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FF:1261-18D4

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Name:eyeball, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs11023
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 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  SAMD00005445
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11023 CAGE DRX008958 DRR009832
Accession ID Mm9

Library idBAMCTSS
CNhs11023 DRZ001257 DRZ002640
Accession ID Mm10

Library idBAMCTSS
CNhs11023 DRZ012607 DRZ013990
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

CNhs11023

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.117
10 0
100 0.162
1000 0
1001 0.102
1002 0.507
1003 0.0707
1004 0.358
1005 --0.0579
1006 0.0936
1007 0.122
1008 0
1009 0.0572
101 0.0531
1010 0
1011 0.0105
1012 0.162
1013 --0.182
1014 0.635
1015 0.214
1016 0.24
1017 0
1018 0.205
1019 0
102 0
1020 0
1021 0
1022 --0.00943
1023 0
1024 --0.0251
1025 0.00122
1026 0
1027 0.462
1028 0
1029 0.411
103 0.435
1030 0
1031 0.265
1032 --0.0145
1033 0.061
1034 0
1035 0.061
1036 0.107
1037 0
1038 0.00183
1039 --0.0828
104 0
1040 0.0755
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: CNhs11023

Jaspar motif P-value
MA0002.2 9.23806e-4
MA0003.1 0.2
MA0004.1 0.256
MA0006.1 0.198
MA0007.1 0.155
MA0009.1 0.266
MA0014.1 0.0887
MA0017.1 4.99677e-9
MA0018.2 0.341
MA0019.1 0.386
MA0024.1 0.00128
MA0025.1 0.00364
MA0027.1 0.913
MA0028.1 0.0314
MA0029.1 0.962
MA0030.1 0.403
MA0031.1 0.00526
MA0035.2 0.0391
MA0038.1 0.0234
MA0039.2 0.00364
MA0040.1 0.0255
MA0041.1 0.224
MA0042.1 0.68
MA0043.1 0.245
MA0046.1 1.95346e-8
MA0047.2 5.54701e-4
MA0048.1 0.753
MA0050.1 2.82702e-6
MA0051.1 1.38275e-6
MA0052.1 0.725
MA0055.1 0.693
MA0057.1 0.189
MA0058.1 0.205
MA0059.1 0.474
MA0060.1 5.47283e-6
MA0061.1 0.016
MA0062.2 1.79216e-7
MA0065.2 2.52591e-8
MA0066.1 0.609
MA0067.1 0.261
MA0068.1 0.938
MA0069.1 0.127
MA0070.1 0.989
MA0071.1 0.277
MA0072.1 0.815
MA0073.1 0.514
MA0074.1 0.126
MA0076.1 0.0753
MA0077.1 0.0371
MA0078.1 0.948
MA0079.2 0.589
MA0080.2 7.95856e-14
MA0081.1 0.0137
MA0083.1 0.849
MA0084.1 0.534
MA0087.1 0.663
MA0088.1 0.151
MA0090.1 0.827
MA0091.1 0.0854
MA0092.1 0.804
MA0093.1 0.277
MA0099.2 4.97896e-6
MA0100.1 0.248
MA0101.1 0.00263
MA0102.2 0.883
MA0103.1 7.00291e-4
MA0104.2 0.973
MA0105.1 0.135
MA0106.1 0.831
MA0107.1 0.00231
MA0108.2 3.21203e-8
MA0111.1 0.916
MA0112.2 5.86761e-4
MA0113.1 0.163
MA0114.1 9.73086e-8
MA0115.1 1.51037e-4
MA0116.1 0.115
MA0117.1 0.318
MA0119.1 0.0602
MA0122.1 0.448
MA0124.1 0.179
MA0125.1 0.00204
MA0131.1 0.647
MA0135.1 0.194
MA0136.1 4.02056e-19
MA0137.2 7.10417e-4
MA0138.2 0.716
MA0139.1 0.0423
MA0140.1 0.363
MA0141.1 4.22844e-6
MA0142.1 0.365
MA0143.1 0.0541
MA0144.1 0.00321
MA0145.1 0.0296
MA0146.1 0.0105
MA0147.1 0.845
MA0148.1 0.00353
MA0149.1 0.0145
MA0150.1 0.00995
MA0152.1 0.136
MA0153.1 3.75895e-9
MA0154.1 0.0132
MA0155.1 0.95
MA0156.1 2.93249e-13
MA0157.1 0.0164
MA0159.1 0.00506
MA0160.1 1.42316e-4
MA0162.1 0.606
MA0163.1 0.0214
MA0164.1 0.801
MA0258.1 0.00268
MA0259.1 0.858



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: CNhs11023

Novel motif P-value
1 0.192
10 0.236
100 0.759
101 0.971
102 0.39
103 0.0445
104 0.51
105 0.418
106 0.0387
107 0.503
108 0.869
109 0.0122
11 0.0293
110 0.133
111 0.00218
112 0.00348
113 0.924
114 0.0289
115 0.807
116 0.342
117 0.0166
118 0.41
119 0.178
12 0.517
120 0.516
121 0.126
122 0.789
123 0.965
124 0.978
125 0.0215
126 0.166
127 0.196
128 0.352
129 0.428
13 0.00295
130 0.922
131 0.559
132 0.509
133 0.877
134 0.424
135 0.43
136 0.00452
137 0.886
138 0.407
139 0.0524
14 0.868
140 0.774
141 0.132
142 0.713
143 0.48
144 0.446
145 0.112
146 0.285
147 0.502
148 0.276
149 0.156
15 0.0248
150 0.238
151 0.246
152 0.0145
153 0.926
154 0.911
155 0.24
156 0.226
157 0.899
158 0.19
159 0.628
160 0.923
161 0.173
162 0.891
163 0.101
164 0.00563
165 0.0213
166 0.449
167 0.61
168 0.415
169 0.00324
17 0.0551
18 0.761
19 0.422
2 0.449
20 0.363
21 0.433
22 0.248
23 0.53
24 0.0419
25 0.392
26 0.131
27 0.464
28 0.263
29 0.0347
3 0.112
30 0.85
31 0.769
32 0.681
33 0.0786
34 0.597
35 0.771
36 0.112
37 0.02
38 0.132
39 0.478
4 0.547
40 0.0395
41 0.106
42 0.451
43 0.196
44 0.198
45 0.275
46 0.32
47 0.146
48 0.0566
49 0.204
5 0.173
50 0.983
51 0.555
52 0.337
53 0.91
54 0.668
55 0.511
56 0.378
57 0.848
58 0.244
59 0.0375
6 0.739
60 0.0414
61 0.561
62 0.141
63 0.117
64 0.536
65 0.0882
66 0.973
67 0.428
68 0.099
69 0.886
7 0.16
70 0.012
71 0.0579
72 0.148
73 0.00331
74 0.955
75 0.0223
76 0.393
77 0.125
78 0.0943
79 0.345
8 0.101
80 0.162
81 0.418
82 0.0197
83 0.726
84 0.494
85 0.0608
86 0.154
87 3.97623e-4
88 0.79
89 0.15
9 0.452
90 0.345
91 0.73
92 0.209
93 0.25
94 0.703
95 0.0107
96 0.75
97 0.55
98 0.259
99 0.853



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: CNhs11023


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)
0000300 (mouse embryonic day 17 sample)
0011521 (mouse eyeball- 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:0006601 (presumptive ectoderm)
UBERON:0003056 (pre-chordal neural plate)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)