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FF:345-16C6

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Name:eyeball, embryo E12
Species:Mouse (Mus musculus)
Library ID:CNhs11016
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 stage12 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  SAMD00005612
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11016 CAGE DRX008955 DRR009829
Accession ID Mm9

Library idBAMCTSS
CNhs11016 DRZ001254 DRZ002637
Accession ID Mm10

Library idBAMCTSS
CNhs11016 DRZ012604 DRZ013987
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

CNhs11016

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.0257
10 0
100 0.1
1000 --0.0355
1001 0.0588
1002 0.354
1003 --0.104
1004 0.654
1005 --0.0978
1006 --0.0752
1007 0.142
1008 0
1009 --0.0469
101 0.158
1010 0
1011 0.0522
1012 0
1013 --0.149
1014 0.267
1015 0.343
1016 0.222
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0531
1022 --0.0709
1023 0
1024 --0.0367
1025 0
1026 0
1027 0.262
1028 0
1029 0.203
103 --0.0136
1030 0
1031 0.199
1032 --0.141
1033 0.0531
1034 0
1035 0
1036 0.129
1037 0
1038 --0.0941
1039 --0.097
104 0
1040 0.0257
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: CNhs11016

Jaspar motif P-value
MA0002.2 1.87475e-5
MA0003.1 0.108
MA0004.1 0.908
MA0006.1 0.282
MA0007.1 0.334
MA0009.1 0.221
MA0014.1 0.196
MA0017.1 2.45987e-4
MA0018.2 0.499
MA0019.1 0.834
MA0024.1 1.25523e-4
MA0025.1 0.0127
MA0027.1 0.12
MA0028.1 0.184
MA0029.1 0.623
MA0030.1 0.0403
MA0031.1 6.71054e-4
MA0035.2 0.00205
MA0038.1 0.00372
MA0039.2 0.00181
MA0040.1 0.0347
MA0041.1 0.198
MA0042.1 0.329
MA0043.1 0.122
MA0046.1 1.3655e-29
MA0047.2 2.83134e-5
MA0048.1 0.21
MA0050.1 2.90774e-7
MA0051.1 2.32766e-5
MA0052.1 1.95362e-6
MA0055.1 0.0769
MA0057.1 0.076
MA0058.1 0.705
MA0059.1 0.314
MA0060.1 2.5449e-13
MA0061.1 0.0645
MA0062.2 0.638
MA0065.2 1.91768e-5
MA0066.1 0.312
MA0067.1 0.53
MA0068.1 0.367
MA0069.1 0.102
MA0070.1 0.781
MA0071.1 0.532
MA0072.1 0.364
MA0073.1 0.166
MA0074.1 0.597
MA0076.1 0.117
MA0077.1 0.00613
MA0078.1 0.39
MA0079.2 0.198
MA0080.2 4.76839e-12
MA0081.1 0.256
MA0083.1 0.0336
MA0084.1 0.757
MA0087.1 0.285
MA0088.1 0.514
MA0090.1 0.42
MA0091.1 0.456
MA0092.1 0.324
MA0093.1 0.869
MA0099.2 1.12308e-6
MA0100.1 0.714
MA0101.1 0.239
MA0102.2 0.197
MA0103.1 0.00351
MA0104.2 0.235
MA0105.1 0.0347
MA0106.1 0.485
MA0107.1 0.101
MA0108.2 0.613
MA0111.1 0.549
MA0112.2 1.426e-4
MA0113.1 0.431
MA0114.1 4.1306e-4
MA0115.1 0.0996
MA0116.1 0.0346
MA0117.1 0.36
MA0119.1 0.00512
MA0122.1 0.855
MA0124.1 0.277
MA0125.1 0.0936
MA0131.1 0.343
MA0135.1 0.552
MA0136.1 2.37768e-8
MA0137.2 0.156
MA0138.2 1.61872e-4
MA0139.1 0.125
MA0140.1 0.029
MA0141.1 0.00557
MA0142.1 0.127
MA0143.1 2.00473e-4
MA0144.1 0.0895
MA0145.1 0.00878
MA0146.1 0.299
MA0147.1 0.368
MA0148.1 9.75145e-6
MA0149.1 0.0289
MA0150.1 0.013
MA0152.1 0.153
MA0153.1 4.85168e-19
MA0154.1 0.0015
MA0155.1 0.755
MA0156.1 0.00237
MA0157.1 0.00419
MA0159.1 0.0318
MA0160.1 0.0237
MA0162.1 0.874
MA0163.1 0.0542
MA0164.1 0.672
MA0258.1 0.00477
MA0259.1 0.501



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: CNhs11016

Novel motif P-value
1 0.127
10 0.378
100 0.656
101 0.68
102 0.68
103 0.118
104 0.947
105 0.129
106 0.00682
107 0.0688
108 0.668
109 0.117
11 0.113
110 0.248
111 0.0514
112 0.0516
113 0.54
114 0.0536
115 0.822
116 0.556
117 0.631
118 0.875
119 0.0425
12 0.853
120 0.46
121 0.808
122 0.895
123 0.156
124 0.142
125 0.211
126 0.498
127 0.12
128 0.0981
129 0.161
13 0.231
130 0.903
131 0.148
132 0.247
133 0.773
134 0.623
135 0.188
136 0.783
137 0.572
138 0.583
139 0.0207
14 0.347
140 0.188
141 0.0303
142 0.312
143 0.467
144 0.983
145 0.299
146 0.192
147 0.375
148 0.297
149 0.0437
15 0.0806
150 0.721
151 0.126
152 0.0255
153 0.637
154 0.977
155 0.771
156 0.47
157 0.674
158 0.604
159 0.872
160 0.737
161 0.748
162 0.802
163 0.0855
164 0.102
165 0.0851
166 0.469
167 0.914
168 0.339
169 0.00397
17 0.0422
18 0.56
19 0.183
2 0.285
20 0.54
21 0.639
22 0.215
23 0.0546
24 0.365
25 0.472
26 0.306
27 0.348
28 0.373
29 0.586
3 0.292
30 0.527
31 0.582
32 0.122
33 0.806
34 0.604
35 0.753
36 0.294
37 0.0638
38 0.174
39 0.652
4 0.333
40 0.227
41 0.44
42 0.644
43 0.154
44 0.125
45 0.308
46 0.322
47 0.192
48 0.179
49 0.195
5 0.145
50 0.889
51 0.571
52 0.151
53 0.489
54 0.35
55 0.657
56 0.305
57 0.662
58 0.242
59 0.0293
6 0.529
60 0.0487
61 0.854
62 0.103
63 0.0976
64 0.464
65 0.0789
66 0.583
67 0.932
68 0.0987
69 0.643
7 0.224
70 0.00244
71 0.24
72 0.217
73 0.0504
74 0.222
75 0.111
76 0.68
77 0.141
78 0.159
79 0.108
8 0.29
80 0.0831
81 0.379
82 0.0246
83 0.682
84 0.437
85 0.0311
86 0.33
87 0.329
88 0.679
89 0.15
9 0.277
90 0.529
91 0.432
92 0.0813
93 0.661
94 0.487
95 0.286
96 0.319
97 0.508
98 0.234
99 0.623



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: CNhs11016


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)
0000295 (mouse embryonic day 12 sample)
0011316 (mouse eyeball- embryo E12 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)