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FF:31-12G4

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Name:eyeball, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10484
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 stageadult
sexmale
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  SAMD00004868
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10484 CAGE DRX008954 DRR009828
Accession ID Mm9

Library idBAMCTSS
CNhs10484 DRZ001253 DRZ002636
Accession ID Mm10

Library idBAMCTSS
CNhs10484 DRZ012603 DRZ013986
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs10484

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.153
10 0
100 0
1000 0.424
1001 0.341
1002 0.138
1003 0.208
1004 0
1005 0.153
1006 0.314
1007 -0.0381
1008 0
1009 0.0225
101 -0.0737
1010 0
1011 0.0569
1012 0.0829
1013 0.339
1014 -0.0851
1015 -0.303
1016 -0.2
1017 0
1018 0.0829
1019 1.677
102 0
1020 0
1021 0
1022 0.495
1023 0
1024 0.0051
1025 0
1026 0
1027 0.307
1028 0
1029 0.217
103 -0.0638
1030 0
1031 -0.315
1032 -0.101
1033 0
1034 0.343
1035 0.0829
1036 -0.365
1037 1.173
1038 -0.0456
1039 0.284
104 0
1040 -0.0036
1041 0.0829



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: CNhs10484
Jaspar motif P-value
MA0002.2 0.931
MA0003.1 0.0558
MA0004.1 0.582
MA0006.1 0.948
MA0007.1 0.668
MA0009.1 0.713
MA0014.1 0.644
MA0017.1 0.389
MA0018.2 0.468
MA0019.1 0.951
MA0024.1 1.27734e-7
MA0025.1 0.0181
MA0027.1 0.0384
MA0028.1 1.49023e-4
MA0029.1 0.94
MA0030.1 0.274
MA0031.1 0.306
MA0035.2 0.464
MA0038.1 0.0252
MA0039.2 0.116
MA0040.1 0.608
MA0041.1 0.504
MA0042.1 0.0888
MA0043.1 0.353
MA0046.1 1.98545e-14
MA0047.2 0.763
MA0048.1 4.65688e-4
MA0050.1 0.938
MA0051.1 0.648
MA0052.1 6.30971e-8
MA0055.1 0.00698
MA0057.1 0.747
MA0058.1 0.55
MA0059.1 0.0447
MA0060.1 6.38549e-4
MA0061.1 1.61497e-4
MA0062.2 1.51531e-7
MA0065.2 0.0412
MA0066.1 0.686
MA0067.1 0.212
MA0068.1 0.011
MA0069.1 0.903
MA0070.1 0.808
MA0071.1 0.0127
MA0072.1 1.08952e-9
MA0073.1 0.578
MA0074.1 0.517
MA0076.1 1.41925e-4
MA0077.1 0.901
MA0078.1 0.116
MA0079.2 0.231
MA0080.2 7.09869e-6
MA0081.1 0.00375
MA0083.1 0.713
MA0084.1 0.618
MA0087.1 0.0299
MA0088.1 0.706
MA0090.1 0.276
MA0091.1 0.431
MA0092.1 0.929
MA0093.1 0.699
MA0099.2 0.759
MA0100.1 0.00791
MA0101.1 0.00612
MA0102.2 0.786
MA0103.1 0.00183
MA0104.2 0.175
MA0105.1 1.67433e-8
MA0106.1 0.549
MA0107.1 0.0223
MA0108.2 0.864
MA0111.1 0.342
MA0112.2 0.666
MA0113.1 0.216
MA0114.1 0.679
MA0115.1 0.333
MA0116.1 0.247
MA0117.1 0.489
MA0119.1 0.236
MA0122.1 0.469
MA0124.1 0.137
MA0125.1 0.253
MA0131.1 0.345
MA0135.1 0.196
MA0136.1 4.62911e-8
MA0137.2 0.0433
MA0138.2 6.86839e-4
MA0139.1 0.979
MA0140.1 0.928
MA0141.1 0.876
MA0142.1 0.858
MA0143.1 0.204
MA0144.1 0.0424
MA0145.1 0.141
MA0146.1 0.682
MA0147.1 0.0328
MA0148.1 0.332
MA0149.1 0.926
MA0150.1 0.0189
MA0152.1 0.962
MA0153.1 8.03714e-12
MA0154.1 0.61
MA0155.1 0.678
MA0156.1 1.48912e-6
MA0157.1 0.91
MA0159.1 0.437
MA0160.1 0.0139
MA0162.1 0.714
MA0163.1 2.73653e-4
MA0164.1 0.417
MA0258.1 0.139
MA0259.1 0.396



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: CNhs10484
Novel motif P-value
1 0.658
10 0.292
100 0.819
101 0.84
102 0.794
103 0.921
104 0.611
105 0.507
106 0.764
107 0.755
108 0.972
109 0.761
11 0.965
110 0.411
111 0.538
112 0.859
113 0.289
114 0.287
115 0.639
116 0.138
117 0.00583
118 0.0212
119 0.111
12 0.0416
120 0.219
121 0.458
122 0.532
123 0.298
124 0.195
125 0.831
126 0.406
127 0.808
128 0.756
129 0.546
13 0.214
130 0.607
131 0.759
132 0.585
133 0.785
134 0.728
135 0.109
136 0.156
137 0.838
138 0.13
139 0.34
14 0.12
140 0.777
141 0.69
142 0.15
143 0.0196
144 0.512
145 0.0596
146 0.339
147 0.568
148 0.708
149 0.74
15 0.817
150 0.318
151 0.0571
152 0.671
153 0.869
154 0.751
155 0.212
156 0.892
157 0.93
158 0.927
159 0.63
160 0.799
161 0.378
162 0.658
163 0.352
164 0.0641
165 0.51
166 0.813
167 0.847
168 0.731
169 0.569
17 0.518
18 0.369
19 0.339
2 0.0962
20 0.0458
21 0.31
22 0.302
23 0.217
24 0.514
25 0.944
26 0.0744
27 0.233
28 0.578
29 0.0735
3 0.625
30 0.23
31 0.767
32 0.698
33 0.138
34 0.873
35 0.568
36 0.25
37 0.735
38 0.738
39 0.863
4 0.328
40 0.924
41 0.739
42 0.513
43 0.896
44 0.954
45 0.236
46 0.662
47 0.672
48 0.88
49 0.775
5 0.981
50 0.921
51 0.707
52 0.341
53 0.0971
54 0.277
55 0.242
56 0.611
57 0.495
58 0.731
59 0.276
6 0.816
60 0.596
61 0.189
62 0.775
63 0.633
64 0.859
65 0.817
66 0.528
67 0.713
68 0.418
69 0.124
7 0.578
70 0.298
71 0.0806
72 0.9
73 0.116
74 0.746
75 0.0435
76 0.0388
77 0.339
78 0.839
79 0.948
8 0.29
80 0.403
81 0.2
82 0.437
83 0.998
84 0.0715
85 0.28
86 0.444
87 0.914
88 0.703
89 0.741
9 0.5
90 0.373
91 0.288
92 0.535
93 0.579
94 0.486
95 0.0581
96 0.986
97 0.742
98 0.0934
99 0.965



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: CNhs10484


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)
0007023 (adult 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)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011309 (mouse eyeball- adult 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)