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FF:11551-120C3

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Name:Mouse Astrocytes - hippocampus, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12077
Sample type:primary cells
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuehippocampus
dev stageNA
sexNA
ageNA
cell typeastrocyte
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:3899
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004768
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12077 CAGE DRX008809 DRR009681
Accession ID Mm9

Library idBAMCTSS
CNhs12077 DRZ001106 DRZ002491
Accession ID Mm10

Library idBAMCTSS
CNhs12077 DRZ012456 DRZ013841
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

CNhs12077

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.715
1001 -0.0491
1002 0.44
1003 0.498
1004 0
1005 -0.00897
1006 0.019
1007 -0.315
1008 0
1009 0.333
101 -0.377
1010 0
1011 -0.0304
1012 0
1013 0.333
1014 -0.00795
1015 0.015
1016 0.288
1017 0
1018 0
1019 0
102 0
1020 0.672
1021 0.0772
1022 0.0693
1023 0
1024 -0.0127
1025 -0.0611
1026 0
1027 0.0772
1028 0.143
1029 -0.176
103 0.188
1030 0
1031 0.179
1032 0.531
1033 -0.0385
1034 0
1035 0
1036 -0.219
1037 0
1038 0.137
1039 0.184
104 0
1040 0.51
1041 0



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: CNhs12077
Jaspar motif P-value
MA0002.2 0.906
MA0003.1 0.232
MA0004.1 0.831
MA0006.1 0.244
MA0007.1 0.131
MA0009.1 0.582
MA0014.1 0.444
MA0017.1 0.0289
MA0018.2 0.61
MA0019.1 0.555
MA0024.1 4.18849e-5
MA0025.1 0.633
MA0027.1 0.35
MA0028.1 0.148
MA0029.1 0.996
MA0030.1 0.652
MA0031.1 0.876
MA0035.2 0.00599
MA0038.1 0.372
MA0039.2 0.176
MA0040.1 0.499
MA0041.1 0.157
MA0042.1 0.557
MA0043.1 0.275
MA0046.1 5.7961e-5
MA0047.2 0.317
MA0048.1 0.654
MA0050.1 0.35
MA0051.1 0.487
MA0052.1 0.437
MA0055.1 0.189
MA0057.1 0.978
MA0058.1 0.95
MA0059.1 0.774
MA0060.1 0.688
MA0061.1 0.422
MA0062.2 8.24389e-4
MA0065.2 0.319
MA0066.1 0.501
MA0067.1 0.792
MA0068.1 0.373
MA0069.1 0.0338
MA0070.1 0.781
MA0071.1 0.389
MA0072.1 0.536
MA0073.1 0.781
MA0074.1 0.836
MA0076.1 0.2
MA0077.1 0.491
MA0078.1 0.852
MA0079.2 0.00704
MA0080.2 9.47975e-7
MA0081.1 0.421
MA0083.1 0.918
MA0084.1 0.151
MA0087.1 0.214
MA0088.1 0.923
MA0090.1 7.88658e-5
MA0091.1 0.0324
MA0092.1 0.866
MA0093.1 0.938
MA0099.2 0.0297
MA0100.1 0.649
MA0101.1 0.0653
MA0102.2 0.486
MA0103.1 0.0182
MA0104.2 0.253
MA0105.1 0.0781
MA0106.1 0.146
MA0107.1 0.0418
MA0108.2 0.53
MA0111.1 0.673
MA0112.2 0.768
MA0113.1 0.658
MA0114.1 0.00148
MA0115.1 0.108
MA0116.1 0.085
MA0117.1 0.866
MA0119.1 0.427
MA0122.1 0.697
MA0124.1 0.329
MA0125.1 0.933
MA0131.1 0.0481
MA0135.1 0.119
MA0136.1 1.20481e-6
MA0137.2 0.84
MA0138.2 0.508
MA0139.1 0.391
MA0140.1 6.74532e-6
MA0141.1 0.588
MA0142.1 0.393
MA0143.1 0.713
MA0144.1 0.836
MA0145.1 0.0475
MA0146.1 0.0205
MA0147.1 0.184
MA0148.1 0.115
MA0149.1 0.839
MA0150.1 0.94
MA0152.1 0.454
MA0153.1 3.19402e-4
MA0154.1 0.493
MA0155.1 0.405
MA0156.1 2.35917e-7
MA0157.1 0.747
MA0159.1 0.233
MA0160.1 0.492
MA0162.1 0.239
MA0163.1 0.564
MA0164.1 0.755
MA0258.1 0.293
MA0259.1 0.174



