Personal tools

FF:11550-120C2

From FANTOM5_SSTAR

Revision as of 11:48, 10 August 2017 by Autoedit (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Name:Mouse Astrocytes - cerebellar, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12076
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
tissuecerebellum
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:3221
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005740
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12076 CAGE DRX008807 DRR009679
Accession ID Mm9

Library idBAMCTSS
CNhs12076 DRZ001104 DRZ002489
Accession ID Mm10

Library idBAMCTSS
CNhs12076 DRZ012454 DRZ013839
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

CNhs12076

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0.0445
1000 0.612
1001 --0.0749
1002 0.141
1003 0.387
1004 0
1005 --0.0389
1006 0.0759
1007 --0.304
1008 0
1009 0.0822
101 --0.443
1010 0
1011 --0.0219
1012 0
1013 0.103
1014 0.131
1015 0.281
1016 0.179
1017 0
1018 0
1019 0
102 0
1020 0.558
1021 0.17
1022 0.0857
1023 0
1024 0
1025 0
1026 0
1027 0.363
1028 0
1029 --0.176
103 0.119
1030 0
1031 0.113
1032 0.677
1033 0
1034 0
1035 0
1036 --0.045
1037 0
1038 --0.00209
1039 0.048
104 0
1040 0.381
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: CNhs12076

Jaspar motif P-value
MA0002.2 0.803
MA0003.1 0.398
MA0004.1 0.709
MA0006.1 0.406
MA0007.1 0.16
MA0009.1 0.371
MA0014.1 0.888
MA0017.1 0.0114
MA0018.2 0.636
MA0019.1 0.527
MA0024.1 0.55
MA0025.1 0.954
MA0027.1 0.729
MA0028.1 0.0756
MA0029.1 0.564
MA0030.1 0.81
MA0031.1 0.451
MA0035.2 0.057
MA0038.1 1
MA0039.2 0.767
MA0040.1 0.456
MA0041.1 0.189
MA0042.1 0.616
MA0043.1 0.255
MA0046.1 3.69195e-6
MA0047.2 0.437
MA0048.1 0.321
MA0050.1 0.00356
MA0051.1 0.0404
MA0052.1 0.384
MA0055.1 0.0378
MA0057.1 0.779
MA0058.1 0.933
MA0059.1 0.246
MA0060.1 0.00163
MA0061.1 0.549
MA0062.2 6.97039e-6
MA0065.2 0.997
MA0066.1 0.699
MA0067.1 0.537
MA0068.1 0.33
MA0069.1 0.0565
MA0070.1 0.524
MA0071.1 0.731
MA0072.1 0.838
MA0073.1 0.752
MA0074.1 0.61
MA0076.1 0.0244
MA0077.1 0.0331
MA0078.1 0.079
MA0079.2 0.12
MA0080.2 1.94472e-7
MA0081.1 0.0985
MA0083.1 0.139
MA0084.1 0.247
MA0087.1 0.298
MA0088.1 0.7
MA0090.1 0.00155
MA0091.1 0.277
MA0092.1 0.634
MA0093.1 0.844
MA0099.2 0.13
MA0100.1 0.379
MA0101.1 0.0661
MA0102.2 0.0608
MA0103.1 0.081
MA0104.2 0.67
MA0105.1 0.341
MA0106.1 0.64
MA0107.1 0.0162
MA0108.2 0.848
MA0111.1 0.687
MA0112.2 0.734
MA0113.1 0.272
MA0114.1 0.0152
MA0115.1 0.232
MA0116.1 0.788
MA0117.1 0.614
MA0119.1 0.153
MA0122.1 0.668
MA0124.1 0.443
MA0125.1 0.985
MA0131.1 0.114
MA0135.1 0.639
MA0136.1 3.22364e-8
MA0137.2 0.298
MA0138.2 0.77
MA0139.1 0.934
MA0140.1 1.70136e-4
MA0141.1 0.278
MA0142.1 0.322
MA0143.1 0.153
MA0144.1 0.2
MA0145.1 0.282
MA0146.1 0.0166
MA0147.1 0.568
MA0148.1 0.19
MA0149.1 0.388
MA0150.1 0.974
MA0152.1 0.215
MA0153.1 2.97743e-4
MA0154.1 0.906
MA0155.1 0.241
MA0156.1 1.01268e-10
MA0157.1 0.428
MA0159.1 0.872
MA0160.1 0.76
MA0162.1 0.0444
MA0163.1 0.441
MA0164.1 0.743
MA0258.1 0.712
MA0259.1 0.476



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: CNhs12076

Novel motif P-value
1 0.487
10 0.452
100 0.598
101 0.707
102 0.636
103 0.0956
104 0.569
105 0.893
106 0.145
107 0.878
108 0.383
109 0.0158
11 0.323
110 0.626
111 0.104
112 0.097
113 0.351
114 0.515
115 0.982
116 0.174
117 0.249
118 0.293
119 0.258
12 0.677
120 0.713
121 0.545
122 0.231
123 0.762
124 0.722
125 0.196
126 0.509
127 0.951
128 0.85
129 0.487
13 0.29
130 0.793
131 0.268
132 0.0469
133 0.182
134 0.684
135 0.251
136 0.099
137 0.169
138 0.907
139 0.15
14 0.38
140 0.0343
141 0.155
142 0.0901
143 0.186
144 0.396
145 0.474
146 0.96
147 0.727
148 0.25
149 0.64
15 0.61
150 0.312
151 0.912
152 0.0186
153 0.0546
154 0.342
155 0.502
156 0.0175
157 0.187
158 0.0491
159 0.0512
160 0.346
161 0.851
162 0.693
163 0.302
164 7.58218e-5
165 0.509
166 0.623
167 0.193
168 0.544
169 0.255
17 0.851
18 0.468
19 0.586
2 0.143
20 0.681
21 0.536
22 0.137
23 0.0499
24 0.636
25 0.517
26 0.257
27 0.533
28 0.241
29 0.883
3 0.787
30 0.482
31 0.402
32 0.293
33 0.783
34 0.0673
35 0.815
36 0.983
37 0.527
38 0.633
39 0.318
4 0.88
40 0.273
41 0.822
42 0.897
43 0.703
44 0.259
45 0.453
46 0.109
47 0.961
48 0.676
49 0.0901
5 0.119
50 0.21
51 0.252
52 0.225
53 0.719
54 0.342
55 0.409
56 0.468
57 0.27
58 0.0686
59 0.0831
6 0.968
60 0.245
61 0.619
62 0.304
63 0.0618
64 0.093
65 0.021
66 0.188
67 0.693
68 0.727
69 0.592
7 0.0611
70 0.568
71 0.487
72 0.451
73 0.0253
74 0.112
75 0.407
76 0.0645
77 0.0561
78 5.3338e-4
79 0.826
8 0.307
80 0.562
81 0.898
82 0.39
83 0.888
84 0.227
85 0.0499
86 0.732
87 3.6079e-4
88 0.28
89 0.671
9 0.623
90 0.903
91 0.828
92 0.399
93 0.0322
94 0.177
95 0.00139
96 0.338
97 0.824
98 0.0752
99 0.158



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: CNhs12076


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)
0002603 (astrocyte of the cerebellum)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0002037 (cerebellum)
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)
0000063 (organ segment)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002680 (regional part of metencephalon)
0002616 (regional part of brain)
0004733 (segmental subdivision of hindbrain)
0004732 (segmental subdivision of nervous system)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001895 (metencephalon)
0002028 (hindbrain)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000105 (mouse astrocyte sample)
0000196 (mouse astrocyte of cerebellum 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)