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FF:11742-123F5

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Name:Mouse Neurons - cortical, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs11947
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 numberRNAMNC3
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005136
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11947 CAGE DRX008832 DRR009704
Accession ID Mm9

Library idBAMCTSS
CNhs11947 DRZ001129 DRZ002514
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

CNhs11947

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.224
10 0
100 0.833
1000 0
1001 --0.0749
1002 0.536
1003 0.853
1004 0.055
1005 --0.194
1006 0.104
1007 --0.00389
1008 0
1009 --0.19
101 --0.135
1010 0
1011 0.264
1012 0.0498
1013 --0.2
1014 0.055
1015 0.405
1016 0.233
1017 0
1018 0
1019 0
102 0
1020 0.672
1021 0.099
1022 --0.124
1023 0
1024 --0.14
1025 0
1026 0
1027 0.555
1028 0
1029 --0.122
103 --0.0754
1030 0
1031 --0.432
1032 --0.177
1033 0.101
1034 0
1035 0
1036 --0.0795
1037 0
1038 0.0822
1039 --0.219
104 0
1040 --0.216
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: CNhs11947

Jaspar motif P-value
MA0002.2 0.00369
MA0003.1 0.109
MA0004.1 0.839
MA0006.1 0.0836
MA0007.1 0.284
MA0009.1 0.719
MA0014.1 0.356
MA0017.1 5.90785e-6
MA0018.2 0.128
MA0019.1 0.316
MA0024.1 0.108
MA0025.1 0.209
MA0027.1 0.692
MA0028.1 0.788
MA0029.1 0.614
MA0030.1 0.293
MA0031.1 0.0552
MA0035.2 0.0266
MA0038.1 0.455
MA0039.2 0.00321
MA0040.1 0.648
MA0041.1 0.398
MA0042.1 0.939
MA0043.1 0.123
MA0046.1 7.96103e-12
MA0047.2 1.44571e-4
MA0048.1 0.958
MA0050.1 3.22891e-9
MA0051.1 6.34719e-4
MA0052.1 2.91227e-4
MA0055.1 0.731
MA0057.1 0.084
MA0058.1 0.687
MA0059.1 0.984
MA0060.1 4.07196e-4
MA0061.1 0.0588
MA0062.2 0.226
MA0065.2 1.18573e-5
MA0066.1 0.286
MA0067.1 0.935
MA0068.1 0.155
MA0069.1 0.0718
MA0070.1 0.477
MA0071.1 0.25
MA0072.1 0.113
MA0073.1 0.825
MA0074.1 0.404
MA0076.1 0.642
MA0077.1 0.00191
MA0078.1 0.00551
MA0079.2 0.717
MA0080.2 3.43002e-11
MA0081.1 0.376
MA0083.1 1.15086e-5
MA0084.1 0.544
MA0087.1 0.914
MA0088.1 0.305
MA0090.1 0.0218
MA0091.1 0.596
MA0092.1 0.38
MA0093.1 0.805
MA0099.2 1.35285e-5
MA0100.1 0.827
MA0101.1 0.13
MA0102.2 0.745
MA0103.1 0.0794
MA0104.2 0.366
MA0105.1 0.103
MA0106.1 0.206
MA0107.1 0.0522
MA0108.2 1.40306e-4
MA0111.1 0.78
MA0112.2 2.2457e-4
MA0113.1 0.705
MA0114.1 1.94333e-5
MA0115.1 0.032
MA0116.1 0.171
MA0117.1 0.754
MA0119.1 0.245
MA0122.1 0.93
MA0124.1 0.978
MA0125.1 0.768
MA0131.1 0.801
MA0135.1 0.893
MA0136.1 3.94315e-9
MA0137.2 0.0378
MA0138.2 0.99
MA0139.1 0.194
MA0140.1 0.00298
MA0141.1 0.019
MA0142.1 0.0116
MA0143.1 0.00276
MA0144.1 0.0229
MA0145.1 0.0235
MA0146.1 0.0754
MA0147.1 0.34
MA0148.1 1.06741e-6
MA0149.1 0.0693
MA0150.1 0.0163
MA0152.1 0.231
MA0153.1 1.27667e-10
MA0154.1 0.0281
MA0155.1 0.721
MA0156.1 1.41388e-6
MA0157.1 0.0205
MA0159.1 0.00406
MA0160.1 0.077
MA0162.1 0.391
MA0163.1 0.0107
MA0164.1 0.957
MA0258.1 0.0131
MA0259.1 0.334



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: CNhs11947

Novel motif P-value
1 0.257
10 0.256
100 0.897
101 0.781
102 0.741
103 0.183
104 0.795
105 0.347
106 0.00914
107 0.0289
108 0.44
109 0.00412
11 0.152
110 0.189
111 0.0856
112 0.0048
113 0.865
114 0.522
115 0.211
116 0.657
117 0.171
118 0.746
119 0.171
12 0.448
120 0.796
121 0.132
122 0.332
123 0.716
124 0.519
125 0.328
126 0.183
127 0.109
128 0.04
129 0.174
13 1.04088e-5
130 0.746
131 0.556
132 0.98
133 0.49
134 0.595
135 0.287
136 0.103
137 0.239
138 0.662
139 0.313
14 0.585
140 0.902
141 0.0776
142 0.086
143 0.925
144 0.834
145 0.0814
146 0.281
147 0.997
148 0.917
149 0.0978
15 0.244
150 0.29
151 0.334
152 0.0341
153 0.689
154 0.97
155 0.871
156 0.00419
157 0.121
158 0.112
159 0.0146
160 0.359
161 0.26
162 0.991
163 0.0397
164 0.0172
165 0.0109
166 0.607
167 0.647
168 0.356
169 0.00691
17 0.0355
18 0.592
19 0.0376
2 0.489
20 0.895
21 0.761
22 0.0721
23 0.262
24 0.0346
25 0.64
26 0.0101
27 0.791
28 0.282
29 0.309
3 0.113
30 0.396
31 0.925
32 0.416
33 0.239
34 0.552
35 0.428
36 0.732
37 0.0058
38 0.44
39 0.246
4 0.533
40 0.189
41 0.824
42 0.369
43 0.186
44 0.796
45 0.411
46 0.266
47 0.277
48 0.233
49 0.22
5 0.192
50 0.313
51 0.669
52 0.0675
53 0.477
54 0.654
55 0.78
56 0.361
57 0.914
58 0.219
59 0.0972
6 0.765
60 0.00915
61 0.339
62 0.137
63 0.186
64 0.94
65 0.49
66 0.872
67 0.715
68 0.813
69 0.465
7 0.0225
70 0.0478
71 0.0414
72 0.334
73 0.0137
74 0.604
75 0.141
76 0.85
77 0.174
78 0.0412
79 0.996
8 0.367
80 0.615
81 0.321
82 0.0839
83 0.115
84 0.642
85 0.0761
86 0.252
87 0.248
88 0.499
89 0.206
9 0.351
90 0.353
91 0.555
92 0.119
93 0.0169
94 0.563
95 0.0473
96 0.259
97 0.85
98 0.637
99 0.275



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: CNhs11947


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)