 0.304
4 0.576
40 0.328
41 0.651
42 0.295
43 0.117
44 0.135
45 0.566
46 0.145
47 0.0905
48 0.0814
49 0.102
5 0.0662
50 0.923
51 0.543
52 0.315
53 0.914
54 0.567
55 0.589
56 0.344
57 0.366
58 0.328
59 0.0908
6 0.721
60 0.0462
61 0.477
62 0.155
63 0.097
64 0.507
65 0.13
66 0.308
67 0.918
68 0.0409
69 0.603
7 0.118
70 0.00708
71 0.0416
72 0.443
73 0.0384
74 0.552
75 0.0266
76 0.458
77 0.169
78 0.114
79 0.128
8 0.0546
80 0.457
81 0.302
82 0.0183
83 0.693
84 0.961
85 0.0208
86 0.158
87 0.924
88 0.697
89 0.17
9 0.495
90 0.0504
91 0.557
92 0.111
93 0.234
94 0.514
95 0.0678
96 0.352
97 0.841
98 0.315
99 0.5



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: CNhs10593


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)
0000298 (mouse embryonic day 15 sample)
0011344 (mouse eyeball- 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:0006601 (presumptive ectoderm)
UBERON:0003056 (pre-chordal neural plate)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)