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FF:16-22A4

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Name:corpora quadrigemina, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10501
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
tissuecorpora quadrigemina
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  SAMD00005905
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10501 CAGE DRX008944 DRR009818
Accession ID Mm9

Library idBAMCTSS
CNhs10501 DRZ001243 DRZ002626
Accession ID Mm10

Library idBAMCTSS
CNhs10501 DRZ012593 DRZ013976
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
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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

CNhs10501

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.774
10 0
100 0
1000 0
1001 0.0707
1002 --0.0795
1003 0.0715
1004 0
1005 0
1006 0.677
1007 --0.0857
1008 0
1009 --0.0572
101 --0.0525
1010 0
1011 0.477
1012 0.204
1013 0.249
1014 --0.0245
1015 --0.0749
1016 --0.127
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.0775
1023 0
1024 0.103
1025 0
1026 0
1027 0.375
1028 0
1029 0.0464
103 --0.0861
1030 0
1031 --0.327
1032 0.43
1033 --0.0665
1034 0
1035 0
1036 --0.179
1037 0
1038 --0.188
1039 0.219
104 0
1040 --0.181
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: CNhs10501

Jaspar motif P-value
MA0002.2 0.0015
MA0003.1 0.321
MA0004.1 0.509
MA0006.1 0.182
MA0007.1 0.334
MA0009.1 0.843
MA0014.1 0.747
MA0017.1 3.45883e-6
MA0018.2 0.0155
MA0019.1 0.527
MA0024.1 0.0613
MA0025.1 5.69827e-4
MA0027.1 0.0785
MA0028.1 0.112
MA0029.1 0.899
MA0030.1 0.937
MA0031.1 0.254
MA0035.2 0.0286
MA0038.1 0.393
MA0039.2 0.0254
MA0040.1 0.377
MA0041.1 0.0691
MA0042.1 0.209
MA0043.1 0.028
MA0046.1 4.26383e-11
MA0047.2 2.02389e-4
MA0048.1 0.032
MA0050.1 9.55222e-5
MA0051.1 0.00102
MA0052.1 0.493
MA0055.1 0.0083
MA0057.1 0.349
MA0058.1 0.501
MA0059.1 0.152
MA0060.1 0.931
MA0061.1 0.0281
MA0062.2 0.00287
MA0065.2 2.47898e-6
MA0066.1 0.0361
MA0067.1 0.442
MA0068.1 0.336
MA0069.1 0.0648
MA0070.1 0.339
MA0071.1 0.168
MA0072.1 0.699
MA0073.1 0.797
MA0074.1 0.134
MA0076.1 0.277
MA0077.1 0.425
MA0078.1 0.803
MA0079.2 0.405
MA0080.2 8.66167e-10
MA0081.1 0.231
MA0083.1 0.00407
MA0084.1 0.674
MA0087.1 0.0976
MA0088.1 0.375
MA0090.1 0.123
MA0091.1 0.0926
MA0092.1 0.159
MA0093.1 0.58
MA0099.2 0.00129
MA0100.1 0.278
MA0101.1 0.0136
MA0102.2 0.556
MA0103.1 0.179
MA0104.2 0.844
MA0105.1 0.00674
MA0106.1 0.0548
MA0107.1 0.03
MA0108.2 2.4474e-4
MA0111.1 0.895
MA0112.2 0.00109
MA0113.1 0.363
MA0114.1 1.09435e-5
MA0115.1 3.14388e-5
MA0116.1 0.0669
MA0117.1 0.964
MA0119.1 0.13
MA0122.1 0.959
MA0124.1 0.509
MA0125.1 0.0364
MA0131.1 0.742
MA0135.1 0.315
MA0136.1 9.90414e-12
MA0137.2 0.314
MA0138.2 9.05945e-5
MA0139.1 0.601
MA0140.1 7.76019e-5
MA0141.1 0.0122
MA0142.1 0.138
MA0143.1 0.623
MA0144.1 0.0859
MA0145.1 0.144
MA0146.1 0.0377
MA0147.1 0.682
MA0148.1 6.90018e-4
MA0149.1 0.158
MA0150.1 0.156
MA0152.1 0.246
MA0153.1 5.98758e-12
MA0154.1 0.0321
MA0155.1 0.412
MA0156.1 1.36334e-7
MA0157.1 0.176
MA0159.1 0.00323
MA0160.1 0.0151
MA0162.1 0.238
MA0163.1 9.61734e-4
MA0164.1 0.882
MA0258.1 0.0184
MA0259.1 0.829



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: CNhs10501

Novel motif P-value
1 0.234
10 0.0523
100 0.38
101 0.827
102 0.933
103 0.104
104 0.962
105 0.581
106 0.029
107 0.109
108 0.611
109 0.0134
11 0.0918
110 0.0472
111 0.281
112 0.0155
113 0.507
114 0.516
115 0.686
116 0.175
117 0.00413
118 0.339
119 0.237
12 0.846
120 1
121 0.673
122 0.61
123 3.04315e-4
124 0.0427
125 0.154
126 0.0208
127 0.244
128 0.0408
129 0.318
13 1.74881e-7
130 0.136
131 0.421
132 0.671
133 0.745
134 0.112
135 0.13
136 0.0559
137 0.703
138 0.969
139 0.216
14 0.766
140 0.022
141 0.972
142 0.531
143 0.251
144 0.734
145 2.06086e-4
146 0.3
147 0.351
148 0.723
149 0.924
15 0.198
150 0.0702
151 0.873
152 0.0926
153 0.781
154 0.726
155 0.463
156 0.00522
157 0.254
158 0.389
159 0.546
160 0.213
161 0.166
162 0.696
163 0.565
164 0.0451
165 0.175
166 0.684
167 0.729
168 0.648
169 0.00435
17 0.0478
18 0.97
19 0.136
2 0.718
20 0.0239
21 0.158
22 0.174
23 0.667
24 0.057
25 0.771
26 3.87928e-9
27 0.399
28 0.752
29 0.0396
3 0.0957
30 0.845
31 0.75
32 0.622
33 0.168
34 0.781
35 0.783
36 0.269
37 0.0316
38 0.528
39 0.314
4 0.237
40 0.104
41 0.407
42 0.228
43 0.139
44 0.369
45 0.73
46 0.0509
47 0.477
48 0.337
49 0.198
5 0.189
50 0.264
51 0.82
52 0.28
53 0.402
54 0.945
55 0.947
56 0.499
57 0.515
58 0.365
59 0.111
6 0.945
60 0.0333
61 0.0671
62 0.237
63 0.164
64 0.654
65 0.406
66 0.871
67 0.785
68 0.891
69 0.514
7 0.0193
70 0.106
71 0.00219
72 0.616
73 0.039
74 0.871
75 0.0552
76 0.374
77 0.357
78 0.00224
79 0.411
8 0.0618
80 0.747
81 0.769
82 0.349
83 0.145
84 0.848
85 0.24
86 0.136
87 0.178
88 0.475
89 0.729
9 0.49
90 0.148
91 0.0432
92 0.34
93 0.0853
94 0.773
95 0.0434
96 0.496
97 0.962
98 0.708
99 0.521



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: CNhs10501


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)
0000955 (brain)
0002259 (corpora quadrigemina)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002950 (regional part of midbrain)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001891 (midbrain)
0002314 (midbrain tectum)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011283 (mouse corpora quadrigemina- 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:0006777 (tectal plate)
UBERON:0010316 (germ layer / neural crest)