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FF:11847-124I2

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Name:GP2+ M cell, pool3
Species:Mouse (Mus musculus)
Library ID:CNhs13240
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
strainBalb/c
tissueileum
dev stageadult
sexmale
ageNA
cell typeM cell
cell lineNA
companyNA
collaborationShinji Fukuda (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberM cell_c
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005004
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13240 CAGE DRX008767 DRR009639
Accession ID Mm9

Library idBAMCTSS
CNhs13240 DRZ001064 DRZ002449
Accession ID Mm10

Library idBAMCTSS
CNhs13240 DRZ012414 DRZ013799
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

CNhs13240

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0749
1002 --0.116
1003 --0.123
1004 0
1005 1.131
1006 --0.364
1007 0.0188
1008 1.884
1009 --0.157
101 --0.137
1010 0
1011 --0.337
1012 0
1013 0.368
1014 --0.0874
1015 --0.258
1016 --0.465
1017 0
1018 0.648
1019 0
102 0
1020 0
1021 0
1022 --0.0931
1023 0
1024 --0.291
1025 --0.00155
1026 0
1027 --0.048
1028 0
1029 --0.0912
103 --0.0887
1030 0
1031 --0.961
1032 0.872
1033 0.00952
1034 0
1035 0
1036 --0.186
1037 0
1038 --0.0435
1039 0.0748
104 0
1040 --0.79
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: CNhs13240

Jaspar motif P-value
MA0002.2 0.034
MA0003.1 0.338
MA0004.1 0.657
MA0006.1 0.105
MA0007.1 0.322
MA0009.1 0.132
MA0014.1 0.0594
MA0017.1 2.5709e-27
MA0018.2 0.266
MA0019.1 0.067
MA0024.1 0.0334
MA0025.1 0.739
MA0027.1 0.908
MA0028.1 0.00967
MA0029.1 0.862
MA0030.1 0.746
MA0031.1 0.488
MA0035.2 1.35321e-5
MA0038.1 0.685
MA0039.2 5.58813e-6
MA0040.1 0.0843
MA0041.1 0.231
MA0042.1 0.278
MA0043.1 0.552
MA0046.1 1.85992e-55
MA0047.2 0.0153
MA0048.1 0.211
MA0050.1 2.88541e-4
MA0051.1 2.3227e-5
MA0052.1 0.24
MA0055.1 0.13
MA0057.1 0.0538
MA0058.1 0.71
MA0059.1 0.874
MA0060.1 0.419
MA0061.1 0.00104
MA0062.2 5.08219e-6
MA0065.2 6.99639e-15
MA0066.1 0.132
MA0067.1 0.812
MA0068.1 0.101
MA0069.1 0.779
MA0070.1 0.158
MA0071.1 0.068
MA0072.1 0.83
MA0073.1 0.972
MA0074.1 0.297
MA0076.1 0.041
MA0077.1 0.365
MA0078.1 0.701
MA0079.2 0.447
MA0080.2 7.24917e-6
MA0081.1 0.739
MA0083.1 0.227
MA0084.1 0.185
MA0087.1 0.263
MA0088.1 0.207
MA0090.1 0.623
MA0091.1 0.298
MA0092.1 0.607
MA0093.1 0.702
MA0099.2 1.06378e-11
MA0100.1 0.903
MA0101.1 2.32481e-6
MA0102.2 0.602
MA0103.1 3.14102e-7
MA0104.2 0.441
MA0105.1 0.0585
MA0106.1 0.313
MA0107.1 1.47958e-6
MA0108.2 6.72333e-4
MA0111.1 0.454
MA0112.2 0.00298
MA0113.1 0.738
MA0114.1 7.61666e-32
MA0115.1 1.20966e-16
MA0116.1 0.245
MA0117.1 0.351
MA0119.1 0.122
MA0122.1 0.877
MA0124.1 0.611
MA0125.1 0.998
MA0131.1 0.93
MA0135.1 0.176
MA0136.1 3.32226e-11
MA0137.2 0.00282
MA0138.2 0.981
MA0139.1 0.151
MA0140.1 0.131
MA0141.1 1.93406e-6
MA0142.1 0.0451
MA0143.1 0.121
MA0144.1 7.38099e-4
MA0145.1 0.0132
MA0146.1 0.101
MA0147.1 0.558
MA0148.1 0.016
MA0149.1 0.0282
MA0150.1 0.0119
MA0152.1 0.165
MA0153.1 1.27712e-45
MA0154.1 0.0503
MA0155.1 0.85
MA0156.1 3.39389e-6
MA0157.1 0.738
MA0159.1 5.20485e-4
MA0160.1 4.31782e-5
MA0162.1 0.64
MA0163.1 0.275
MA0164.1 0.834
MA0258.1 0.0558
MA0259.1 0.841



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: CNhs13240

Novel motif P-value
1 0.172
10 0.205
100 0.895
101 0.69
102 0.85
103 0.465
104 0.969
105 0.193
106 0.0197
107 0.142
108 0.651
109 0.0345
11 0.143
110 0.404
111 0.155
112 0.0284
113 0.164
114 0.213
115 0.892
116 0.0915
117 0.027
118 0.589
119 0.143
12 0.654
120 0.442
121 0.247
122 0.995
123 0.0974
124 0.108
125 0.592
126 0.0665
127 0.235
128 0.22
129 0.19
13 3.16139e-5
130 0.871
131 0.897
132 0.743
133 0.493
134 0.958
135 0.103
136 0.00744
137 0.81
138 0.265
139 0.188
14 0.751
140 0.882
141 0.153
142 0.988
143 0.146
144 0.166
145 0.148
146 0.24
147 0.792
148 0.839
149 0.857
15 0.117
150 0.421
151 0.985
152 0.0268
153 0.85
154 0.742
155 0.366
156 0.0715
157 0.409
158 0.661
159 0.714
160 0.872
161 0.805
162 0.551
163 0.061
164 0.0963
165 0.153
166 0.647
167 0.771
168 0.938
169 0.0262
17 0.0401
18 0.85
19 0.297
2 0.846
20 0.308
21 0.981
22 0.276
23 0.539
24 0.456
25 0.455
26 0.0126
27 0.995
28 0.34
29 0.0798
3 0.196
30 0.353
31 0.923
32 0.257
33 0.195
34 0.881
35 0.968
36 0.581
37 0.0254
38 0.429
39 0.386
4 0.202
40 0.214
41 0.134
42 0.75
43 0.311
44 0.152
45 0.365
46 0.408
47 0.417
48 0.224
49 0.445
5 0.738
50 0.387
51 0.677
52 0.164
53 0.458
54 0.43
55 0.503
56 0.5
57 0.844
58 0.274
59 0.246
6 0.65
60 0.031
61 0.303
62 0.227
63 0.0951
64 0.722
65 0.296
66 0.826
67 0.479
68 0.0769
69 0.957
7 0.0651
70 0.0142
71 0.169
72 0.256
73 0.0226
74 0.663
75 0.0171
76 0.733
77 0.0558
78 0.0195
79 0.803
8 0.334
80 0.913
81 0.973
82 0.16
83 0.533
84 0.123
85 0.149
86 0.151
87 0.00562
88 0.259
89 0.281
9 0.979
90 0.311
91 0.925
92 0.562
93 0.23
94 0.745
95 0.00213
96 0.979
97 0.813
98 0.509
99 0.42



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: CNhs13240


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)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000473 (defensive cell)
0000255 (eukaryotic cell)
0000627 (transporting cell)
0000682 (M cell of gut)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0011159 (mouse GP2-positive M cell 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

NA