Personal tools

FF:11647-122D9

From FANTOM5_SSTAR

Jump to: navigation, search


Name:Mouse Neurons - cortical, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs12112
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 numberRNAMNC1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004767
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12112 CAGE DRX008833 DRR009705
Accession ID Mm9

Library idBAMCTSS
CNhs12112 DRZ001130 DRZ002515
Accession ID Mm10

Library idBAMCTSS
CNhs12112 DRZ012480 DRZ013865
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

CNhs12112

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.185
10 0
100 0.734
1000 0
1001 --0.0749
1002 0.424
1003 0.514
1004 0.0415
1005 --0.283
1006 0.0684
1007 --0.00142
1008 0
1009 --0.19
101 --0.0884
1010 0
1011 0.235
1012 0
1013 --0.217
1014 0.0829
1015 0.396
1016 0.215
1017 0
1018 0
1019 0
102 0
1020 0.461
1021 0.152
1022 --0.124
1023 0
1024 --0.14
1025 0.0517
1026 0
1027 0.413
1028 0
1029 --0.0989
103 --0.0787
1030 0
1031 --0.415
1032 --0.184
1033 --0.00479
1034 0
1035 0
1036 --0.13
1037 0
1038 0.073
1039 --0.244
104 0
1040 --0.155
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: CNhs12112

Jaspar motif P-value
MA0002.2 0.00327
MA0003.1 0.105
MA0004.1 0.905
MA0006.1 0.104
MA0007.1 0.338
MA0009.1 0.586
MA0014.1 0.389
MA0017.1 1.40466e-5
MA0018.2 0.0335
MA0019.1 0.301
MA0024.1 0.0804
MA0025.1 0.233
MA0027.1 0.796
MA0028.1 0.993
MA0029.1 0.389
MA0030.1 0.613
MA0031.1 0.115
MA0035.2 0.0654
MA0038.1 0.127
MA0039.2 0.00781
MA0040.1 0.817
MA0041.1 0.369
MA0042.1 0.927
MA0043.1 0.0326
MA0046.1 6.28547e-12
MA0047.2 5.06443e-4
MA0048.1 0.933
MA0050.1 1.38617e-9
MA0051.1 4.87098e-4
MA0052.1 3.66777e-4
MA0055.1 0.723
MA0057.1 0.0777
MA0058.1 0.729
MA0059.1 0.889
MA0060.1 3.69902e-6
MA0061.1 0.0574
MA0062.2 0.544
MA0065.2 2.52739e-5
MA0066.1 0.216
MA0067.1 0.942
MA0068.1 0.135
MA0069.1 0.048
MA0070.1 0.413
MA0071.1 0.241
MA0072.1 0.116
MA0073.1 0.849
MA0074.1 0.368
MA0076.1 0.396
MA0077.1 6.53206e-4
MA0078.1 0.00313
MA0079.2 0.853
MA0080.2 2.49737e-10
MA0081.1 0.465
MA0083.1 4.78437e-6
MA0084.1 0.563
MA0087.1 0.459
MA0088.1 0.31
MA0090.1 0.0227
MA0091.1 0.48
MA0092.1 0.29
MA0093.1 0.867
MA0099.2 2.78736e-5
MA0100.1 0.64
MA0101.1 0.19
MA0102.2 0.857
MA0103.1 0.0498
MA0104.2 0.424
MA0105.1 0.0548
MA0106.1 0.171
MA0107.1 0.059
MA0108.2 0.00167
MA0111.1 0.763
MA0112.2 2.80417e-4
MA0113.1 0.59
MA0114.1 7.59143e-5
MA0115.1 0.0341
MA0116.1 0.0936
MA0117.1 0.764
MA0119.1 0.21
MA0122.1 0.878
MA0124.1 0.779
MA0125.1 0.446
MA0131.1 0.564
MA0135.1 0.834
MA0136.1 2.28455e-7
MA0137.2 0.0854
MA0138.2 0.824
MA0139.1 0.128
MA0140.1 0.00437
MA0141.1 0.0118
MA0142.1 0.0113
MA0143.1 0.00167
MA0144.1 0.0767
MA0145.1 0.024
MA0146.1 0.0978
MA0147.1 0.409
MA0148.1 2.70966e-6
MA0149.1 0.076
MA0150.1 0.0466
MA0152.1 0.408
MA0153.1 9.4975e-11
MA0154.1 0.0151
MA0155.1 0.658
MA0156.1 3.89421e-5
MA0157.1 0.0193
MA0159.1 0.00326
MA0160.1 0.0939
MA0162.1 0.39
MA0163.1 0.00401
MA0164.1 0.991
MA0258.1 0.0134
MA0259.1 0.381



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: CNhs12112

Novel motif P-value
1 0.201
10 0.207
100 0.938
101 0.663
102 0.718
103 0.156
104 0.855
105 0.414
106 0.00847
107 0.0317
108 0.48
109 0.00384
11 0.148
110 0.158
111 0.0425
112 0.00529
113 0.905
114 0.276
115 0.0853
116 0.562
117 0.199
118 0.64
119 0.141
12 0.547
120 0.882
121 0.23
122 0.365
123 0.669
124 0.741
125 0.53
126 0.268
127 0.184
128 0.0328
129 0.155
13 3.47606e-5
130 0.675
131 0.64
132 0.843
133 0.386
134 0.562
135 0.162
136 0.0843
137 0.23
138 0.696
139 0.281
14 0.568
140 0.338
141 0.0736
142 0.117
143 0.798
144 0.903
145 0.0969
146 0.38
147 0.94
148 0.868
149 0.0725
15 0.258
150 0.265
151 0.335
152 0.0356
153 0.794
154 0.928
155 0.578
156 0.00454
157 0.163
158 0.205
159 0.02
160 0.372
161 0.26
162 0.844
163 0.0699
164 0.0188
165 0.00938
166 0.587
167 0.949
168 0.651
169 0.00668
17 0.031
18 0.784
19 0.0376
2 0.448
20 0.905
21 0.689
22 0.0819
23 0.21
24 0.0355
25 0.623
26 0.00516
27 0.65
28 0.334
29 0.277
3 0.106
30 0.439
31 0.84
32 0.346
33 0.244
34 0.576
35 0.54
36 0.693
37 0.00536
38 0.382
39 0.165
4 0.643
40 0.201
41 0.952
42 0.41
43 0.146
44 0.533
45 0.427
46 0.283
47 0.297
48 0.233
49 0.19
5 0.214
50 0.276
51 0.563
52 0.0654
53 0.495
54 0.547
55 0.733
56 0.297
57 0.918
58 0.224
59 0.0782
6 0.61
60 0.00961
61 0.359
62 0.132
63 0.145
64 0.971
65 0.357
66 0.614
67 0.954
68 0.919
69 0.411
7 0.0284
70 0.0452
71 0.0412
72 0.339
73 0.0148
74 0.72
75 0.154
76 0.873
77 0.145
78 0.0576
79 0.75
8 0.318
80 0.971
81 0.284
82 0.0674
83 0.251
84 0.962
85 0.0514
86 0.236
87 0.262
88 0.531
89 0.163
9 0.337
90 0.415
91 0.353
92 0.081
93 0.0781
94 0.641
95 0.0416
96 0.206
97 0.818
98 0.663
99 0.136



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: CNhs12112


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)