Personal tools

FF:11811-124E2

From FANTOM5_SSTAR

Jump to: navigation, search


Name:neurospheres - enteric neuron derived, biol_rep2
Species:Mouse (Mus musculus)
Library ID:CNhs13088
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
tissueANATOMICAL SYSTEM
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companyNA
collaborationHideki Enomoto (RIKEN CDB)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberEN2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005784
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13088 CAGE DRX008863 DRR009735
Accession ID Mm9

Library idBAMCTSS
CNhs13088 DRZ001160 DRZ002545
Accession ID Mm10

Library idBAMCTSS
CNhs13088 DRZ012510 DRZ013895
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

CNhs13088

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.0216
10 0
100 0
1000 0
1001 --0.0749
1002 --0.116
1003 --0.0693
1004 0
1005 --0.0824
1006 0
1007 --0.144
1008 0
1009 --0.0468
101 0.0454
1010 0
1011 --0.132
1012 0
1013 --0.0382
1014 --0.0229
1015 0.101
1016 0.289
1017 0
1018 0
1019 0
102 0
1020 0.251
1021 0.202
1022 --0.124
1023 0
1024 --0.164
1025 0
1026 0
1027 0.476
1028 0
1029 --0.115
103 --0.0532
1030 0
1031 0.322
1032 0.112
1033 0.143
1034 0
1035 0
1036 0.129
1037 0
1038 --0.0109
1039 --0.13
104 0
1040 0.26
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: CNhs13088

Jaspar motif P-value
MA0002.2 6.33801e-4
MA0003.1 0.0133
MA0004.1 0.731
MA0006.1 0.421
MA0007.1 0.497
MA0009.1 0.0337
MA0014.1 0.699
MA0017.1 6.96045e-6
MA0018.2 0.00458
MA0019.1 0.218
MA0024.1 0.00185
MA0025.1 0.508
MA0027.1 0.207
MA0028.1 0.315
MA0029.1 0.0627
MA0030.1 0.13
MA0031.1 0.0163
MA0035.2 9.2183e-4
MA0038.1 0.00527
MA0039.2 0.138
MA0040.1 0.971
MA0041.1 0.407
MA0042.1 0.857
MA0043.1 0.253
MA0046.1 5.23907e-16
MA0047.2 1.39905e-4
MA0048.1 0.801
MA0050.1 0.00193
MA0051.1 0.0093
MA0052.1 0.00581
MA0055.1 0.878
MA0057.1 0.0532
MA0058.1 0.385
MA0059.1 0.719
MA0060.1 9.26713e-8
MA0061.1 0.0525
MA0062.2 0.82
MA0065.2 1.68393e-6
MA0066.1 0.189
MA0067.1 0.573
MA0068.1 0.073
MA0069.1 0.367
MA0070.1 0.316
MA0071.1 0.541
MA0072.1 0.605
MA0073.1 0.866
MA0074.1 0.76
MA0076.1 0.244
MA0077.1 0.026
MA0078.1 0.155
MA0079.2 0.802
MA0080.2 1.36667e-8
MA0081.1 0.539
MA0083.1 0.95
MA0084.1 0.91
MA0087.1 0.824
MA0088.1 0.736
MA0090.1 0.77
MA0091.1 0.63
MA0092.1 0.953
MA0093.1 0.678
MA0099.2 0.141
MA0100.1 0.537
MA0101.1 0.254
MA0102.2 0.776
MA0103.1 7.03716e-4
MA0104.2 0.7
MA0105.1 9.87127e-4
MA0106.1 0.148
MA0107.1 0.105
MA0108.2 0.14
MA0111.1 0.751
MA0112.2 1.59787e-5
MA0113.1 0.084
MA0114.1 3.12686e-5
MA0115.1 0.013
MA0116.1 6.74547e-4
MA0117.1 0.817
MA0119.1 0.0617
MA0122.1 0.988
MA0124.1 0.913
MA0125.1 0.376
MA0131.1 0.461
MA0135.1 0.234
MA0136.1 2.61218e-5
MA0137.2 0.564
MA0138.2 0.178
MA0139.1 0.106
MA0140.1 6.79003e-5
MA0141.1 0.0129
MA0142.1 0.019
MA0143.1 0.0565
MA0144.1 0.352
MA0145.1 0.0444
MA0146.1 0.44
MA0147.1 0.945
MA0148.1 0.00255
MA0149.1 0.509
MA0150.1 0.141
MA0152.1 0.521
MA0153.1 1.04044e-13
MA0154.1 0.00358
MA0155.1 0.354
MA0156.1 0.00466
MA0157.1 0.05
MA0159.1 0.263
MA0160.1 0.104
MA0162.1 0.38
MA0163.1 0.00939
MA0164.1 0.932
MA0258.1 0.00976
MA0259.1 0.796



