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FF:777-19A2

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Name:eyeball, neonate N16
Species:Mouse (Mus musculus)
Library ID:CNhs11188
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 stage16 days neonate
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  SAMD00004878
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11188 CAGE DRX008962 DRR009836
Accession ID Mm9

Library idBAMCTSS
CNhs11188 DRZ001261 DRZ002644
Accession ID Mm10

Library idBAMCTSS
CNhs11188 DRZ012611 DRZ013994
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

CNhs11188

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.315
10 0
100 0
1000 0.428
1001 0.537
1002 0.38
1003 0.145
1004 0
1005 0
1006 0.524
1007 0.0262
1008 0
1009 0.0594
101 --0.0531
1010 0
1011 0.142
1012 0.249
1013 0.21
1014 --0.0874
1015 --0.223
1016 --0.128
1017 0
1018 0.0999
1019 0.826
102 0
1020 0
1021 0
1022 0.415
1023 0
1024 0.0534
1025 0
1026 0
1027 0.359
1028 0
1029 0.632
103 0.309
1030 0
1031 0.122
1032 0.0362
1033 0.0683
1034 0.0137
1035 0
1036 --0.102
1037 0.873
1038 0.118
1039 0.184
104 0
1040 0.0594
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: CNhs11188

Jaspar motif P-value
MA0002.2 0.0432
MA0003.1 0.925
MA0004.1 0.0591
MA0006.1 0.497
MA0007.1 0.376
MA0009.1 0.439
MA0014.1 0.193
MA0017.1 4.23705e-5
MA0018.2 0.224
MA0019.1 0.591
MA0024.1 1.29563e-4
MA0025.1 0.202
MA0027.1 0.0712
MA0028.1 1.09633e-6
MA0029.1 0.635
MA0030.1 0.84
MA0031.1 0.431
MA0035.2 0.194
MA0038.1 0.085
MA0039.2 0.001
MA0040.1 0.0944
MA0041.1 0.366
MA0042.1 0.857
MA0043.1 0.0726
MA0046.1 3.42394e-20
MA0047.2 0.0355
MA0048.1 0.00268
MA0050.1 0.0014
MA0051.1 0.00222
MA0052.1 3.02831e-5
MA0055.1 1.0938e-4
MA0057.1 0.592
MA0058.1 0.0443
MA0059.1 0.0094
MA0060.1 0.00518
MA0061.1 0.00141
MA0062.2 1.54222e-14
MA0065.2 0.0142
MA0066.1 0.508
MA0067.1 0.899
MA0068.1 0.253
MA0069.1 0.124
MA0070.1 0.624
MA0071.1 0.0348
MA0072.1 1.83047e-7
MA0073.1 0.87
MA0074.1 0.141
MA0076.1 1.01701e-7
MA0077.1 0.866
MA0078.1 0.0579
MA0079.2 0.633
MA0080.2 5.31992e-12
MA0081.1 5.65111e-4
MA0083.1 0.497
MA0084.1 0.545
MA0087.1 0.174
MA0088.1 0.322
MA0090.1 0.724
MA0091.1 0.0789
MA0092.1 0.658
MA0093.1 0.0755
MA0099.2 0.00947
MA0100.1 0.00654
MA0101.1 4.79221e-4
MA0102.2 0.143
MA0103.1 0.783
MA0104.2 0.156
MA0105.1 0.00223
MA0106.1 0.298
MA0107.1 0.00676
MA0108.2 0.5
MA0111.1 0.426
MA0112.2 0.172
MA0113.1 0.0545
MA0114.1 5.36783e-5
MA0115.1 7.17512e-4
MA0116.1 0.178
MA0117.1 0.831
MA0119.1 0.997
MA0122.1 0.413
MA0124.1 0.897
MA0125.1 0.0491
MA0131.1 0.291
MA0135.1 0.637
MA0136.1 2.96964e-22
MA0137.2 0.00295
MA0138.2 2.88863e-5
MA0139.1 0.368
MA0140.1 0.113
MA0141.1 0.147
MA0142.1 0.521
MA0143.1 0.457
MA0144.1 0.0025
MA0145.1 1
MA0146.1 0.0486
MA0147.1 0.0601
MA0148.1 0.00632
MA0149.1 0.328
MA0150.1 0.905
MA0152.1 0.93
MA0153.1 6.50512e-19
MA0154.1 0.203
MA0155.1 0.746
MA0156.1 4.28237e-18
MA0157.1 0.124
MA0159.1 0.175
MA0160.1 0.509
MA0162.1 0.549
MA0163.1 6.14381e-4
MA0164.1 0.851
MA0258.1 0.578
MA0259.1 0.361



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: CNhs11188

Novel motif P-value
1 0.981
10 0.213
100 0.96
101 0.702
102 0.866
103 0.636
104 0.877
105 0.918
106 0.65
107 0.638
108 0.631
109 0.16
11 0.216
110 0.135
111 0.0633
112 0.186
113 0.229
114 0.85
115 0.891
116 0.298
117 7.59083e-4
118 0.00494
119 0.57
12 0.154
120 0.492
121 0.885
122 0.49
123 0.019
124 0.194
125 0.677
126 0.16
127 0.699
128 0.919
129 0.884
13 1.1698e-6
130 0.295
131 0.303
132 0.831
133 0.881
134 0.786
135 0.557
136 0.00119
137 0.791
138 0.0499
139 0.567
14 0.159
140 0.67
141 0.763
142 0.82
143 0.0973
144 0.97
145 0.0254
146 0.818
147 0.705
148 0.811
149 0.713
15 0.131
150 0.0635
151 0.406
152 0.0285
153 0.92
154 0.537
155 0.163
156 0.846
157 0.466
158 0.983
159 0.176
160 0.991
161 0.215
162 0.974
163 0.953
164 6.93209e-4
165 0.0934
166 0.696
167 0.852
168 0.59
169 0.0413
17 0.451
18 0.694
19 0.906
2 0.193
20 0.00104
21 0.165
22 0.597
23 0.226
24 0.0398
25 0.353
26 3.37492e-4
27 0.465
28 0.826
29 0.00142
3 0.2
30 0.521
31 0.658
32 0.584
33 0.038
34 0.766
35 0.649
36 0.279
37 0.0745
38 0.453
39 0.536
4 0.547
40 0.285
41 0.321
42 0.224
43 0.668
44 0.631
45 0.897
46 0.445
47 0.722
48 0.396
49 0.744
5 0.299
50 0.592
51 0.822
52 0.973
53 0.0483
54 0.342
55 0.202
56 0.967
57 0.851
58 0.602
59 0.109
6 0.871
60 0.19
61 0.0778
62 0.509
63 0.419
64 0.915
65 0.609
66 0.828
67 0.415
68 0.327
69 0.271
7 0.101
70 0.842
71 0.00949
72 0.359
73 0.0012
74 0.406
75 0.0132
76 0.0666
77 0.981
78 0.0122
79 0.906
8 0.0498
80 0.591
81 0.316
82 0.92
83 0.199
84 0.768
85 0.931
86 0.225
87 0.00248
88 0.462
89 0.609
9 0.759
90 0.696
91 0.836
92 0.942
93 0.501
94 0.722
95 0.00261
96 0.768
97 0.961
98 0.396
99 0.628



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: CNhs11188


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000306 (mouse neonate N16 sample)
0011423 (mouse eyeball- neonate N16 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)