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FF:12-14D5

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Name:cortex, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10473
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
tissuecortex
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  SAMD00005968
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10473 CAGE DRX008947 DRR009821
Accession ID Mm9

Library idBAMCTSS
CNhs10473 DRZ001246 DRZ002629
Accession ID Mm10

Library idBAMCTSS
CNhs10473 DRZ012596 DRZ013979
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

CNhs10473

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.839
10 0
100 0
1000 0
1001 0
1002 --0.0592
1003 0.265
1004 0
1005 0.13
1006 0.739
1007 --0.0572
1008 0
1009 --0.0774
101 --0.05
1010 0
1011 0.985
1012 0.34
1013 0.147
1014 --0.0155
1015 --0.133
1016 --0.166
1017 0
1018 0
1019 0
102 0
1020 0
1021 --0.0487
1022 --0.016
1023 0
1024 0
1025 --0.0312
1026 0
1027 0.375
1028 0
1029 --0.0369
103 --0.0861
1030 0
1031 --0.502
1032 0.0951
1033 0.0696
1034 0
1035 0.0106
1036 --0.255
1037 0
1038 0.0186
1039 0.092
104 0
1040 --0.165
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: CNhs10473

Jaspar motif P-value
MA0002.2 0.00288
MA0003.1 0.298
MA0004.1 0.596
MA0006.1 0.137
MA0007.1 0.382
MA0009.1 0.792
MA0014.1 0.711
MA0017.1 7.90756e-7
MA0018.2 0.00495
MA0019.1 0.312
MA0024.1 0.0641
MA0025.1 0.00195
MA0027.1 0.0669
MA0028.1 0.0928
MA0029.1 0.964
MA0030.1 0.902
MA0031.1 0.183
MA0035.2 0.0157
MA0038.1 0.397
MA0039.2 0.0312
MA0040.1 0.128
MA0041.1 0.274
MA0042.1 0.35
MA0043.1 0.0695
MA0046.1 3.20088e-10
MA0047.2 4.70009e-4
MA0048.1 0.0549
MA0050.1 1.95729e-4
MA0051.1 0.0278
MA0052.1 0.459
MA0055.1 0.0112
MA0057.1 0.522
MA0058.1 0.456
MA0059.1 0.147
MA0060.1 0.651
MA0061.1 0.035
MA0062.2 0.0033
MA0065.2 1.03847e-6
MA0066.1 0.032
MA0067.1 0.518
MA0068.1 0.615
MA0069.1 0.0531
MA0070.1 0.498
MA0071.1 0.0195
MA0072.1 0.138
MA0073.1 0.856
MA0074.1 0.132
MA0076.1 0.223
MA0077.1 0.675
MA0078.1 0.704
MA0079.2 0.376
MA0080.2 1.84505e-9
MA0081.1 0.321
MA0083.1 0.0231
MA0084.1 0.832
MA0087.1 0.485
MA0088.1 0.346
MA0090.1 0.157
MA0091.1 0.165
MA0092.1 0.271
MA0093.1 0.638
MA0099.2 0.0116
MA0100.1 0.317
MA0101.1 0.0218
MA0102.2 0.51
MA0103.1 0.205
MA0104.2 0.886
MA0105.1 0.0117
MA0106.1 0.0518
MA0107.1 0.0423
MA0108.2 7.43124e-4
MA0111.1 0.917
MA0112.2 5.77001e-4
MA0113.1 0.355
MA0114.1 4.51823e-6
MA0115.1 2.2026e-5
MA0116.1 0.0683
MA0117.1 0.908
MA0119.1 0.11
MA0122.1 0.907
MA0124.1 0.522
MA0125.1 0.0383
MA0131.1 0.778
MA0135.1 0.496
MA0136.1 8.37649e-11
MA0137.2 0.283
MA0138.2 9.61154e-4
MA0139.1 0.643
MA0140.1 2.20598e-4
MA0141.1 4.62552e-4
MA0142.1 0.473
MA0143.1 0.623
MA0144.1 0.148
MA0145.1 0.138
MA0146.1 0.0178
MA0147.1 0.765
MA0148.1 2.81477e-4
MA0149.1 0.0903
MA0150.1 0.209
MA0152.1 0.302
MA0153.1 8.39011e-11
MA0154.1 0.0472
MA0155.1 0.338
MA0156.1 2.94094e-7
MA0157.1 0.11
MA0159.1 0.00121
MA0160.1 0.00331
MA0162.1 0.145
MA0163.1 6.3365e-4
MA0164.1 0.957
MA0258.1 0.0168
MA0259.1 0.921



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: CNhs10473

Novel motif P-value
1 0.215
10 0.0492
100 0.39
101 0.698
102 0.925
103 0.0467
104 0.94
105 0.881
106 0.059
107 0.195
108 0.599
109 0.00468
11 0.086
110 0.0612
111 0.118
112 0.00607
113 0.38
114 0.38
115 0.975
116 0.302
117 0.00367
118 0.373
119 0.249
12 0.993
120 0.921
121 0.517
122 0.772
123 0.0026
124 0.0629
125 0.223
126 0.0206
127 0.361
128 0.038
129 0.223
13 1.43024e-7
130 0.112
131 0.622
132 0.756
133 0.833
134 0.106
135 0.373
136 0.063
137 0.692
138 0.874
139 0.305
14 0.952
140 0.0479
141 0.667
142 0.837
143 0.391
144 0.731
145 3.06758e-4
146 0.279
147 0.256
148 0.399
149 0.553
15 0.195
150 0.0579
151 0.826
152 0.125
153 0.831
154 0.983
155 0.294
156 0.00336
157 0.289
158 0.131
159 0.902
160 0.17
161 0.093
162 0.67
163 0.699
164 0.0699
165 0.0916
166 0.884
167 0.674
168 0.549
169 0.00363
17 0.0497
18 0.756
19 0.0911
2 0.775
20 0.0483
21 0.244
22 0.142
23 0.731
24 0.0315
25 0.779
26 4.52714e-7
27 0.53
28 0.712
29 0.0234
3 0.0406
30 0.829
31 0.967
32 0.55
33 0.216
34 0.679
35 0.895
36 0.25
37 0.0203
38 0.551
39 0.252
4 0.172
40 0.12
41 0.524
42 0.15
43 0.141
44 0.398
45 0.717
46 0.133
47 0.463
48 0.323
49 0.213
5 0.186
50 0.243
51 0.777
52 0.25
53 0.434
54 0.92
55 0.903
56 0.468
57 0.657
58 0.364
59 0.114
6 0.952
60 0.0368
61 0.028
62 0.284
63 0.156
64 0.632
65 0.464
66 0.769
67 0.614
68 0.789
69 0.15
7 0.016
70 0.0963
71 0.00606
72 0.59
73 0.0339
74 0.893
75 0.0427
76 0.501
77 0.307
78 0.00306
79 0.633
8 0.0648
80 0.626
81 0.904
82 0.238
83 0.0947
84 0.73
85 0.163
86 0.195
87 0.16
88 0.467
89 0.798
9 0.506
90 0.215
91 0.0789
92 0.258
93 0.195
94 0.806
95 0.0262
96 0.45
97 0.972
98 0.496
99 0.429



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: CNhs10473


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)
0000956 (cerebral cortex)
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)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011525 (cortex- 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:0010316 (germ layer / neural crest)