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FF:11810-124E1

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Name:neurospheres - enteric neuron derived, biol_rep1
Species:Mouse (Mus musculus)
Library ID:CNhs13087
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 numberEN1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005149
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13087 CAGE DRX008862 DRR009734
Accession ID Mm9

Library idBAMCTSS
CNhs13087 DRZ001159 DRZ002544
Accession ID Mm10

Library idBAMCTSS
CNhs13087 DRZ012509 DRZ013894
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

CNhs13087

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.0166
10 0
100 0
1000 --0.0121
1001 --0.0749
1002 --0.0644
1003 --0.089
1004 0
1005 --0.0219
1006 --0.071
1007 --0.194
1008 0
1009 --0.0572
101 0.0135
1010 0
1011 --0.215
1012 0
1013 --0.0031
1014 0.119
1015 0.159
1016 0.354
1017 0
1018 0
1019 0
102 0
1020 0.289
1021 0.119
1022 --0.251
1023 0
1024 --0.188
1025 --0.0417
1026 0
1027 0.619
1028 0
1029 --0.1
103 --0.0528
1030 0
1031 0.369
1032 --0.0575
1033 0.0488
1034 0
1035 0
1036 0.0451
1037 0
1038 0.0127
1039 --0.151
104 0
1040 0.0916
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: CNhs13087

Jaspar motif P-value
MA0002.2 4.33091e-5
MA0003.1 0.0151
MA0004.1 0.65
MA0006.1 0.407
MA0007.1 0.457
MA0009.1 0.0294
MA0014.1 0.828
MA0017.1 6.14993e-5
MA0018.2 0.00683
MA0019.1 0.15
MA0024.1 7.07538e-4
MA0025.1 0.277
MA0027.1 0.19
MA0028.1 0.388
MA0029.1 0.321
MA0030.1 0.274
MA0031.1 0.0581
MA0035.2 0.00337
MA0038.1 0.0266
MA0039.2 0.125
MA0040.1 0.803
MA0041.1 0.572
MA0042.1 0.532
MA0043.1 0.112
MA0046.1 1.21583e-9
MA0047.2 0.00126
MA0048.1 0.997
MA0050.1 0.00783
MA0051.1 0.0277
MA0052.1 1.10125e-5
MA0055.1 0.645
MA0057.1 0.129
MA0058.1 0.325
MA0059.1 0.756
MA0060.1 7.36756e-7
MA0061.1 0.0457
MA0062.2 0.993
MA0065.2 1.81272e-5
MA0066.1 0.322
MA0067.1 0.625
MA0068.1 0.0237
MA0069.1 0.377
MA0070.1 0.0952
MA0071.1 0.409
MA0072.1 0.457
MA0073.1 0.876
MA0074.1 0.762
MA0076.1 0.282
MA0077.1 0.0333
MA0078.1 0.256
MA0079.2 0.955
MA0080.2 4.13058e-10
MA0081.1 0.611
MA0083.1 0.74
MA0084.1 0.461
MA0087.1 0.637
MA0088.1 0.99
MA0090.1 0.975
MA0091.1 0.922
MA0092.1 0.973
MA0093.1 0.568
MA0099.2 0.0745
MA0100.1 0.492
MA0101.1 0.346
MA0102.2 0.583
MA0103.1 5.91639e-4
MA0104.2 0.714
MA0105.1 7.31107e-4
MA0106.1 0.225
MA0107.1 0.153
MA0108.2 0.119
MA0111.1 0.829
MA0112.2 7.37614e-6
MA0113.1 0.182
MA0114.1 2.16519e-4
MA0115.1 0.0182
MA0116.1 0.00114
MA0117.1 0.768
MA0119.1 0.0865
MA0122.1 0.813
MA0124.1 0.773
MA0125.1 0.324
MA0131.1 0.402
MA0135.1 0.143
MA0136.1 4.15299e-6
MA0137.2 0.687
MA0138.2 0.115
MA0139.1 0.0959
MA0140.1 1.44815e-4
MA0141.1 0.0118
MA0142.1 0.0685
MA0143.1 0.215
MA0144.1 0.333
MA0145.1 0.0429
MA0146.1 0.408
MA0147.1 0.99
MA0148.1 0.00469
MA0149.1 0.468
MA0150.1 0.0815
MA0152.1 0.229
MA0153.1 8.21048e-10
MA0154.1 0.00522
MA0155.1 0.428
MA0156.1 0.00115
MA0157.1 0.0359
MA0159.1 0.155
MA0160.1 0.066
MA0162.1 0.348
MA0163.1 0.00411
MA0164.1 0.573
MA0258.1 0.00873
MA0259.1 0.642



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: CNhs13087

Novel motif P-value
1 0.168
10 0.095
100 0.676
101 0.569
102 0.613
103 0.194
104 0.878
105 0.0408
106 0.0327
107 0.0606
108 0.861
109 0.0826
11 0.178
110 0.182
111 0.00579
112 0.026
113 0.405
114 0.0307
115 0.397
116 0.632
117 0.5
118 0.447
119 0.0527
12 0.605
120 0.538
121 0.0737
122 0.21
123 0.315
124 0.297
125 0.665
126 0.621
127 0.091
128 0.0231
129 0.212
13 0.0539
130 0.769
131 0.856
132 0.353
133 0.7
134 0.969
135 0.768
136 0.904
137 0.522
138 0.596
139 0.0741
14 0.348
140 0.00323
141 0.204
142 0.703
143 0.757
144 0.773
145 0.47
146 0.552
147 0.794
148 0.342
149 0.107
15 0.127
150 0.416
151 0.295
152 0.101
153 0.898
154 0.719
155 0.874
156 4.36168e-12
157 0.53
158 0.346
159 0.0306
160 0.0972
161 0.315
162 0.758
163 0.9
164 0.12
165 0.116
166 0.837
167 0.536
168 0.462
169 0.0157
17 0.0409
18 0.713
19 0.176
2 0.371
20 0.814
21 0.269
22 0.314
23 0.203
24 0.193
25 0.471
26 0.0719
27 0.29
28 0.271
29 0.718
3 0.157
30 0.454
31 0.674
32 0.0592
33 0.658
34 0.367
35 0.965
36 0.994
37 0.0663
38 0.259
39 0.498
4 0.54
40 0.606
41 0.582
42 0.368
43 0.194
44 0.163
45 0.251
46 0.272
47 0.242
48 0.161
49 0.144
5 0.255
50 0.607
51 0.587
52 0.331
53 0.295
54 0.477
55 0.938
56 0.577
57 0.706
58 0.115
59 0.0273
6 0.701
60 0.0855
61 0.317
62 0.0604
63 0.101
64 0.522
65 0.146
66 0.41
67 0.747
68 0.453
69 0.865
7 0.123
70 0.00144
71 0.176
72 0.309
73 0.217
74 0.84
75 0.197
76 0.976
77 0.176
78 0.0617
79 0.176
8 0.246
80 0.537
81 0.628
82 0.0121
83 0.273
84 0.4
85 0.131
86 0.241
87 0.436
88 0.618
89 0.0831
9 0.406
90 0.844
91 0.408
92 0.153
93 0.565
94 0.521
95 0.238
96 0.661
97 0.499
98 0.0896
99 0.292



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: CNhs13087


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)