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: CNhs12077
Novel motif P-value
1 0.134
10 0.103
100 0.468
101 0.874
102 0.542
103 0.106
104 0.798
105 0.902
106 0.234
107 0.897
108 0.705
109 0.0609
11 0.606
110 0.981
111 0.214
112 0.217
113 0.342
114 0.772
115 0.689
116 0.419
117 0.0874
118 0.101
119 0.279
12 0.976
120 0.554
121 0.653
122 0.439
123 0.994
124 0.578
125 0.625
126 0.239
127 0.913
128 0.92
129 0.158
13 0.187
130 0.652
131 0.993
132 0.247
133 0.48
134 0.842
135 0.387
136 0.00965
137 0.103
138 0.645
139 0.487
14 0.411
140 0.00495
141 0.588
142 0.0871
143 0.536
144 0.77
145 0.49
146 0.926
147 0.866
148 0.332
149 0.478
15 0.779
150 0.461
151 0.785
152 0.00323
153 0.0606
154 0.219
155 0.455
156 0.0059
157 0.662
158 0.0256
159 0.0832
160 0.133
161 0.762
162 0.949
163 0.219
164 0.00292
165 0.696
166 0.793
167 0.0785
168 0.326
169 0.212
17 0.958
18 0.641
19 0.446
2 0.049
20 0.922
21 0.695
22 0.122
23 0.134
24 0.386
25 0.288
26 0.143
27 0.986
28 0.526
29 0.552
3 0.29
30 0.246
31 0.497
32 0.0435
33 0.614
34 0.334
35 0.324
36 0.0347
37 0.323
38 0.772
39 0.456
4 0.947
40 0.586
41 0.843
42 0.606
43 0.335
44 0.297
45 0.24
46 0.0433
47 0.958
48 0.821
49 0.0395
5 0.066
50 0.194
51 0.149
52 0.221
53 0.885
54 0.39
55 0.686
56 0.818
57 0.879
58 0.0377
59 0.13
6 0.859
60 0.238
61 0.6
62 0.12
63 0.233
64 0.865
65 0.261
66 0.508
67 0.982
68 0.465
69 0.258
7 0.233
70 0.582
71 0.0403
72 0.499
73 0.00303
74 0.291
75 0.229
76 0.161
77 0.0646
78 0.0135
79 0.892
8 0.407
80 0.219
81 0.643
82 0.778
83 0.95
84 0.266
85 0.338
86 0.88
87 2.5117e-4
88 0.427
89 0.597
9 0.376
90 0.331
91 0.842
92 0.36
93 0.0441
94 0.0158
95 0.00691
96 0.0681
97 0.825
98 0.27
99 0.256



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: CNhs12077


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

CL: Cell type
0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000128 (oligodendrocyte)
0000126 (macroglial cell)
0000125 (glial cell)
0000255 (eukaryotic cell)
0000127 (astrocyte)
0002605 (astrocyte of the cerebral cortex)
0002604 (astrocyte of the hippocampus)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0001954 (Ammon's horn)
0000956 (cerebral cortex)
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)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0003022 (lobe parts of cerebral cortex)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002421 (hippocampal formation)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0000349 (limbic system)
0002600 (limbic lobe)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000105 (mouse astrocyte sample)
0000197 (mouse astrocyte of hippocampus 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


CL:0000133 (neurectodermal cell)
CL:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)