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FF:1551-44G8

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Name:eyeball, neonate N02
Species:Mouse (Mus musculus)
Library ID:CNhs11205
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 stage2 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  SAMD00005344
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11205 CAGE DRX008961 DRR009835
Accession ID Mm9

Library idBAMCTSS
CNhs11205 DRZ001260 DRZ002643
Accession ID Mm10

Library idBAMCTSS
CNhs11205 DRZ012610 DRZ013993
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

CNhs11205

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.171
10 0
100 0.138
1000 0.0567
1001 0.197
1002 0.274
1003 0.0359
1004 0.123
1005 0
1006 0.255
1007 0.0605
1008 0
1009 0.0059
101 0.0024
1010 0
1011 0.107
1012 0.108
1013 --0.121
1014 0.167
1015 0.164
1016 0.223
1017 0
1018 0.0389
1019 0
102 0
1020 0
1021 0.0896
1022 0.0324
1023 0
1024 5.312076e-4
1025 0
1026 0.0746
1027 0.924
1028 0
1029 0.209
103 0.38
1030 0
1031 0.278
1032 0.0575
1033 0.0104
1034 0
1035 0.0389
1036 --0.106
1037 0
1038 0.121
1039 --0.135
104 0
1040 --0.073
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: CNhs11205

Jaspar motif P-value
MA0002.2 1.4735e-5
MA0003.1 0.235
MA0004.1 0.351
MA0006.1 0.289
MA0007.1 0.211
MA0009.1 0.147
MA0014.1 0.18
MA0017.1 1.19383e-7
MA0018.2 0.203
MA0019.1 0.548
MA0024.1 0.0311
MA0025.1 0.102
MA0027.1 0.218
MA0028.1 0.222
MA0029.1 0.462
MA0030.1 0.884
MA0031.1 0.244
MA0035.2 0.00583
MA0038.1 9.23695e-4
MA0039.2 0.0539
MA0040.1 0.101
MA0041.1 0.453
MA0042.1 0.909
MA0043.1 0.821
MA0046.1 1.19065e-21
MA0047.2 1.26985e-4
MA0048.1 0.483
MA0050.1 2.33294e-4
MA0051.1 0.00434
MA0052.1 0.236
MA0055.1 0.723
MA0057.1 0.158
MA0058.1 0.345
MA0059.1 0.266
MA0060.1 5.65431e-9
MA0061.1 0.0223
MA0062.2 0.00333
MA0065.2 5.12979e-7
MA0066.1 0.179
MA0067.1 0.948
MA0068.1 0.0333
MA0069.1 0.0178
MA0070.1 0.533
MA0071.1 0.952
MA0072.1 0.0236
MA0073.1 0.608
MA0074.1 0.363
MA0076.1 0.588
MA0077.1 0.0166
MA0078.1 0.738
MA0079.2 0.541
MA0080.2 1.17088e-12
MA0081.1 0.039
MA0083.1 0.739
MA0084.1 0.0758
MA0087.1 0.449
MA0088.1 0.0829
MA0090.1 0.628
MA0091.1 0.0831
MA0092.1 0.418
MA0093.1 0.37
MA0099.2 2.10329e-5
MA0100.1 0.56
MA0101.1 0.0465
MA0102.2 0.253
MA0103.1 0.00345
MA0104.2 0.827
MA0105.1 0.00163
MA0106.1 0.239
MA0107.1 0.0525
MA0108.2 0.0013
MA0111.1 0.961
MA0112.2 3.89883e-4
MA0113.1 0.148
MA0114.1 1.44287e-6
MA0115.1 5.81015e-6
MA0116.1 0.00789
MA0117.1 0.683
MA0119.1 0.0811
MA0122.1 0.873
MA0124.1 0.537
MA0125.1 4.57794e-4
MA0131.1 0.724
MA0135.1 0.802
MA0136.1 2.99219e-15
MA0137.2 0.00322
MA0138.2 0.355
MA0139.1 0.0752
MA0140.1 5.25301e-4
MA0141.1 5.49875e-4
MA0142.1 0.351
MA0143.1 0.126
MA0144.1 0.0117
MA0145.1 0.0613
MA0146.1 0.0762
MA0147.1 0.593
MA0148.1 2.67633e-4
MA0149.1 0.0255
MA0150.1 0.0411
MA0152.1 0.339
MA0153.1 1.92566e-25
MA0154.1 0.00487
MA0155.1 0.943
MA0156.1 1.65215e-7
MA0157.1 0.0992
MA0159.1 0.00822
MA0160.1 0.00448
MA0162.1 0.351
MA0163.1 3.44755e-4
MA0164.1 0.802
MA0258.1 0.0166
MA0259.1 0.897



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: CNhs11205

Novel motif P-value
1 0.113
10 0.0816
100 0.824
101 0.556
102 0.641
103 0.0109
104 0.63
105 0.573
106 0.0756
107 0.21
108 0.906
109 0.0085
11 0.0451
110 0.0931
111 5.23853e-4
112 0.00289
113 0.92
114 0.0214
115 0.98
116 0.275
117 0.0141
118 0.295
119 0.103
12 0.304
120 0.213
121 0.598
122 0.811
123 0.547
124 0.703
125 0.0535
126 0.167
127 0.0612
128 0.126
129 0.311
13 0.00279
130 0.97
131 0.473
132 0.577
133 0.684
134 0.584
135 0.23
136 0.0981
137 0.329
138 0.179
139 0.0333
14 0.911
140 0.0927
141 0.0257
142 0.718
143 0.149
144 0.786
145 0.05
146 0.447
147 0.717
148 0.332
149 0.183
15 0.0626
150 0.241
151 0.393
152 0.049
153 0.639
154 0.977
155 0.187
156 0.617
157 0.68
158 0.18
159 0.417
160 0.344
161 0.195
162 0.826
163 0.582
164 0.00458
165 0.00809
166 0.705
167 0.711
168 0.762
169 0.00368
17 0.0452
18 0.477
19 0.301
2 0.582
20 0.496
21 0.232
22 0.242
23 0.387
24 0.0773
25 0.482
26 0.012
27 0.447
28 0.312
29 0.0437
3 0.0587
30 0.9
31 0.535
32 0.303
33 0.239
34 0.761
35 0.599
36 0.269
37 0.0209
38 0.262
39 0.389
4 0.604
40 0.307
41 0.364
42 0.231
43 0.179
44 0.109
45 0.52
46 0.127
47 0.0848
48 0.0826
49 0.162
5 0.132
50 0.696
51 0.582
52 0.353
53 0.866
54 0.685
55 0.466
56 0.312
57 0.647
58 0.211
59 0.033
6 0.608
60 0.0393
61 0.244
62 0.0799
63 0.0803
64 0.496
65 0.157
66 0.563
67 0.969
68 0.131
69 0.984
7 0.0674
70 0.00804
71 0.0135
72 0.279
73 0.0184
74 0.285
75 0.0241
76 0.59
77 0.166
78 0.0313
79 0.0908
8 0.0362
80 0.332
81 0.27
82 0.00952
83 0.51
84 0.168
85 0.0466
86 0.117
87 0.178
88 0.466
89 0.0824
9 0.613
90 0.0875
91 0.741
92 0.063
93 0.238
94 0.311
95 0.0213
96 0.451
97 0.923
98 0.372
99 0.504



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: CNhs11205


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)
0000307 (mouse neonate N2 sample)
0011281 (mouse eyeball- neonate N02 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)


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