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FF:13-16E8

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Name:hippocampus, adult, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuehippocampus
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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs10478

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.782
10 0
100 0
1000 --0.0205
1001 0.0406
1002 --0.0856
1003 0.26
1004 0
1005 0.106
1006 0.575
1007 --0.0278
1008 0
1009 --0.162
101 --0.036
1010 0
1011 0.835
1012 0.265
1013 0.12
1014 --0.0874
1015 --0.0888
1016 --0.227
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.0285
1023 0
1024 0.0129
1025 0
1026 0
1027 0.368
1028 0
1029 0.172
103 --0.0848
1030 0
1031 --0.476
1032 0.227
1033 0.0312
1034 0
1035 0
1036 --0.195
1037 0
1038 --0.0319
1039 0.152
104 0
1040 --0.163
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
no result for this sample


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: CNhs10478

Jaspar motif P-value
MA0002.2 0.00627
MA0003.1 0.324
MA0004.1 0.533
MA0006.1 0.133
MA0007.1 0.568
MA0009.1 0.482
MA0014.1 0.716
MA0017.1 6.27848e-7
MA0018.2 0.0256
MA0019.1 0.278
MA0024.1 0.0251
MA0025.1 0.00664
MA0027.1 0.053
MA0028.1 0.093
MA0029.1 0.861
MA0030.1 0.419
MA0031.1 0.268
MA0035.2 0.0235
MA0038.1 0.415
MA0039.2 0.0324
MA0040.1 0.332
MA0041.1 0.0624
MA0042.1 0.168
MA0043.1 0.109
MA0046.1 9.59254e-10
MA0047.2 1.66036e-4
MA0048.1 0.0675
MA0050.1 2.8484e-4
MA0051.1 0.0516
MA0052.1 0.832
MA0055.1 0.0229
MA0057.1 0.437
MA0058.1 0.422
MA0059.1 0.163
MA0060.1 0.759
MA0061.1 0.0351
MA0062.2 0.00471
MA0065.2 6.75888e-7
MA0066.1 0.0147
MA0067.1 0.689
MA0068.1 0.732
MA0069.1 0.0585
MA0070.1 0.271
MA0071.1 0.0267
MA0072.1 0.138
MA0073.1 0.997
MA0074.1 0.108
MA0076.1 0.247
MA0077.1 0.301
MA0078.1 0.683
MA0079.2 0.338
MA0080.2 2.12652e-9
MA0081.1 0.362
MA0083.1 0.015
MA0084.1 0.835
MA0087.1 0.236
MA0088.1 0.44
MA0090.1 0.218
MA0091.1 0.219
MA0092.1 0.247
MA0093.1 0.587
MA0099.2 0.00273
MA0100.1 0.291
MA0101.1 0.0174
MA0102.2 0.475
MA0103.1 0.126
MA0104.2 0.885
MA0105.1 0.00894
MA0106.1 0.0592
MA0107.1 0.0339
MA0108.2 0.00152
MA0111.1 0.967
MA0112.2 5.47942e-4
MA0113.1 0.461
MA0114.1 6.3393e-6
MA0115.1 6.27948e-5
MA0116.1 0.0737
MA0117.1 0.907
MA0119.1 0.125
MA0122.1 0.96
MA0124.1 0.396
MA0125.1 0.0247
MA0131.1 0.741
MA0135.1 0.352
MA0136.1 3.96042e-11
MA0137.2 0.141
MA0138.2 6.55491e-4
MA0139.1 0.598
MA0140.1 1.98063e-4
MA0141.1 3.16374e-4
MA0142.1 0.486
MA0143.1 0.716
MA0144.1 0.101
MA0145.1 0.127
MA0146.1 0.0161
MA0147.1 0.762
MA0148.1 9.25497e-5
MA0149.1 0.126
MA0150.1 0.131
MA0152.1 0.213
MA0153.1 3.38615e-10
MA0154.1 0.0479
MA0155.1 0.355
MA0156.1 3.29603e-7
MA0157.1 0.0874
MA0159.1 0.00109
MA0160.1 0.00189
MA0162.1 0.143
MA0163.1 3.08128e-4
MA0164.1 0.788
MA0258.1 0.0162
MA0259.1 0.923



