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FF:11722-123D3

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Name:Mouse Neurons - raphe, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs12631
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
tissueraphe nuclei
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 numberRNARAP2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005499
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12631 CAGE DRX008840 DRR009712
Accession ID Mm9

Library idBAMCTSS
CNhs12631 DRZ001137 DRZ002522
Accession ID Mm10

Library idBAMCTSS
CNhs12631 DRZ012487 DRZ013872
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

CNhs12631

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.733
10 0
100 0
1000 0
1001 0
1002 --0.0941
1003 --0.0029
1004 0
1005 0
1006 0.693
1007 --0.198
1008 0
1009 --0.2
101 --0.246
1010 0
1011 0.19
1012 0
1013 0.407
1014 --0.0851
1015 --0.212
1016 0.0537
1017 0
1018 0
1019 0
102 0
1020 0.322
1021 --0.0487
1022 --0.0704
1023 0
1024 --0.0899
1025 0
1026 0
1027 0.416
1028 0
1029 --0.148
103 --0.0848
1030 0
1031 --0.46
1032 0.638
1033 0.247
1034 0
1035 0
1036 --0.328
1037 0
1038 --0.194
1039 3.171674e-4
104 0
1040 --0.268
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: CNhs12631

Jaspar motif P-value
MA0002.2 0.074
MA0003.1 0.371
MA0004.1 0.455
MA0006.1 0.166
MA0007.1 0.339
MA0009.1 0.771
MA0014.1 0.727
MA0017.1 2.18456e-5
MA0018.2 0.0071
MA0019.1 0.406
MA0024.1 0.00277
MA0025.1 0.00113
MA0027.1 0.129
MA0028.1 0.00447
MA0029.1 0.851
MA0030.1 0.977
MA0031.1 0.223
MA0035.2 0.0723
MA0038.1 0.569
MA0039.2 0.00433
MA0040.1 0.741
MA0041.1 0.188
MA0042.1 0.395
MA0043.1 0.0848
MA0046.1 3.37696e-6
MA0047.2 0.00303
MA0048.1 0.0136
MA0050.1 1.7241e-8
MA0051.1 1.99282e-6
MA0052.1 0.525
MA0055.1 4.46814e-4
MA0057.1 0.388
MA0058.1 0.471
MA0059.1 0.324
MA0060.1 0.0853
MA0061.1 0.0276
MA0062.2 2.18002e-6
MA0065.2 3.99705e-5
MA0066.1 0.162
MA0067.1 0.653
MA0068.1 0.288
MA0069.1 0.11
MA0070.1 0.179
MA0071.1 0.437
MA0072.1 0.618
MA0073.1 0.553
MA0074.1 0.278
MA0076.1 0.00989
MA0077.1 0.118
MA0078.1 0.429
MA0079.2 0.631
MA0080.2 1.10516e-9
MA0081.1 0.171
MA0083.1 7.51594e-4
MA0084.1 0.351
MA0087.1 0.0793
MA0088.1 0.312
MA0090.1 0.177
MA0091.1 0.465
MA0092.1 0.0956
MA0093.1 0.482
MA0099.2 0.0109
MA0100.1 0.216
MA0101.1 0.00431
MA0102.2 0.5
MA0103.1 0.582
MA0104.2 0.959
MA0105.1 0.021
MA0106.1 0.0675
MA0107.1 0.0119
MA0108.2 2.26836e-4
MA0111.1 0.715
MA0112.2 0.00518
MA0113.1 0.525
MA0114.1 2.50348e-5
MA0115.1 0.00154
MA0116.1 0.139
MA0117.1 0.982
MA0119.1 0.174
MA0122.1 0.883
MA0124.1 0.716
MA0125.1 0.252
MA0131.1 0.247
MA0135.1 0.806
MA0136.1 1.15751e-11
MA0137.2 0.153
MA0138.2 5.96329e-6
MA0139.1 0.783
MA0140.1 0.00185
MA0141.1 0.211
MA0142.1 0.0174
MA0143.1 0.442
MA0144.1 0.0461
MA0145.1 0.178
MA0146.1 0.0436
MA0147.1 0.877
MA0148.1 0.0103
MA0149.1 0.753
MA0150.1 0.344
MA0152.1 0.0234
MA0153.1 5.60953e-7
MA0154.1 0.0667
MA0155.1 0.535
MA0156.1 5.96345e-12
MA0157.1 0.158
MA0159.1 0.0511
MA0160.1 0.175
MA0162.1 0.305
MA0163.1 0.00338
MA0164.1 0.846
MA0258.1 0.094
MA0259.1 0.767



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: CNhs12631

Novel motif P-value
1 0.346
10 0.0723
100 0.243
101 0.391
102 0.62
103 0.295
104 0.975
105 0.494
106 0.0607
107 0.361
108 0.41
109 0.0158
11 0.272
110 0.0732
111 0.725
112 0.0229
113 0.387
114 0.901
115 0.644
116 0.416
117 0.00138
118 0.599
119 0.375
12 0.908
120 0.683
121 0.489
122 0.975
123 2.10001e-5
124 0.0333
125 0.186
126 0.076
127 0.605
128 0.126
129 0.371
13 4.08607e-10
130 0.216
131 0.448
132 0.618
133 0.838
134 0.0199
135 0.0444
136 0.0889
137 0.751
138 0.645
139 0.732
14 0.463
140 0.366
141 0.885
142 0.351
143 0.797
144 0.932
145 9.90991e-6
146 0.363
147 0.112
148 0.55
149 0.644
15 0.405
150 0.0457
151 0.759
152 0.0857
153 0.774
154 0.435
155 0.478
156 0.00986
157 0.0402
158 0.298
159 0.62
160 0.377
161 0.423
162 0.366
163 0.953
164 0.0355
165 0.422
166 0.351
167 0.776
168 0.88
169 0.00634
17 0.108
18 0.342
19 0.149
2 0.352
20 0.00368
21 0.195
22 0.169
23 0.893
24 0.0291
25 0.944
26 1.37344e-9
27 0.113
28 0.917
29 0.0449
3 0.13
30 0.796
31 0.423
32 0.853
33 0.0935
34 0.993
35 0.294
36 0.292
37 0.0213
38 0.635
39 0.326
4 0.372
40 0.0816
41 0.88
42 0.285
43 0.207
44 0.952
45 0.685
46 0.0701
47 0.773
48 0.573
49 0.396
5 0.386
50 0.173
51 0.825
52 0.368
53 0.361
54 0.923
55 0.7
56 0.605
57 0.959
58 0.465
59 0.395
6 0.968
60 0.0466
61 0.0409
62 0.37
63 0.264
64 0.924
65 0.552
66 0.751
67 0.86
68 0.878
69 0.71
7 0.0186
70 0.384
71 0.00167
72 0.521
73 0.0325
74 0.911
75 0.0701
76 0.249
77 0.765
78 0.00144
79 0.0635
8 0.138
80 0.659
81 0.415
82 0.458
83 0.35
84 0.569
85 0.455
86 0.196
87 0.436
88 0.516
89 0.85
9 0.547
90 0.506
91 0.142
92 0.893
93 0.256
94 0.956
95 0.0323
96 0.66
97 0.747
98 0.689
99 0.633



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: CNhs12631


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)
0002610 (raphe nuclei neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0004121 (ectoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0004684 (raphe nuclei)
0001016 (nervous system)
0002275 (reticular formation)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000205 (mouse raphe nuclei 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)