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FF:11846-124I1

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Name:GP2+ M cell, pool2
Species:Mouse (Mus musculus)
Library ID:CNhs13231
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_b
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005557
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13231 CAGE DRX008766 DRR009638
Accession ID Mm9

Library idBAMCTSS
CNhs13231 DRZ001063 DRZ002448
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

CNhs13231

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 1.267
1006 --0.436
1007 --0.0093
1008 1.685
1009 --0.19
101 --0.243
1010 0
1011 --0.337
1012 0
1013 0.31
1014 --0.0874
1015 --0.325
1016 --0.581
1017 0
1018 0.604
1019 0
102 0
1020 0
1021 0
1022 --0.0704
1023 0
1024 --0.2
1025 0
1026 0
1027 --0.048
1028 0
1029 --0.148
103 --0.0887
1030 0
1031 --0.961
1032 1.045
1033 0
1034 0
1035 0
1036 --0.183
1037 0
1038 0.0712
1039 0.08
104 0
1040 --0.983
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: CNhs13231

Jaspar motif P-value
MA0002.2 0.0186
MA0003.1 0.342
MA0004.1 0.691
MA0006.1 0.0783
MA0007.1 0.178
MA0009.1 0.166
MA0014.1 0.0838
MA0017.1 1.80682e-28
MA0018.2 0.596
MA0019.1 0.0509
MA0024.1 0.00476
MA0025.1 0.533
MA0027.1 0.933
MA0028.1 0.0437
MA0029.1 0.963
MA0030.1 0.478
MA0031.1 0.349
MA0035.2 6.03306e-5
MA0038.1 0.452
MA0039.2 9.58271e-6
MA0040.1 0.0959
MA0041.1 0.223
MA0042.1 0.222
MA0043.1 0.749
MA0046.1 1.08992e-55
MA0047.2 0.0085
MA0048.1 0.28
MA0050.1 2.21285e-4
MA0051.1 1.09003e-5
MA0052.1 0.389
MA0055.1 0.253
MA0057.1 0.0717
MA0058.1 0.801
MA0059.1 0.831
MA0060.1 0.0892
MA0061.1 0.00232
MA0062.2 7.52286e-5
MA0065.2 2.17264e-15
MA0066.1 0.0648
MA0067.1 0.999
MA0068.1 0.101
MA0069.1 0.617
MA0070.1 0.135
MA0071.1 0.0303
MA0072.1 0.94
MA0073.1 0.844
MA0074.1 0.244
MA0076.1 0.135
MA0077.1 0.442
MA0078.1 0.507
MA0079.2 0.468
MA0080.2 2.12839e-5
MA0081.1 0.954
MA0083.1 0.46
MA0084.1 0.208
MA0087.1 0.238
MA0088.1 0.243
MA0090.1 0.471
MA0091.1 0.323
MA0092.1 0.595
MA0093.1 0.759
MA0099.2 7.2398e-11
MA0100.1 0.723
MA0101.1 6.52458e-6
MA0102.2 0.564
MA0103.1 7.95617e-7
MA0104.2 0.263
MA0105.1 0.115
MA0106.1 0.296
MA0107.1 8.79905e-6
MA0108.2 0.0014
MA0111.1 0.593
MA0112.2 0.00189
MA0113.1 0.55
MA0114.1 7.3462e-33
MA0115.1 7.95636e-15
MA0116.1 0.303
MA0117.1 0.385
MA0119.1 0.0743
MA0122.1 0.786
MA0124.1 0.596
MA0125.1 0.678
MA0131.1 0.721
MA0135.1 0.243
MA0136.1 1.21742e-9
MA0137.2 0.0082
MA0138.2 0.896
MA0139.1 0.193
MA0140.1 0.151
MA0141.1 1.63856e-7
MA0142.1 0.0786
MA0143.1 0.229
MA0144.1 0.00134
MA0145.1 0.014
MA0146.1 0.0744
MA0147.1 0.341
MA0148.1 0.00633
MA0149.1 0.0403
MA0150.1 0.013
MA0152.1 0.105
MA0153.1 7.69532e-45
MA0154.1 0.075
MA0155.1 0.832
MA0156.1 6.74088e-5
MA0157.1 0.817
MA0159.1 1.85653e-4
MA0160.1 2.33813e-5
MA0162.1 0.762
MA0163.1 0.416
MA0164.1 0.917
MA0258.1 0.0289
MA0259.1 0.663



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: CNhs13231

Novel motif P-value
1 0.168
10 0.284
100 0.881
101 0.783
102 0.888
103 0.382
104 0.998
105 0.112
106 0.0107
107 0.123
108 0.645
109 0.031
11 0.142
110 0.466
111 0.121
112 0.0164
113 0.206
114 0.145
115 0.857
116 0.0785
117 0.0343
118 0.579
119 0.144
12 0.583
120 0.692
121 0.338
122 0.951
123 0.0733
124 0.227
125 0.234
126 0.0582
127 0.187
128 0.134
129 0.127
13 9.40537e-5
130 0.807
131 0.746
132 0.639
133 0.293
134 0.917
135 0.135
136 0.0155
137 0.765
138 0.155
139 0.143
14 0.67
140 0.804
141 0.125
142 0.841
143 0.219
144 0.287
145 0.167
146 0.21
147 0.59
148 0.695
149 0.804
15 0.123
150 0.405
151 0.847
152 0.0159
153 0.77
154 0.758
155 0.289
156 0.0964
157 0.34
158 0.561
159 0.627
160 0.705
161 0.788
162 0.772
163 0.251
164 0.1
165 0.09
166 0.916
167 0.787
168 0.91
169 0.0331
17 0.0274
18 0.999
19 0.314
2 0.685
20 0.322
21 0.998
22 0.241
23 0.455
24 0.548
25 0.446
26 0.0115
27 0.957
28 0.324
29 0.0686
3 0.207
30 0.372
31 0.774
32 0.363
33 0.275
34 0.729
35 0.833
36 0.584
37 0.0324
38 0.421
39 0.441
4 0.261
40 0.176
41 0.0953
42 0.716
43 0.288
44 0.277
45 0.337
46 0.368
47 0.48
48 0.264
49 0.351
5 0.633
50 0.417
51 0.605
52 0.128
53 0.509
54 0.391
55 0.541
56 0.502
57 0.94
58 0.239
59 0.243
6 0.638
60 0.0314
61 0.341
62 0.214
63 0.0955
64 0.752
65 0.284
66 0.997
67 0.655
68 0.0548
69 0.988
7 0.0672
70 0.00331
71 0.153
72 0.3
73 0.0183
74 0.981
75 0.0184
76 0.689
77 0.0711
78 0.0267
79 0.924
8 0.279
80 0.749
81 0.955
82 0.0942
83 0.334
84 0.0759
85 0.115
86 0.139
87 0.0115
88 0.268
89 0.247
9 0.94
90 0.335
91 0.66
92 0.54
93 0.222
94 0.783
95 0.00465
96 0.922
97 0.809
98 0.626
99 0.418



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: CNhs13231


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