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FF:11741-123F4

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Name:Mouse Neurons - striatal, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12360
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
tissuecorpus striatum
dev stageNA
sexNA
ageNA
cell typeneuron
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMNS1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005038
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12360 CAGE DRX008844 DRR009716
Accession ID Mm9

Library idBAMCTSS
CNhs12360 DRZ001141 DRZ002526
Accession ID Mm10

Library idBAMCTSS
CNhs12360 DRZ012491 DRZ013876
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

CNhs12360

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.423
10 0
100 0.423
1000 0
1001 -0.0668
1002 0.0456
1003 0.0293
1004 0.0717
1005 0
1006 0.37
1007 -0.0312
1008 0
1009 -0.2
101 -0.163
1010 0
1011 0.198
1012 0
1013 -0.0266
1014 0.0503
1015 0.444
1016 0.236
1017 0
1018 0
1019 0
102 0
1020 0.552
1021 0.135
1022 -0.0704
1023 0
1024 -0.14
1025 0
1026 0
1027 0.375
1028 0
1029 -0.115
103 -0.0709
1030 0
1031 -0.568
1032 0.01
1033 0.0234
1034 0
1035 0
1036 -0.225
1037 0
1038 0.108
1039 -0.213
104 0
1040 -0.271
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: CNhs12360
Jaspar motif P-value
MA0002.2 0.00164
MA0003.1 0.173
MA0004.1 0.604
MA0006.1 0.085
MA0007.1 0.154
MA0009.1 0.805
MA0014.1 0.424
MA0017.1 1.64739e-5
MA0018.2 0.0154
MA0019.1 0.429
MA0024.1 0.953
MA0025.1 0.533
MA0027.1 0.533
MA0028.1 0.679
MA0029.1 0.62
MA0030.1 0.339
MA0031.1 0.0575
MA0035.2 0.0873
MA0038.1 0.427
MA0039.2 0.0173
MA0040.1 0.688
MA0041.1 0.253
MA0042.1 0.539
MA0043.1 0.0696
MA0046.1 2.65618e-8
MA0047.2 0.00146
MA0048.1 0.396
MA0050.1 6.31981e-9
MA0051.1 1.53189e-4
MA0052.1 0.0453
MA0055.1 0.485
MA0057.1 0.115
MA0058.1 0.566
MA0059.1 0.372
MA0060.1 0.00769
MA0061.1 0.0565
MA0062.2 0.207
MA0065.2 1.78908e-5
MA0066.1 0.201
MA0067.1 0.767
MA0068.1 0.887
MA0069.1 0.124
MA0070.1 0.453
MA0071.1 0.208
MA0072.1 0.143
MA0073.1 0.891
MA0074.1 0.355
MA0076.1 0.63
MA0077.1 0.0134
MA0078.1 0.0945
MA0079.2 0.613
MA0080.2 3.50162e-10
MA0081.1 0.363
MA0083.1 0.0061
MA0084.1 0.696
MA0087.1 0.528
MA0088.1 0.224
MA0090.1 0.0084
MA0091.1 0.191
MA0092.1 0.138
MA0093.1 0.621
MA0099.2 1.13922e-4
MA0100.1 0.821
MA0101.1 0.0577
MA0102.2 0.923
MA0103.1 0.168
MA0104.2 0.623
MA0105.1 0.0541
MA0106.1 0.12
MA0107.1 0.0518
MA0108.2 0.0681
MA0111.1 0.99
MA0112.2 8.5774e-5
MA0113.1 0.295
MA0114.1 1.05204e-4
MA0115.1 0.0102
MA0116.1 0.0848
MA0117.1 0.821
MA0119.1 0.0418
MA0122.1 0.677
MA0124.1 0.813
MA0125.1 0.208
MA0131.1 0.842
MA0135.1 0.128
MA0136.1 7.65572e-8
MA0137.2 0.0233
MA0138.2 0.21
MA0139.1 0.304
MA0140.1 0.00174
MA0141.1 0.00903
MA0142.1 0.0977
MA0143.1 0.0119
MA0144.1 0.0208
MA0145.1 0.0416
MA0146.1 0.0458
MA0147.1 0.712
MA0148.1 1.06855e-5
MA0149.1 0.0575
MA0150.1 0.0195
MA0152.1 0.0768
MA0153.1 1.77314e-7
MA0154.1 0.023
MA0155.1 0.698
MA0156.1 2.66772e-5
MA0157.1 0.0584
MA0159.1 0.003
MA0160.1 0.0766
MA0162.1 0.319
MA0163.1 0.00311
MA0164.1 0.996
MA0258.1 0.00769
MA0259.1 0.56



