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FF:11721-123D2

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Name:Mouse Neurons - hippocampal, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs12133
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
tissuehippocampus
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 numberRNAMNh1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005801
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12133 CAGE DRX008837 DRR009709
Accession ID Mm9

Library idBAMCTSS
CNhs12133 DRZ001134 DRZ002519
Accession ID Mm10

Library idBAMCTSS
CNhs12133 DRZ012484 DRZ013869
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

CNhs12133

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.238
10 0
100 0.568
1000 --0.0104
1001 --0.0498
1002 0.202
1003 0.0522
1004 0.0251
1005 --0.184
1006 0.158
1007 0.00165
1008 0
1009 --0.2
101 --0.0723
1010 0
1011 0.1
1012 0.0446
1013 --0.16
1014 0
1015 0.433
1016 0.034
1017 0
1018 0
1019 0
102 0
1020 0.568
1021 0.191
1022 --0.124
1023 0
1024 --0.171
1025 --0.0611
1026 0
1027 0.489
1028 0
1029 --0.148
103 --0.0861
1030 0
1031 --0.529
1032 --0.177
1033 --0.025
1034 0
1035 0
1036 --0.0877
1037 0
1038 0.0726
1039 --0.233
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: CNhs12133

Jaspar motif P-value
MA0002.2 0.00226
MA0003.1 0.126
MA0004.1 0.882
MA0006.1 0.0885
MA0007.1 0.197
MA0009.1 0.961
MA0014.1 0.374
MA0017.1 2.03512e-5
MA0018.2 0.0114
MA0019.1 0.263
MA0024.1 0.015
MA0025.1 0.299
MA0027.1 0.647
MA0028.1 0.878
MA0029.1 0.513
MA0030.1 0.383
MA0031.1 0.06
MA0035.2 0.11
MA0038.1 0.0134
MA0039.2 0.0108
MA0040.1 0.857
MA0041.1 0.215
MA0042.1 0.476
MA0043.1 0.0162
MA0046.1 1.8521e-9
MA0047.2 6.1223e-4
MA0048.1 0.673
MA0050.1 1.0469e-8
MA0051.1 0.00106
MA0052.1 0.00618
MA0055.1 0.8
MA0057.1 0.0552
MA0058.1 0.819
MA0059.1 0.757
MA0060.1 2.36763e-9
MA0061.1 0.05
MA0062.2 0.783
MA0065.2 3.85793e-5
MA0066.1 0.187
MA0067.1 0.849
MA0068.1 0.303
MA0069.1 0.0814
MA0070.1 0.552
MA0071.1 0.23
MA0072.1 0.238
MA0073.1 0.921
MA0074.1 0.337
MA0076.1 0.289
MA0077.1 0.00344
MA0078.1 0.00582
MA0079.2 0.761
MA0080.2 9.09905e-11
MA0081.1 0.448
MA0083.1 1.07457e-5
MA0084.1 0.529
MA0087.1 0.58
MA0088.1 0.401
MA0090.1 0.0099
MA0091.1 0.409
MA0092.1 0.21
MA0093.1 0.882
MA0099.2 8.14343e-5
MA0100.1 0.651
MA0101.1 0.136
MA0102.2 0.731
MA0103.1 0.0705
MA0104.2 0.356
MA0105.1 0.0833
MA0106.1 0.155
MA0107.1 0.0761
MA0108.2 0.00877
MA0111.1 0.889
MA0112.2 2.70533e-4
MA0113.1 0.525
MA0114.1 1.30914e-4
MA0115.1 0.0425
MA0116.1 0.112
MA0117.1 0.838
MA0119.1 0.132
MA0122.1 0.914
MA0124.1 0.929
MA0125.1 0.133
MA0131.1 0.556
MA0135.1 0.36
MA0136.1 4.65355e-7
MA0137.2 0.0521
MA0138.2 0.741
MA0139.1 0.224
MA0140.1 0.00723
MA0141.1 0.0089
MA0142.1 0.00167
MA0143.1 9.53859e-4
MA0144.1 0.0485
MA0145.1 0.0261
MA0146.1 0.0496
MA0147.1 0.415
MA0148.1 1.55932e-5
MA0149.1 0.092
MA0150.1 0.0658
MA0152.1 0.381
MA0153.1 1.94808e-8
MA0154.1 0.0209
MA0155.1 0.629
MA0156.1 2.94742e-4
MA0157.1 0.0198
MA0159.1 0.00361
MA0160.1 0.0914
MA0162.1 0.277
MA0163.1 0.00775
MA0164.1 0.935
MA0258.1 0.00965
MA0259.1 0.403



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: CNhs12133

Novel motif P-value
1 0.179
10 0.203
100 0.995
101 0.955
102 0.796
103 0.073
104 0.933
105 0.229
106 0.00517
107 0.0281
108 0.666
109 0.00285
11 0.0766
110 0.146
111 0.0265
112 0.00372
113 0.992
114 0.13
115 0.279
116 0.557
117 0.198
118 0.474
119 0.144
12 0.477
120 0.963
121 0.285
122 0.662
123 0.584
124 0.567
125 0.505
126 0.205
127 0.102
128 0.0142
129 0.0992
13 3.42542e-5
130 0.775
131 0.532
132 0.756
133 0.228
134 0.488
135 0.208
136 0.0773
137 0.335
138 0.579
139 0.151
14 0.606
140 0.398
141 0.12
142 0.23
143 0.812
144 0.859
145 0.0425
146 0.439
147 0.965
148 0.5
149 0.0465
15 0.194
150 0.199
151 0.388
152 0.0289
153 0.961
154 0.989
155 0.384
156 0.00409
157 0.168
158 0.301
159 0.0178
160 0.228
161 0.368
162 0.752
163 0.167
164 0.0254
165 0.0132
166 0.618
167 0.572
168 0.729
169 0.00697
17 0.021
18 0.772
19 0.0375
2 0.506
20 0.869
21 0.546
22 0.0664
23 0.181
24 0.0365
25 0.841
26 0.00123
27 0.671
28 0.432
29 0.314
3 0.0964
30 0.519
31 0.701
32 0.225
33 0.283
34 0.534
35 0.521
36 0.917
37 0.00977
38 0.348
39 0.152
4 0.569
40 0.289
41 0.856
42 0.355
43 0.142
44 0.54
45 0.38
46 0.184
47 0.194
48 0.161
49 0.175
5 0.192
50 0.226
51 0.581
52 0.0756
53 0.634
54 0.579
55 0.921
56 0.305
57 0.717
58 0.306
59 0.0604
6 0.628
60 0.00987
61 0.267
62 0.163
63 0.106
64 0.927
65 0.28
66 0.572
67 0.711
68 0.447
69 0.379
7 0.0393
70 0.013
71 0.0394
72 0.382
73 0.0136
74 0.339
75 0.131
76 0.851
77 0.138
78 0.0383
79 0.611
8 0.222
80 0.865
81 0.374
82 0.0302
83 0.0992
84 0.866
85 0.0303
86 0.304
87 0.338
88 0.347
89 0.318
9 0.315
90 0.409
91 0.27
92 0.117
93 0.0364
94 0.93
95 0.0444
96 0.314
97 0.876
98 0.701
99 0.168



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: CNhs12133


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)
0002608 (hippocampal neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0001954 (Ammon's horn)
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)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0003022 (lobe parts of cerebral cortex)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002421 (hippocampal formation)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0000349 (limbic system)
0002600 (limbic lobe)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000201 (hippocampal neuron sample)
0000203 (mouse neuron samples)
0000202 (mouse hippocampal 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)