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FF:11740-123F3

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Name:Mouse Neurons - raphe, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12636
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 numberRNARAP3
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004769
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12636 CAGE DRX008841 DRR009713
Accession ID Mm9

Library idBAMCTSS
CNhs12636 DRZ001138 DRZ002523
Accession ID Mm10

Library idBAMCTSS
CNhs12636 DRZ012488 DRZ013873
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

CNhs12636

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.777
10 0
100 0
1000 0
1001 0.097
1002 0.00416
1003 --0.0108
1004 0
1005 --0.00803
1006 0.624
1007 --0.116
1008 0
1009 --0.0912
101 --0.141
1010 0
1011 0.443
1012 0.141
1013 0.284
1014 --0.0408
1015 --0.0519
1016 --0.016
1017 0
1018 0
1019 0
102 0
1020 0.518
1021 0.0522
1022 0.0169
1023 0
1024 0
1025 0
1026 0
1027 0.356
1028 0
1029 --0.0488
103 --0.0788
1030 0
1031 --0.413
1032 0.459
1033 --0.0665
1034 0
1035 0
1036 --0.24
1037 0
1038 --0.0615
1039 0.117
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: CNhs12636

Jaspar motif P-value
MA0002.2 9.96019e-4
MA0003.1 0.302
MA0004.1 0.504
MA0006.1 0.19
MA0007.1 0.267
MA0009.1 0.763
MA0014.1 0.8
MA0017.1 4.48578e-6
MA0018.2 0.0118
MA0019.1 0.528
MA0024.1 0.0824
MA0025.1 0.00112
MA0027.1 0.109
MA0028.1 0.0838
MA0029.1 0.874
MA0030.1 0.912
MA0031.1 0.198
MA0035.2 0.0284
MA0038.1 0.898
MA0039.2 0.0286
MA0040.1 0.568
MA0041.1 0.177
MA0042.1 0.32
MA0043.1 0.0543
MA0046.1 2.67482e-8
MA0047.2 0.00107
MA0048.1 0.0531
MA0050.1 3.45223e-6
MA0051.1 3.84505e-4
MA0052.1 0.967
MA0055.1 0.0155
MA0057.1 0.355
MA0058.1 0.501
MA0059.1 0.187
MA0060.1 0.859
MA0061.1 0.025
MA0062.2 0.00192
MA0065.2 5.4068e-6
MA0066.1 0.101
MA0067.1 0.355
MA0068.1 0.212
MA0069.1 0.0458
MA0070.1 0.573
MA0071.1 0.219
MA0072.1 0.841
MA0073.1 0.943
MA0074.1 0.133
MA0076.1 0.218
MA0077.1 0.255
MA0078.1 0.932
MA0079.2 0.324
MA0080.2 2.37523e-10
MA0081.1 0.28
MA0083.1 0.00516
MA0084.1 0.658
MA0087.1 0.112
MA0088.1 0.28
MA0090.1 0.0807
MA0091.1 0.188
MA0092.1 0.14
MA0093.1 0.551
MA0099.2 0.00451
MA0100.1 0.205
MA0101.1 0.0115
MA0102.2 0.581
MA0103.1 0.236
MA0104.2 0.886
MA0105.1 0.00408
MA0106.1 0.062
MA0107.1 0.0297
MA0108.2 7.39012e-4
MA0111.1 0.926
MA0112.2 8.18438e-4
MA0113.1 0.378
MA0114.1 1.41811e-5
MA0115.1 8.97439e-5
MA0116.1 0.0637
MA0117.1 0.906
MA0119.1 0.104
MA0122.1 0.752
MA0124.1 0.663
MA0125.1 0.0447
MA0131.1 0.701
MA0135.1 0.48
MA0136.1 5.91469e-12
MA0137.2 0.115
MA0138.2 1.87678e-4
MA0139.1 0.45
MA0140.1 1.58507e-4
MA0141.1 0.0195
MA0142.1 0.447
MA0143.1 0.814
MA0144.1 0.0735
MA0145.1 0.116
MA0146.1 0.0371
MA0147.1 0.73
MA0148.1 3.98357e-4
MA0149.1 0.185
MA0150.1 0.166
MA0152.1 0.0565
MA0153.1 1.09703e-9
MA0154.1 0.0422
MA0155.1 0.417
MA0156.1 1.17721e-8
MA0157.1 0.142
MA0159.1 0.00869
MA0160.1 0.043
MA0162.1 0.233
MA0163.1 7.60967e-4
MA0164.1 0.848
MA0258.1 0.0208
MA0259.1 0.855



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: CNhs12636

Novel motif P-value
1 0.211
10 0.0448
100 0.278
101 0.94
102 0.921
103 0.0818
104 0.927
105 0.575
106 0.0564
107 0.145
108 0.493
109 0.00718
11 0.109
110 0.0495
111 0.275
112 0.00911
113 0.647
114 0.482
115 0.974
116 0.379
117 0.00421
118 0.471
119 0.169
12 0.835
120 0.762
121 0.416
122 0.832
123 2.68192e-4
124 0.181
125 0.186
126 0.0575
127 0.517
128 0.0562
129 0.197
13 3.01135e-7
130 0.128
131 0.297
132 0.682
133 0.949
134 0.0818
135 0.296
136 0.225
137 0.664
138 0.657
139 0.26
14 0.874
140 0.227
141 0.818
142 0.813
143 0.349
144 0.603
145 2.74394e-4
146 0.253
147 0.254
148 0.992
149 0.774
15 0.205
150 0.0736
151 0.777
152 0.137
153 0.432
154 0.754
155 0.41
156 0.00385
157 0.155
158 0.147
159 0.567
160 0.237
161 0.223
162 0.666
163 0.947
164 0.0442
165 0.198
166 0.44
167 0.681
168 0.523
169 0.0028
17 0.0638
18 0.807
19 0.103
2 0.678
20 0.0355
21 0.215
22 0.148
23 0.661
24 0.0579
25 0.723
26 6.88064e-8
27 0.38
28 0.754
29 0.0485
3 0.0709
30 0.808
31 0.718
32 0.572
33 0.0956
34 0.752
35 0.716
36 0.109
37 0.036
38 0.426
39 0.389
4 0.235
40 0.0827
41 0.568
42 0.149
43 0.117
44 0.944
45 0.673
46 0.0532
47 0.378
48 0.296
49 0.14
5 0.165
50 0.256
51 0.715
52 0.3
53 0.574
54 0.958
55 0.976
56 0.478
57 0.526
58 0.247
59 0.179
6 0.9
60 0.0395
61 0.041
62 0.169
63 0.156
64 0.711
65 0.366
66 0.697
67 0.668
68 0.8
69 0.435
7 0.0122
70 0.0828
71 0.00338
72 0.508
73 0.0521
74 0.969
75 0.0517
76 0.392
77 0.514
78 0.00337
79 0.0636
8 0.0649
80 0.718
81 0.795
82 0.291
83 0.142
84 0.843
85 0.191
86 0.135
87 0.462
88 0.684
89 0.617
9 0.382
90 0.0983
91 0.126
92 0.349
93 0.0471
94 0.654
95 0.0623
96 0.218
97 0.743
98 0.637
99 0.474



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: CNhs12636


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)