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FF:11724-123D5

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Name:Mouse Neurons - cortical, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs12025
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
tissuecortex
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 numberRNAMNC2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005346
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12025 CAGE DRX008831 DRR009703
Accession ID Mm9

Library idBAMCTSS
CNhs12025 DRZ001128 DRZ002513
Accession ID Mm10

Library idBAMCTSS
CNhs12025 DRZ012478 DRZ013863
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

CNhs12025

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.189
10 0
100 0.767
1000 --0.0157
1001 --0.0631
1002 0.46
1003 0.537
1004 0.0428
1005 --0.282
1006 0.0527
1007 0.0592
1008 0
1009 --0.2
101 --0.0748
1010 0
1011 0.0739
1012 0.0428
1013 --0.184
1014 0.118
1015 0.426
1016 0.249
1017 0
1018 0
1019 0
102 0
1020 0.389
1021 0.118
1022 --0.124
1023 0
1024 --0.14
1025 0
1026 0
1027 0.568
1028 0
1029 --0.101
103 --0.0719
1030 0
1031 --0.477
1032 --0.177
1033 --0.0236
1034 0
1035 0
1036 --0.12
1037 0
1038 0.186
1039 --0.231
104 0
1040 --0.173
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: CNhs12025

Jaspar motif P-value
MA0002.2 0.00258
MA0003.1 0.0931
MA0004.1 0.835
MA0006.1 0.132
MA0007.1 0.348
MA0009.1 0.683
MA0014.1 0.402
MA0017.1 1.17954e-5
MA0018.2 0.053
MA0019.1 0.347
MA0024.1 0.0552
MA0025.1 0.214
MA0027.1 0.754
MA0028.1 0.915
MA0029.1 0.419
MA0030.1 0.417
MA0031.1 0.0713
MA0035.2 0.0417
MA0038.1 0.106
MA0039.2 0.0152
MA0040.1 0.581
MA0041.1 0.314
MA0042.1 0.996
MA0043.1 0.0356
MA0046.1 1.4892e-14
MA0047.2 2.86339e-4
MA0048.1 0.882
MA0050.1 1.1127e-8
MA0051.1 0.00103
MA0052.1 5.49273e-5
MA0055.1 0.664
MA0057.1 0.0799
MA0058.1 0.692
MA0059.1 0.685
MA0060.1 1.67427e-6
MA0061.1 0.0734
MA0062.2 0.639
MA0065.2 1.54522e-5
MA0066.1 0.2
MA0067.1 0.782
MA0068.1 0.212
MA0069.1 0.0436
MA0070.1 0.449
MA0071.1 0.208
MA0072.1 0.111
MA0073.1 0.703
MA0074.1 0.302
MA0076.1 0.33
MA0077.1 0.00362
MA0078.1 0.00675
MA0079.2 0.936
MA0080.2 2.16772e-11
MA0081.1 0.489
MA0083.1 6.59244e-6
MA0084.1 0.657
MA0087.1 0.673
MA0088.1 0.306
MA0090.1 0.0195
MA0091.1 0.404
MA0092.1 0.318
MA0093.1 0.829
MA0099.2 1.11985e-5
MA0100.1 0.641
MA0101.1 0.247
MA0102.2 0.963
MA0103.1 0.0481
MA0104.2 0.528
MA0105.1 0.0431
MA0106.1 0.22
MA0107.1 0.133
MA0108.2 8.82552e-5
MA0111.1 0.742
MA0112.2 1.40191e-4
MA0113.1 0.483
MA0114.1 9.61006e-5
MA0115.1 0.0169
MA0116.1 0.0675
MA0117.1 0.871
MA0119.1 0.175
MA0122.1 0.814
MA0124.1 0.995
MA0125.1 0.404
MA0131.1 0.554
MA0135.1 0.717
MA0136.1 2.35308e-8
MA0137.2 0.0789
MA0138.2 0.743
MA0139.1 0.134
MA0140.1 0.00444
MA0141.1 0.00651
MA0142.1 0.0079
MA0143.1 0.00177
MA0144.1 0.0577
MA0145.1 0.0194
MA0146.1 0.0867
MA0147.1 0.584
MA0148.1 1.37487e-6
MA0149.1 0.0558
MA0150.1 0.0388
MA0152.1 0.42
MA0153.1 2.73981e-12
MA0154.1 0.0154
MA0155.1 0.591
MA0156.1 4.86293e-5
MA0157.1 0.0136
MA0159.1 0.00227
MA0160.1 0.057
MA0162.1 0.337
MA0163.1 0.00336
MA0164.1 0.92
MA0258.1 0.00595
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: CNhs12025

Novel motif P-value
1 0.207
10 0.202
100 0.981
101 0.704
102 0.703
103 0.119
104 0.896
105 0.433
106 0.00943
107 0.0511
108 0.644
109 0.00341
11 0.134
110 0.176
111 0.0423
112 0.00557
113 0.907
114 0.236
115 0.11
116 0.463
117 0.164
118 0.647
119 0.104
12 0.535
120 0.8
121 0.135
122 0.402
123 0.685
124 0.923
125 0.325
126 0.235
127 0.133
128 0.0227
129 0.172
13 1.27472e-4
130 0.738
131 0.436
132 0.705
133 0.526
134 0.531
135 0.184
136 0.109
137 0.294
138 0.782
139 0.234
14 0.581
140 0.508
141 0.0418
142 0.157
143 0.579
144 0.765
145 0.0852
146 0.34
147 0.992
148 0.78
149 0.0486
15 0.236
150 0.309
151 0.331
152 0.0359
153 0.945
154 0.978
155 0.574
156 0.00127
157 0.16
158 0.254
159 0.0954
160 0.327
161 0.242
162 0.989
163 0.0834
164 0.0263
165 0.00464
166 0.588
167 0.605
168 0.461
169 0.00575
17 0.0285
18 0.929
19 0.0442
2 0.42
20 0.807
21 0.542
22 0.0893
23 0.195
24 0.0299
25 0.553
26 0.00743
27 0.596
28 0.397
29 0.282
3 0.0838
30 0.405
31 0.768
32 0.258
33 0.235
34 0.488
35 0.666
36 0.562
37 0.00787
38 0.395
39 0.225
4 0.587
40 0.171
41 0.773
42 0.313
43 0.178
44 0.495
45 0.409
46 0.222
47 0.21
48 0.19
49 0.203
5 0.173
50 0.301
51 0.602
52 0.0714
53 0.44
54 0.532
55 0.472
56 0.279
57 0.932
58 0.197
59 0.0466
6 0.666
60 0.0137
61 0.352
62 0.108
63 0.142
64 0.874
65 0.279
66 0.728
67 0.734
68 0.725
69 0.256
7 0.0413
70 0.0175
71 0.0426
72 0.292
73 0.016
74 0.427
75 0.128
76 0.871
77 0.126
78 0.0644
79 0.899
8 0.277
80 0.891
81 0.28
82 0.0622
83 0.0447
84 0.695
85 0.0292
86 0.295
87 0.203
88 0.63
89 0.156
9 0.335
90 0.387
91 0.371
92 0.091
93 0.0577
94 0.643
95 0.0479
96 0.238
97 0.832
98 0.516
99 0.194



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: CNhs12025


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)
0002609 (neuron of cerebral cortex)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
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)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000204 (cortical mouse 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)