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FF:11845-124H9

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Name:GP2+ M cell, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs13228
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_a
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004773
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13228 CAGE DRX008765 DRR009637
Accession ID Mm9

Library idBAMCTSS
CNhs13228 DRZ001062 DRZ002447
Accession ID Mm10

Library idBAMCTSS
CNhs13228 DRZ012412 DRZ013797
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

CNhs13228

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 --0.175
1004 0
1005 1.179
1006 --0.264
1007 --0.0374
1008 1.218
1009 --0.177
101 --0.344
1010 0
1011 --0.337
1012 0
1013 0.348
1014 --0.0874
1015 --0.428
1016 --0.594
1017 0
1018 0.518
1019 0
102 0
1020 0
1021 0
1022 --0.0704
1023 0
1024 --0.307
1025 0
1026 0
1027 --0.048
1028 0
1029 --0.176
103 --0.0887
1030 0
1031 --0.911
1032 1.065
1033 0
1034 0
1035 0
1036 --0.0428
1037 0
1038 --0.0166
1039 0.00176
104 0
1040 --0.728
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: CNhs13228

Jaspar motif P-value
MA0002.2 0.0107
MA0003.1 0.387
MA0004.1 0.845
MA0006.1 0.0771
MA0007.1 0.284
MA0009.1 0.0663
MA0014.1 0.0541
MA0017.1 4.20677e-29
MA0018.2 0.207
MA0019.1 0.0535
MA0024.1 4.97107e-4
MA0025.1 0.933
MA0027.1 0.895
MA0028.1 0.0769
MA0029.1 0.901
MA0030.1 0.635
MA0031.1 0.195
MA0035.2 6.97773e-6
MA0038.1 0.517
MA0039.2 5.01859e-6
MA0040.1 0.0777
MA0041.1 0.278
MA0042.1 0.286
MA0043.1 0.665
MA0046.1 1.37008e-49
MA0047.2 0.0231
MA0048.1 0.358
MA0050.1 0.00136
MA0051.1 4.56306e-5
MA0052.1 0.594
MA0055.1 0.256
MA0057.1 0.0752
MA0058.1 0.948
MA0059.1 0.736
MA0060.1 0.222
MA0061.1 0.00521
MA0062.2 3.44942e-4
MA0065.2 1.94103e-16
MA0066.1 0.126
MA0067.1 0.714
MA0068.1 0.0766
MA0069.1 0.741
MA0070.1 0.289
MA0071.1 0.042
MA0072.1 0.683
MA0073.1 0.829
MA0074.1 0.167
MA0076.1 0.204
MA0077.1 0.448
MA0078.1 0.892
MA0079.2 0.482
MA0080.2 4.3483e-5
MA0081.1 0.805
MA0083.1 0.396
MA0084.1 0.138
MA0087.1 0.295
MA0088.1 0.451
MA0090.1 0.462
MA0091.1 0.253
MA0092.1 0.404
MA0093.1 0.908
MA0099.2 1.30744e-11
MA0100.1 0.886
MA0101.1 6.14946e-5
MA0102.2 0.642
MA0103.1 1.47984e-6
MA0104.2 0.118
MA0105.1 0.157
MA0106.1 0.287
MA0107.1 7.56356e-5
MA0108.2 6.25441e-4
MA0111.1 0.424
MA0112.2 0.00268
MA0113.1 0.936
MA0114.1 2.75589e-34
MA0115.1 1.55177e-16
MA0116.1 0.388
MA0117.1 0.243
MA0119.1 0.0821
MA0122.1 0.816
MA0124.1 0.468
MA0125.1 0.92
MA0131.1 0.556
MA0135.1 0.392
MA0136.1 6.21259e-8
MA0137.2 0.017
MA0138.2 0.868
MA0139.1 0.201
MA0140.1 0.147
MA0141.1 8.01488e-8
MA0142.1 0.071
MA0143.1 0.233
MA0144.1 0.00173
MA0145.1 0.00795
MA0146.1 0.14
MA0147.1 0.156
MA0148.1 0.0239
MA0149.1 0.0187
MA0150.1 0.00498
MA0152.1 0.133
MA0153.1 9.61844e-42
MA0154.1 0.0444
MA0155.1 0.812
MA0156.1 3.03693e-4
MA0157.1 0.836
MA0159.1 1.56802e-4
MA0160.1 6.87295e-6
MA0162.1 0.68
MA0163.1 0.589
MA0164.1 0.995
MA0258.1 0.0614
MA0259.1 0.557



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: CNhs13228

Novel motif P-value
1 0.178
10 0.304
100 0.867
101 0.958
102 0.799
103 0.52
104 0.88
105 0.0859
106 0.0128
107 0.126
108 0.597
109 0.0469
11 0.13
110 0.393
111 0.216
112 0.0177
113 0.22
114 0.12
115 0.488
116 0.095
117 0.0564
118 0.541
119 0.141
12 0.74
120 0.64
121 0.378
122 0.72
123 0.134
124 0.242
125 0.716
126 0.0476
127 0.167
128 0.176
129 0.15
13 7.56184e-5
130 0.938
131 0.795
132 0.6
133 0.473
134 0.752
135 0.152
136 0.0387
137 0.977
138 0.347
139 0.093
14 0.63
140 0.842
141 0.108
142 0.754
143 0.237
144 0.236
145 0.112
146 0.234
147 0.588
148 1
149 0.844
15 0.129
150 0.347
151 0.799
152 0.0231
153 0.683
154 0.644
155 0.256
156 0.19
157 0.439
158 0.444
159 0.71
160 0.799
161 0.595
162 0.99
163 0.0778
164 0.096
165 0.129
166 0.595
167 0.997
168 0.942
169 0.0341
17 0.0304
18 0.979
19 0.325
2 0.706
20 0.361
21 0.968
22 0.256
23 0.268
24 0.611
25 0.463
26 0.021
27 0.921
28 0.269
29 0.155
3 0.154
30 0.282
31 0.854
32 0.198
33 0.208
34 0.857
35 0.849
36 0.647
37 0.0325
38 0.409
39 0.418
4 0.432
40 0.221
41 0.126
42 0.712
43 0.316
44 0.123
45 0.375
46 0.478
47 0.471
48 0.25
49 0.318
5 0.666
50 0.455
51 0.562
52 0.112
53 0.499
54 0.319
55 0.529
56 0.534
57 0.892
58 0.217
59 0.163
6 0.674
60 0.0294
61 0.436
62 0.204
63 0.123
64 0.702
65 0.279
66 0.813
67 0.583
68 0.125
69 0.931
7 0.0844
70 0.00307
71 0.21
72 0.293
73 0.0222
74 0.931
75 0.0261
76 0.939
77 0.0597
78 0.0296
79 0.868
8 0.389
80 0.886
81 0.906
82 0.0595
83 0.423
84 0.0673
85 0.117
86 0.11
87 0.0177
88 0.278
89 0.309
9 0.994
90 0.511
91 0.652
92 0.459
93 0.242
94 0.816
95 0.0043
96 0.64
97 0.914
98 0.447
99 0.35



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: CNhs13228


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