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: CNhs12360
Novel motif P-value
1 0.141
10 0.104
100 0.795
101 0.9
102 0.978
103 0.137
104 0.914
105 0.173
106 0.00488
107 0.0329
108 0.42
109 0.00459
11 0.112
110 0.0966
111 0.167
112 0.00951
113 0.942
114 0.341
115 0.999
116 0.555
117 0.0616
118 0.499
119 0.115
12 0.603
120 0.746
121 0.383
122 0.821
123 0.123
124 0.676
125 0.371
126 0.242
127 0.0906
128 0.0184
129 0.245
13 6.65885e-6
130 0.25
131 0.295
132 0.957
133 0.356
134 0.293
135 0.941
136 0.222
137 0.295
138 0.709
139 0.154
14 0.618
140 0.094
141 0.245
142 0.027
143 0.598
144 0.982
145 0.0166
146 0.384
147 0.938
148 0.409
149 0.178
15 0.181
150 0.127
151 0.41
152 0.0407
153 0.45
154 0.609
155 0.72
156 0.00657
157 0.0785
158 0.14
159 0.103
160 0.209
161 0.42
162 0.873
163 0.43
164 0.0164
165 0.0439
166 0.763
167 0.911
168 0.541
169 0.00281
17 0.0256
18 0.686
19 0.0458
2 0.889
20 0.577
21 0.481
22 0.0762
23 0.256
24 0.0402
25 0.616
26 7.1553e-4
27 0.898
28 0.368
29 0.111
3 0.0915
30 0.713
31 0.948
32 0.524
33 0.147
34 0.489
35 0.512
36 0.321
37 0.0114
38 0.319
39 0.207
4 0.585
40 0.271
41 0.752
42 0.202
43 0.136
44 0.817
45 0.518
46 0.139
47 0.197
48 0.14
49 0.155
5 0.126
50 0.27
51 0.515
52 0.0948
53 0.658
54 0.629
55 0.875
56 0.329
57 0.568
58 0.219
59 0.0889
6 0.607
60 0.0128
61 0.145
62 0.108
63 0.0989
64 0.944
65 0.242
66 0.621
67 0.769
68 0.291
69 0.505
7 0.0192
70 0.0248
71 0.0138
72 0.364
73 0.0203
74 0.358
75 0.126
76 0.775
77 0.281
78 0.0162
79 0.59
8 0.161
80 0.704
81 0.515
82 0.102
83 0.155
84 0.844
85 0.143
86 0.259
87 0.256
88 0.306
89 0.378
9 0.288
90 0.106
91 0.25
92 0.322
93 0.0112
94 0.752
95 0.0598
96 0.292
97 0.886
98 0.82
99 0.36



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: CNhs12360


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)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000117 (CNS neuron (sensu Vertebrata))
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0002613 (striatum neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0000369 (corpus striatum)
0002435 (striatum)
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)
0001062 (anatomical entity)
0000480 (anatomical group)
0002420 (basal ganglion)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0007245 (nuclear complex of neuraxis)
0010317 (germ layer / neural crest derived structure)
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0001893 (telencephalon)
0001890 (forebrain)
0010011 (collection of basal ganglia)
0000204 (ventral part of telencephalon)
0000454 (cerebral subcortex)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000209 (mouse striatal neuron 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:0000337 (neuroblast (sensu Vertebrata))
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)