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FF:11853-124I8

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Name:CD326++ enterocyte isolated from mice, treated with RANKL, day03, pool2
Species:Mouse (Mus musculus)
Library ID:CNhs13210
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 typeenterocyte
cell lineNA
companyNA
collaborationShinji Fukuda (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRANKL_Ephigh_b
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005805
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13210 CAGE DRX008789 DRR009661
Accession ID Mm9

Library idBAMCTSS
CNhs13210 DRZ001086 DRZ002471
Accession ID Mm10

Library idBAMCTSS
CNhs13210 DRZ012436 DRZ013821
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

CNhs13210

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 --0.156
1004 0
1005 1.167
1006 --0.344
1007 0.0296
1008 2.264
1009 --0.19
101 --0.0219
1010 0
1011 --0.337
1012 0
1013 0.238
1014 --0.0874
1015 --0.206
1016 --0.378
1017 0
1018 0.606
1019 0
102 0
1020 0
1021 0.409
1022 --0.0704
1023 0
1024 --0.18
1025 0
1026 0
1027 --0.048
1028 0
1029 --0.0989
103 --0.0861
1030 0
1031 -1.026
1032 0.577
1033 0.0913
1034 0
1035 0
1036 --0.0104
1037 0
1038 0.0677
1039 --0.0327
104 0
1040 --0.564
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: CNhs13210

Jaspar motif P-value
MA0002.2 0.103
MA0003.1 0.287
MA0004.1 0.517
MA0006.1 0.0969
MA0007.1 0.323
MA0009.1 0.0895
MA0014.1 0.0378
MA0017.1 3.36802e-23
MA0018.2 0.02
MA0019.1 0.186
MA0024.1 0.754
MA0025.1 0.695
MA0027.1 0.49
MA0028.1 0.00977
MA0029.1 0.91
MA0030.1 0.653
MA0031.1 0.452
MA0035.2 1.17015e-5
MA0038.1 0.495
MA0039.2 5.8337e-6
MA0040.1 0.274
MA0041.1 0.192
MA0042.1 0.286
MA0043.1 0.129
MA0046.1 4.26875e-45
MA0047.2 0.00168
MA0048.1 0.141
MA0050.1 0.00262
MA0051.1 1.12068e-4
MA0052.1 0.181
MA0055.1 0.0496
MA0057.1 0.0624
MA0058.1 0.601
MA0059.1 0.409
MA0060.1 0.228
MA0061.1 7.7545e-5
MA0062.2 1.55812e-5
MA0065.2 3.52239e-12
MA0066.1 0.398
MA0067.1 0.583
MA0068.1 0.194
MA0069.1 0.686
MA0070.1 0.121
MA0071.1 0.1
MA0072.1 0.491
MA0073.1 0.778
MA0074.1 0.527
MA0076.1 0.0574
MA0077.1 0.196
MA0078.1 0.393
MA0079.2 0.658
MA0080.2 2.58896e-5
MA0081.1 0.75
MA0083.1 0.76
MA0084.1 0.305
MA0087.1 0.263
MA0088.1 0.243
MA0090.1 0.678
MA0091.1 0.718
MA0092.1 0.832
MA0093.1 0.577
MA0099.2 6.51633e-8
MA0100.1 0.691
MA0101.1 3.36269e-8
MA0102.2 0.435
MA0103.1 8.97431e-9
MA0104.2 0.972
MA0105.1 0.0527
MA0106.1 0.198
MA0107.1 5.19768e-8
MA0108.2 3.08393e-5
MA0111.1 0.508
MA0112.2 0.0461
MA0113.1 0.816
MA0114.1 1.65353e-27
MA0115.1 7.85144e-12
MA0116.1 0.341
MA0117.1 0.441
MA0119.1 0.281
MA0122.1 0.964
MA0124.1 0.42
MA0125.1 0.856
MA0131.1 0.867
MA0135.1 0.167
MA0136.1 7.90358e-10
MA0137.2 0.00324
MA0138.2 0.729
MA0139.1 0.224
MA0140.1 0.103
MA0141.1 3.38426e-5
MA0142.1 0.139
MA0143.1 0.0514
MA0144.1 5.37654e-4
MA0145.1 0.0302
MA0146.1 0.222
MA0147.1 0.781
MA0148.1 0.00129
MA0149.1 0.0162
MA0150.1 0.0488
MA0152.1 0.057
MA0153.1 1.58466e-35
MA0154.1 0.174
MA0155.1 0.555
MA0156.1 1.73224e-5
MA0157.1 0.799
MA0159.1 1.23679e-4
MA0160.1 1.53059e-4
MA0162.1 0.913
MA0163.1 0.36
MA0164.1 0.565
MA0258.1 0.186
MA0259.1 0.976



