Personal tools

FF:20-12F2

From FANTOM5_SSTAR

Jump to: navigation, search


Name:diencephalon, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10482
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
tissuediencephalon
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  SAMD00005882
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10482 CAGE DRX008949 DRR009823
Accession ID Mm9

Library idBAMCTSS
CNhs10482 DRZ001248 DRZ002631
Accession ID Mm10

Library idBAMCTSS
CNhs10482 DRZ012598 DRZ013981
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

CNhs10482

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.771
10 0
100 0
1000 0
1001 0.124
1002 --0.0751
1003 0.132
1004 0.082
1005 0.0345
1006 0.579
1007 --0.103
1008 0
1009 --0.19
101 --0.0855
1010 0
1011 0.549
1012 0.151
1013 0.272
1014 --0.0851
1015 --0.0251
1016 --0.00199
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.0347
1023 0
1024 0.0114
1025 0
1026 0
1027 0.425
1028 0
1029 0.0344
103 --0.0861
1030 0.082
1031 --0.336
1032 0.395
1033 --0.0665
1034 0
1035 0
1036 --0.133
1037 0
1038 --0.0167
1039 0.129
104 0
1040 --0.189
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: CNhs10482

Jaspar motif P-value
MA0002.2 0.00127
MA0003.1 0.341
MA0004.1 0.466
MA0006.1 0.195
MA0007.1 0.297
MA0009.1 0.754
MA0014.1 0.744
MA0017.1 1.60245e-6
MA0018.2 0.00956
MA0019.1 0.617
MA0024.1 0.0519
MA0025.1 0.00199
MA0027.1 0.0852
MA0028.1 0.0554
MA0029.1 0.896
MA0030.1 0.842
MA0031.1 0.287
MA0035.2 0.0206
MA0038.1 0.599
MA0039.2 0.0341
MA0040.1 0.39
MA0041.1 0.0369
MA0042.1 0.252
MA0043.1 0.0792
MA0046.1 1.97573e-10
MA0047.2 7.2676e-4
MA0048.1 0.0226
MA0050.1 4.72246e-5
MA0051.1 0.00274
MA0052.1 0.741
MA0055.1 0.00489
MA0057.1 0.334
MA0058.1 0.488
MA0059.1 0.158
MA0060.1 0.84
MA0061.1 0.0263
MA0062.2 5.19664e-4
MA0065.2 1.69034e-6
MA0066.1 0.049
MA0067.1 0.489
MA0068.1 0.625
MA0069.1 0.0504
MA0070.1 0.493
MA0071.1 0.147
MA0072.1 0.809
MA0073.1 0.981
MA0074.1 0.178
MA0076.1 0.134
MA0077.1 0.416
MA0078.1 0.891
MA0079.2 0.327
MA0080.2 5.88263e-10
MA0081.1 0.27
MA0083.1 0.00883
MA0084.1 0.815
MA0087.1 0.138
MA0088.1 0.233
MA0090.1 0.125
MA0091.1 0.188
MA0092.1 0.142
MA0093.1 0.527
MA0099.2 0.00499
MA0100.1 0.253
MA0101.1 0.0107
MA0102.2 0.482
MA0103.1 0.211
MA0104.2 0.804
MA0105.1 0.0056
MA0106.1 0.0354
MA0107.1 0.0259
MA0108.2 0.0017
MA0111.1 0.944
MA0112.2 8.2926e-4
MA0113.1 0.515
MA0114.1 6.47116e-6
MA0115.1 1.60724e-5
MA0116.1 0.0922
MA0117.1 0.934
MA0119.1 0.153
MA0122.1 0.702
MA0124.1 0.379
MA0125.1 0.0304
MA0131.1 0.642
MA0135.1 0.352
MA0136.1 1.76918e-12
MA0137.2 0.182
MA0138.2 2.3374e-5
MA0139.1 0.639
MA0140.1 6.45205e-5
MA0141.1 0.00946
MA0142.1 0.162
MA0143.1 0.654
MA0144.1 0.0721
MA0145.1 0.162
MA0146.1 0.0344
MA0147.1 0.647
MA0148.1 7.7385e-4
MA0149.1 0.0797
MA0150.1 0.271
MA0152.1 0.156
MA0153.1 2.11423e-10
MA0154.1 0.0526
MA0155.1 0.401
MA0156.1 1.65051e-8
MA0157.1 0.129
MA0159.1 0.00323
MA0160.1 0.0148
MA0162.1 0.207
MA0163.1 4.89598e-4
MA0164.1 0.871
MA0258.1 0.0189
MA0259.1 0.767



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: CNhs10482

Novel motif P-value
1 0.207
10 0.0395
100 0.342
101 0.757
102 0.984
103 0.0761
104 0.873
105 0.551
106 0.0575
107 0.158
108 0.528
109 0.0141
11 0.0926
110 0.0469
111 0.234
112 0.00717
113 0.473
114 0.444
115 0.889
116 0.221
117 0.00294
118 0.359
119 0.218
12 0.997
120 0.838
121 0.72
122 0.638
123 5.5466e-4
124 0.038
125 0.197
126 0.0317
127 0.222
128 0.0528
129 0.343
13 8.83796e-8
130 0.226
131 0.546
132 0.748
133 0.613
134 0.0915
135 0.117
136 0.0788
137 0.797
138 0.892
139 0.239
14 0.805
140 0.0713
141 0.97
142 0.817
143 0.299
144 0.706
145 1.5917e-4
146 0.351
147 0.25
148 0.878
149 0.971
15 0.205
150 0.0639
151 0.988
152 0.137
153 0.796
154 0.788
155 0.318
156 0.00597
157 0.127
158 0.31
159 0.937
160 0.206
161 0.149
162 0.649
163 0.69
164 0.0382
165 0.219
166 0.598
167 0.686
168 0.573
169 0.00302
17 0.0709
18 0.919
19 0.114
2 0.63
20 0.0214
21 0.192
22 0.167
23 0.78
24 0.0657
25 0.729
26 2.05798e-8
27 0.398
28 0.795
29 0.0307
3 0.069
30 0.738
31 0.666
32 0.597
33 0.154
34 0.757
35 0.699
36 0.179
37 0.0327
38 0.495
39 0.348
4 0.222
40 0.0896
41 0.523
42 0.161
43 0.122
44 0.502
45 0.78
46 0.0817
47 0.464
48 0.325
49 0.176
5 0.156
50 0.271
51 0.795
52 0.396
53 0.386
54 0.959
55 0.807
56 0.554
57 0.478
58 0.331
59 0.143
6 0.894
60 0.058
61 0.0452
62 0.233
63 0.201
64 0.76
65 0.445
66 0.951
67 0.856
68 0.465
69 0.502
7 0.0177
70 0.128
71 0.00258
72 0.502
73 0.0517
74 0.996
75 0.0484
76 0.315
77 0.489
78 0.00195
79 0.318
8 0.0599
80 0.62
81 0.769
82 0.333
83 0.245
84 0.849
85 0.321
86 0.145
87 0.334
88 0.516
89 0.803
9 0.519
90 0.126
91 0.0939
92 0.329
93 0.164
94 0.814
95 0.0519
96 0.301
97 0.971
98 0.752
99 0.505



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: CNhs10482


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)
0001894 (diencephalon)
0000479 (tissue)
0004121 (ectoderm-derived structure)
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)
0002780 (regional part of forebrain)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001890 (forebrain)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0010193 (human diencephalon - 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:0006222 (future diencephalon)
UBERON:0010316 (germ layer / neural crest)