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: CNhs10478

Novel motif P-value
1 0.194
10 0.0504
100 0.375
101 0.676
102 0.912
103 0.0492
104 0.896
105 0.82
106 0.0421
107 0.22
108 0.66
109 0.00571
11 0.0702
110 0.0497
111 0.106
112 0.00365
113 0.44
114 0.386
115 0.948
116 0.22
117 0.0041
118 0.373
119 0.215
12 0.872
120 0.893
121 0.423
122 0.715
123 0.00317
124 0.066
125 0.144
126 0.0209
127 0.32
128 0.0266
129 0.265
13 4.82902e-7
130 0.12
131 0.64
132 0.761
133 0.993
134 0.0962
135 0.243
136 0.064
137 0.714
138 0.855
139 0.402
14 0.959
140 0.0131
141 0.585
142 0.698
143 0.223
144 0.877
145 9.41431e-4
146 0.504
147 0.264
148 0.613
149 0.621
15 0.223
150 0.0485
151 0.772
152 0.0816
153 0.959
154 0.99
155 0.258
156 0.00633
157 0.354
158 0.115
159 0.638
160 0.142
161 0.0818
162 0.515
163 0.834
164 0.0617
165 0.0513
166 0.693
167 0.834
168 0.695
169 0.00408
17 0.0441
18 0.657
19 0.0919
2 0.864
20 0.0532
21 0.241
22 0.143
23 0.66
24 0.055
25 0.756
26 2.80597e-7
27 0.616
28 0.654
29 0.035
3 0.0411
30 0.715
31 0.944
32 0.514
33 0.202
34 0.78
35 0.931
36 0.348
37 0.0276
38 0.508
39 0.249
4 0.143
40 0.127
41 0.51
42 0.187
43 0.138
44 0.33
45 0.754
46 0.103
47 0.386
48 0.341
49 0.228
5 0.167
50 0.214
51 0.734
52 0.25
53 0.443
54 0.901
55 0.921
56 0.488
57 0.764
58 0.305
59 0.098
6 0.948
60 0.0364
61 0.0388
62 0.258
63 0.162
64 0.677
65 0.415
66 0.695
67 0.6
68 0.858
69 0.312
7 0.0207
70 0.105
71 0.00597
72 0.604
73 0.0269
74 0.861
75 0.044
76 0.473
77 0.342
78 0.00159
79 0.991
8 0.0731
80 0.472
81 0.974
82 0.232
83 0.165
84 0.933
85 0.202
86 0.184
87 0.197
88 0.468
89 0.796
9 0.509
90 0.136
91 0.0822
92 0.229
93 0.0711
94 0.72
95 0.0212
96 0.426
97 0.868
98 0.564
99 0.37



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: CNhs10478


FANTOM5 (FF) ontology


Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000073 (regional part of nervous system)
0000153 (anterior region of body)
0000349 (limbic system)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000955 (brain)
0000956 (cerebral cortex)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001869 (cerebral hemisphere)
0001890 (forebrain)
0001893 (telencephalon)
0001954 (Ammon's horn)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002421 (hippocampal formation)
0002532 (epiblast (generic))
0002600 (limbic lobe)
0002616 (regional part of brain)
0002619 (regional part of cerebral cortex)
0002780 (regional part of forebrain)
0002791 (regional part of telencephalon)
0003022 (lobe parts of cerebral cortex)
0003056 (pre-chordal neural plate)
0003075 (neural plate)
0003080 (anterior neural tube)
0004121 (ectoderm-derived structure)
0005068 (neural rod)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007023 (adult organism)
0007135 (neural keel)
0007284 (presumptive neural plate)

FF: FANTOM5
NA

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

NA