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: CNhs13210

Novel motif P-value
1 0.239
10 0.186
100 0.627
101 0.552
102 0.977
103 0.91
104 0.942
105 0.408
106 0.0116
107 0.151
108 0.543
109 0.0423
11 0.219
110 0.433
111 0.271
112 0.0515
113 0.0875
114 0.311
115 0.821
116 0.0962
117 0.0151
118 0.707
119 0.208
12 0.341
120 0.487
121 0.247
122 0.907
123 0.0673
124 0.0829
125 0.296
126 0.00505
127 0.277
128 0.143
129 0.407
13 1.17612e-5
130 0.864
131 0.581
132 0.808
133 0.627
134 0.706
135 0.0305
136 7.02375e-4
137 0.501
138 0.541
139 0.523
14 0.877
140 0.857
141 0.312
142 0.486
143 0.292
144 0.056
145 0.0622
146 0.265
147 0.907
148 0.804
149 0.514
15 0.259
150 0.422
151 0.716
152 0.0167
153 0.462
154 0.855
155 0.461
156 0.0539
157 0.359
158 0.813
159 0.685
160 0.575
161 0.668
162 0.596
163 0.251
164 0.0998
165 0.193
166 0.522
167 0.494
168 0.422
169 0.0849
17 0.0428
18 0.695
19 0.564
2 0.823
20 0.261
21 0.61
22 0.537
23 0.995
24 0.494
25 0.388
26 0.00505
27 0.802
28 0.567
29 0.0376
3 0.292
30 0.463
31 0.726
32 0.555
33 0.207
34 0.787
35 0.945
36 0.365
37 0.0575
38 0.714
39 0.483
4 0.152
40 0.124
41 0.159
42 0.746
43 0.639
44 0.246
45 0.525
46 0.339
47 0.615
48 0.316
49 0.898
5 0.9
50 0.656
51 0.897
52 0.177
53 0.332
54 0.618
55 0.838
56 0.566
57 0.871
58 0.39
59 0.476
6 0.927
60 0.0313
61 0.252
62 0.329
63 0.218
64 0.915
65 0.508
66 0.578
67 0.635
68 0.13
69 0.964
7 0.0664
70 0.0204
71 0.115
72 0.411
73 0.012
74 0.206
75 0.0129
76 0.643
77 0.0533
78 0.0575
79 1
8 0.267
80 0.663
81 0.632
82 0.449
83 0.842
84 0.149
85 0.224
86 0.102
87 0.00129
88 0.186
89 0.43
9 0.837
90 0.24
91 0.824
92 0.918
93 0.143
94 0.735
95 0.00553
96 0.854
97 0.724
98 0.664
99 0.47



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: CNhs13210


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)
0000075 (columnar/cuboidal epithelial cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002563 (intestinal epithelial cell)
0000255 (eukaryotic cell)
0000239 (brush border epithelial cell)
0000677 (gut absorptive cell)
0000212 (absorptive cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)
0000584 (enterocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000160 (intestine)
0000483 (epithelium)
0001242 (intestinal mucosa)
0000479 (tissue)
0001007 (digestive system)
0000344 (mucosa)
0000064 (organ part)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0005911 (endo-epithelium)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0001262 (wall of intestine)
0004786 (gastrointestinal system mucosa)
0000485 (simple columnar epithelium)
0003350 (epithelium of mucosa)
0003929 (gut epithelium)
0004808 (gastrointestinal system epithelium)
0001277 (intestinal epithelium)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal 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)
0000383 (3 days sample)
0000627 (RANK ligand treatment sample)
0011445 (CD326-positive+ enterocyte isolated from mice- treated with RANKL- day03)

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:0000223 (endodermal cell)