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: CNhs13088

Novel motif P-value
1 0.142
10 0.109
100 0.728
101 0.972
102 0.794
103 0.136
104 0.851
105 0.0655
106 0.0167
107 0.114
108 0.824
109 0.0573
11 0.131
110 0.206
111 0.0298
112 0.0297
113 0.424
114 0.0534
115 0.642
116 0.685
117 0.35
118 0.353
119 0.0223
12 0.676
120 0.643
121 0.323
122 0.315
123 0.53
124 0.549
125 0.941
126 0.247
127 0.124
128 0.0501
129 0.13
13 0.0371
130 0.542
131 0.292
132 0.289
133 0.549
134 0.895
135 0.824
136 0.999
137 0.295
138 0.747
139 0.122
14 0.37
140 3.30797e-4
141 0.502
142 0.712
143 0.573
144 0.81
145 0.533
146 0.692
147 0.888
148 0.455
149 0.169
15 0.141
150 0.495
151 0.325
152 0.0857
153 0.64
154 0.886
155 0.974
156 3.82151e-9
157 0.599
158 0.251
159 0.0451
160 0.127
161 0.275
162 0.981
163 0.806
164 0.212
165 0.363
166 0.759
167 0.472
168 0.688
169 0.00654
17 0.0457
18 0.718
19 0.138
2 0.457
20 0.796
21 0.483
22 0.236
23 0.161
24 0.181
25 0.432
26 0.0303
27 0.37
28 0.318
29 0.694
3 0.0996
30 0.459
31 0.626
32 0.0499
33 0.578
34 0.337
35 0.791
36 0.933
37 0.0545
38 0.255
39 0.253
4 0.682
40 0.53
41 0.79
42 0.313
43 0.176
44 0.248
45 0.3
46 0.218
47 0.208
48 0.121
49 0.137
5 0.249
50 0.526
51 0.437
52 0.364
53 0.324
54 0.428
55 0.781
56 0.584
57 0.697
58 0.0819
59 0.0234
6 0.864
60 0.0942
61 0.205
62 0.0408
63 0.076
64 0.463
65 0.112
66 0.487
67 0.577
68 0.304
69 0.497
7 0.0993
70 0.00192
71 0.181
72 0.358
73 0.203
74 0.989
75 0.175
76 0.84
77 0.172
78 0.0645
79 0.147
8 0.157
80 0.504
81 0.607
82 0.0165
83 0.369
84 0.343
85 0.0783
86 0.256
87 0.267
88 0.607
89 0.0317
9 0.373
90 0.604
91 0.231
92 0.194
93 0.611
94 0.573
95 0.19
96 0.645
97 0.634
98 0.133
99 0.29



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: CNhs13088


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)
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0000107 (autonomic neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0002410 (autonomic nervous system)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0010313 (neural crest-derived structure)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0000010 (peripheral nervous system)
0002005 (enteric nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0011142 (mouse neurospheres - enteric neuron derived 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:0000031 (neuroblast)
CL:0000221 (ectodermal cell)