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FF:11723-123D4

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Name:Mouse Neurons - striatal, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs12134
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 numberRNAMNS2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005105
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12134 CAGE DRX008843 DRR009715
Accession ID Mm9

Library idBAMCTSS
CNhs12134 DRZ001140 DRZ002525
Accession ID Mm10

Library idBAMCTSS
CNhs12134 DRZ012490 DRZ013875
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

CNhs12134

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.38
10 0
100 0.412
1000 --0.0355
1001 --0.0749
1002 --0.0618
1003 --0.00666
1004 0.0269
1005 --0.166
1006 0.297
1007 --0.0387
1008 0
1009 --0.2
101 --0.189
1010 0
1011 0.117
1012 0
1013 --0.0029
1014 0.0143
1015 0.377
1016 0.314
1017 0
1018 0
1019 0
102 0
1020 0.646
1021 0.053
1022 --0.0704
1023 0
1024 --0.221
1025 --0.016
1026 0
1027 0.223
1028 0
1029 --0.148
103 --0.0848
1030 0
1031 --0.467
1032 0.06
1033 0.0538
1034 0
1035 0
1036 --0.208
1037 0
1038 0.0708
1039 --0.219
104 0
1040 --0.162
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: CNhs12134

Jaspar motif P-value
MA0002.2 0.00401
MA0003.1 0.184
MA0004.1 0.627
MA0006.1 0.0938
MA0007.1 0.152
MA0009.1 0.915
MA0014.1 0.412
MA0017.1 4.29699e-5
MA0018.2 0.0103
MA0019.1 0.314
MA0024.1 0.896
MA0025.1 0.697
MA0027.1 0.619
MA0028.1 0.504
MA0029.1 0.505
MA0030.1 0.326
MA0031.1 0.0816
MA0035.2 0.156
MA0038.1 0.252
MA0039.2 0.0235
MA0040.1 0.785
MA0041.1 0.23
MA0042.1 0.561
MA0043.1 0.0541
MA0046.1 2.23386e-7
MA0047.2 0.0022
MA0048.1 0.346
MA0050.1 2.95862e-9
MA0051.1 2.92578e-4
MA0052.1 0.0985
MA0055.1 0.362
MA0057.1 0.0881
MA0058.1 0.581
MA0059.1 0.408
MA0060.1 0.00105
MA0061.1 0.0474
MA0062.2 0.146
MA0065.2 2.791e-5
MA0066.1 0.147
MA0067.1 0.888
MA0068.1 0.821
MA0069.1 0.0918
MA0070.1 0.357
MA0071.1 0.253
MA0072.1 0.222
MA0073.1 0.936
MA0074.1 0.37
MA0076.1 0.807
MA0077.1 0.00881
MA0078.1 0.0557
MA0079.2 0.622
MA0080.2 8.0982e-10
MA0081.1 0.353
MA0083.1 0.00623
MA0084.1 0.653
MA0087.1 0.406
MA0088.1 0.188
MA0090.1 0.00821
MA0091.1 0.216
MA0092.1 0.135
MA0093.1 0.632
MA0099.2 1.66632e-4
MA0100.1 0.943
MA0101.1 0.054
MA0102.2 0.914
MA0103.1 0.168
MA0104.2 0.618
MA0105.1 0.0312
MA0106.1 0.108
MA0107.1 0.048
MA0108.2 0.107
MA0111.1 0.995
MA0112.2 1.27478e-4
MA0113.1 0.236
MA0114.1 1.1707e-4
MA0115.1 0.00722
MA0116.1 0.0636
MA0117.1 0.738
MA0119.1 0.0437
MA0122.1 0.556
MA0124.1 0.866
MA0125.1 0.151
MA0131.1 0.879
MA0135.1 0.15
MA0136.1 1.29154e-7
MA0137.2 0.00749
MA0138.2 0.224
MA0139.1 0.261
MA0140.1 0.00484
MA0141.1 0.0112
MA0142.1 0.0218
MA0143.1 0.00618
MA0144.1 0.0192
MA0145.1 0.0565
MA0146.1 0.0514
MA0147.1 0.686
MA0148.1 1.64095e-5
MA0149.1 0.0816
MA0150.1 0.0342
MA0152.1 0.152
MA0153.1 5.91923e-7
MA0154.1 0.0154
MA0155.1 0.639
MA0156.1 4.83295e-5
MA0157.1 0.0566
MA0159.1 0.0034
MA0160.1 0.0723
MA0162.1 0.294
MA0163.1 0.0023
MA0164.1 0.908
MA0258.1 0.0121
MA0259.1 0.554



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: CNhs12134

Novel motif P-value
1 0.145
10 0.09
100 0.758
101 0.977
102 0.894
103 0.0893
104 0.97
105 0.155
106 0.00713
107 0.0454
108 0.53
109 0.00372
11 0.0839
110 0.0912
111 0.0951
112 0.00627
113 0.962
114 0.305
115 0.564
116 0.492
117 0.0474
118 0.428
119 0.142
12 0.682
120 0.878
121 0.448
122 0.782
123 0.181
124 0.642
125 0.384
126 0.233
127 0.134
128 0.0216
129 0.279
13 5.77667e-6
130 0.359
131 0.384
132 0.946
133 0.231
134 0.364
135 0.638
136 0.204
137 0.223
138 0.646
139 0.105
14 0.674
140 0.0429
141 0.261
142 0.0179
143 0.536
144 0.995
145 0.0126
146 0.406
147 0.789
148 0.409
149 0.116
15 0.18
150 0.132
151 0.457
152 0.0521
153 0.522
154 0.703
155 0.663
156 0.00879
157 0.111
158 0.22
159 0.124
160 0.198
161 0.444
162 0.74
163 0.37
164 0.0175
165 0.0411
166 0.69
167 0.948
168 0.443
169 0.00382
17 0.0216
18 0.727
19 0.054
2 0.913
20 0.481
21 0.459
22 0.0852
23 0.236
24 0.0361
25 0.694
26 6.93915e-4
27 0.868
28 0.379
29 0.11
3 0.0712
30 0.676
31 0.912
32 0.385
33 0.167
34 0.551
35 0.505
36 0.36
37 0.00999
38 0.268
39 0.162
4 0.56
40 0.294
41 0.904
42 0.223
43 0.13
44 0.624
45 0.517
46 0.132
47 0.174
48 0.116
49 0.147
5 0.138
50 0.234
51 0.532
52 0.103
53 0.681
54 0.662
55 0.831
56 0.391
57 0.571
58 0.215
59 0.0717
6 0.512
60 0.0115
61 0.152
62 0.114
63 0.101
64 0.892
65 0.226
66 0.698
67 0.796
68 0.281
69 0.611
7 0.0167
70 0.0212
71 0.0139
72 0.345
73 0.026
74 0.35
75 0.119
76 0.709
77 0.239
78 0.0152
79 0.468
8 0.131
80 0.864
81 0.501
82 0.0862
83 0.174
84 0.816
85 0.0995
86 0.287
87 0.316
88 0.277
89 0.287
9 0.317
90 0.132
91 0.238
92 0.288
93 0.0452
94 0.765
95 0.0464
96 0.344
97 0.85
98 0.787
99 0.321



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: CNhs12134


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)
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)