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FF:11709-123B8

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Name:Mouse Astrocytes - hippocampus, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs12129
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:5772
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004686
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12129 CAGE DRX008808 DRR009680
Accession ID Mm9

Library idBAMCTSS
CNhs12129 DRZ001105 DRZ002490
Accession ID Mm10

Library idBAMCTSS
CNhs12129 DRZ012455 DRZ013840
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

CNhs12129

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.598
1001 --0.0668
1002 0.268
1003 0.502
1004 0
1005 0
1006 0.247
1007 --0.368
1008 0
1009 0.281
101 --0.477
1010 0
1011 0.0299
1012 0
1013 0.172
1014 --0.0083
1015 0.132
1016 0.317
1017 0
1018 0
1019 0
102 0
1020 0.404
1021 0.0871
1022 0.0862
1023 0
1024 0.0941
1025 --0.0611
1026 0
1027 0.0383
1028 0
1029 --0.176
103 0.181
1030 0
1031 0.146
1032 0.583
1033 --0.00544
1034 0
1035 0
1036 --0.223
1037 0
1038 0.0889
1039 0.0561
104 0
1040 0.563
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: CNhs12129

Jaspar motif P-value
MA0002.2 0.707
MA0003.1 0.243
MA0004.1 0.89
MA0006.1 0.285
MA0007.1 0.078
MA0009.1 0.601
MA0014.1 0.543
MA0017.1 0.13
MA0018.2 0.369
MA0019.1 0.382
MA0024.1 8.68507e-6
MA0025.1 0.821
MA0027.1 0.377
MA0028.1 0.0184
MA0029.1 0.959
MA0030.1 0.736
MA0031.1 0.812
MA0035.2 0.03
MA0038.1 0.157
MA0039.2 0.226
MA0040.1 0.659
MA0041.1 0.171
MA0042.1 0.584
MA0043.1 0.758
MA0046.1 4.33986e-4
MA0047.2 0.596
MA0048.1 0.649
MA0050.1 0.139
MA0051.1 0.708
MA0052.1 0.453
MA0055.1 0.272
MA0057.1 0.854
MA0058.1 0.936
MA0059.1 0.874
MA0060.1 0.444
MA0061.1 0.973
MA0062.2 2.09459e-6
MA0065.2 0.932
MA0066.1 0.92
MA0067.1 0.489
MA0068.1 0.326
MA0069.1 0.0526
MA0070.1 0.526
MA0071.1 0.535
MA0072.1 0.634
MA0073.1 0.815
MA0074.1 0.618
MA0076.1 0.00269
MA0077.1 0.515
MA0078.1 0.836
MA0079.2 0.0117
MA0080.2 8.33241e-6
MA0081.1 0.0944
MA0083.1 0.734
MA0084.1 0.131
MA0087.1 0.201
MA0088.1 0.812
MA0090.1 3.69544e-5
MA0091.1 0.0739
MA0092.1 0.506
MA0093.1 0.901
MA0099.2 2.68476e-4
MA0100.1 0.778
MA0101.1 0.175
MA0102.2 0.247
MA0103.1 0.0892
MA0104.2 0.489
MA0105.1 0.699
MA0106.1 0.101
MA0107.1 0.102
MA0108.2 0.741
MA0111.1 0.848
MA0112.2 0.2
MA0113.1 0.309
MA0114.1 0.0487
MA0115.1 0.125
MA0116.1 0.982
MA0117.1 0.609
MA0119.1 0.0832
MA0122.1 0.765
MA0124.1 0.497
MA0125.1 0.922
MA0131.1 0.0365
MA0135.1 0.27
MA0136.1 5.13925e-7
MA0137.2 0.545
MA0138.2 0.787
MA0139.1 0.816
MA0140.1 5.23638e-5
MA0141.1 0.899
MA0142.1 0.93
MA0143.1 0.54
MA0144.1 0.788
MA0145.1 0.0249
MA0146.1 0.0242
MA0147.1 0.504
MA0148.1 0.206
MA0149.1 0.766
MA0150.1 0.76
MA0152.1 0.346
MA0153.1 0.00105
MA0154.1 0.722
MA0155.1 0.221
MA0156.1 6.54047e-10
MA0157.1 0.8
MA0159.1 0.523
MA0160.1 0.577
MA0162.1 0.155
MA0163.1 0.821
MA0164.1 0.84
MA0258.1 0.803
MA0259.1 0.184



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: CNhs12129

Novel motif P-value
1 0.33
10 0.315
100 0.674
101 0.975
102 0.43
103 0.103
104 0.822
105 0.694
106 0.0181
107 0.394
108 0.488
109 0.0211
11 0.242
110 0.913
111 0.555
112 0.59
113 0.412
114 0.528
115 0.853
116 0.153
117 0.252
118 0.152
119 0.69
12 0.861
120 0.648
121 0.617
122 0.564
123 0.962
124 0.718
125 0.766
126 0.303
127 0.71
128 0.214
129 0.296
13 0.324
130 0.764
131 0.93
132 0.0389
133 0.408
134 0.756
135 0.235
136 0.0475
137 0.216
138 0.875
139 0.901
14 0.246
140 0.0145
141 0.903
142 0.12
143 0.245
144 0.77
145 0.676
146 0.688
147 0.896
148 0.627
149 0.536
15 0.936
150 0.198
151 0.826
152 0.00401
153 0.052
154 0.295
155 0.299
156 0.0156
157 0.436
158 0.0231
159 0.139
160 0.371
161 0.747
162 0.586
163 0.353
164 0.00691
165 0.809
166 0.804
167 0.0316
168 0.434
169 0.142
17 0.317
18 0.984
19 0.27
2 0.0763
20 0.794
21 0.325
22 0.0645
23 0.0711
24 0.236
25 0.214
26 0.396
27 0.738
28 0.648
29 0.548
3 0.884
30 0.194
31 0.33
32 0.00984
33 0.774
34 0.15
35 0.493
36 0.129
37 0.148
38 0.528
39 0.262
4 0.778
40 0.871
41 0.819
42 0.951
43 0.734
44 0.209
45 0.228
46 0.222
47 0.656
48 0.737
49 0.171
5 0.176
50 0.12
51 0.462
52 0.0627
53 0.814
54 0.511
55 0.477
56 0.406
57 0.56
58 0.124
59 0.079
6 0.798
60 0.099
61 0.705
62 0.435
63 0.0454
64 0.386
65 0.0583
66 0.313
67 0.963
68 0.713
69 0.257
7 0.223
70 0.0814
71 0.583
72 0.708
73 0.00507
74 0.186
75 0.642
76 0.114
77 0.00442
78 0.0129
79 0.883
8 0.645
80 0.327
81 0.936
82 0.903
83 0.8
84 0.202
85 0.0499
86 0.946
87 8.85116e-4
88 0.421
89 0.75
9 0.574
90 0.487
91 0.561
92 0.768
93 0.148
94 0.0428
95 0.0276
96 0.14
97 0.832
98 0.105
99 0.281



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: CNhs12129


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), 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)