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FF:11852-124I7

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Name:CD326++ enterocyte isolated from mice, treated with RANKL, day03, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs13236
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_a
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004708
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13236 CAGE DRX008764 DRR009636
Accession ID Mm9

Library idBAMCTSS
CNhs13236 DRZ001061 DRZ002446
Accession ID Mm10

Library idBAMCTSS
CNhs13236 DRZ012411 DRZ013796
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

CNhs13236

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 1.1
1006 --0.19
1007 0.182
1008 1.638
1009 --0.19
101 --0.0436
1010 0
1011 --0.337
1012 0
1013 0.266
1014 --0.0874
1015 --0.166
1016 --0.465
1017 0
1018 0.4
1019 0
102 0
1020 0
1021 0
1022 --0.0704
1023 0
1024 --0.14
1025 0
1026 0
1027 --0.048
1028 0
1029 --0.148
103 --0.0887
1030 0
1031 -1.067
1032 0.661
1033 0.102
1034 0
1035 0
1036 0.0598
1037 0
1038 0.081
1039 0.0257
104 0
1040 --0.603
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: CNhs13236

Jaspar motif P-value
MA0002.2 0.0696
MA0003.1 0.476
MA0004.1 0.371
MA0006.1 0.0724
MA0007.1 0.216
MA0009.1 0.121
MA0014.1 0.0335
MA0017.1 9.16996e-22
MA0018.2 8.37433e-5
MA0019.1 0.0842
MA0024.1 0.999
MA0025.1 0.173
MA0027.1 0.403
MA0028.1 5.86277e-4
MA0029.1 0.966
MA0030.1 0.224
MA0031.1 0.217
MA0035.2 8.46445e-6
MA0038.1 0.944
MA0039.2 1.06561e-5
MA0040.1 0.145
MA0041.1 0.181
MA0042.1 0.272
MA0043.1 0.00349
MA0046.1 1.20228e-54
MA0047.2 1.00082e-4
MA0048.1 0.121
MA0050.1 0.00466
MA0051.1 4.56543e-5
MA0052.1 0.765
MA0055.1 0.0254
MA0057.1 0.0557
MA0058.1 0.444
MA0059.1 0.855
MA0060.1 0.00361
MA0061.1 9.78695e-5
MA0062.2 1.74093e-9
MA0065.2 1.54978e-10
MA0066.1 0.468
MA0067.1 0.317
MA0068.1 0.219
MA0069.1 0.755
MA0070.1 0.362
MA0071.1 0.126
MA0072.1 0.787
MA0073.1 0.998
MA0074.1 0.478
MA0076.1 0.00483
MA0077.1 0.0813
MA0078.1 0.396
MA0079.2 0.1
MA0080.2 4.43844e-6
MA0081.1 0.431
MA0083.1 0.752
MA0084.1 0.197
MA0087.1 0.257
MA0088.1 0.545
MA0090.1 0.439
MA0091.1 0.393
MA0092.1 0.68
MA0093.1 0.406
MA0099.2 1.80478e-9
MA0100.1 0.626
MA0101.1 2.25768e-10
MA0102.2 0.98
MA0103.1 9.5557e-9
MA0104.2 0.75
MA0105.1 0.713
MA0106.1 0.586
MA0107.1 4.803e-9
MA0108.2 3.04079e-6
MA0111.1 0.261
MA0112.2 0.507
MA0113.1 0.567
MA0114.1 9.30992e-32
MA0115.1 1.39109e-11
MA0116.1 0.517
MA0117.1 0.228
MA0119.1 0.522
MA0122.1 0.677
MA0124.1 0.482
MA0125.1 0.758
MA0131.1 0.77
MA0135.1 0.0987
MA0136.1 2.87744e-11
MA0137.2 0.00646
MA0138.2 0.298
MA0139.1 0.592
MA0140.1 0.263
MA0141.1 2.47823e-4
MA0142.1 0.0696
MA0143.1 0.0454
MA0144.1 5.94089e-4
MA0145.1 0.0303
MA0146.1 0.0826
MA0147.1 0.891
MA0148.1 6.30158e-4
MA0149.1 0.0333
MA0150.1 0.0189
MA0152.1 0.192
MA0153.1 6.99264e-35
MA0154.1 0.66
MA0155.1 0.372
MA0156.1 2.9341e-7
MA0157.1 0.931
MA0159.1 0.00102
MA0160.1 1.01971e-4
MA0162.1 0.619
MA0163.1 0.342
MA0164.1 0.842
MA0258.1 0.701
MA0259.1 0.997



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: CNhs13236

Novel motif P-value
1 0.485
10 0.546
100 0.82
101 0.45
102 0.882
103 0.5
104 0.992
105 0.205
106 0.00365
107 0.132
108 0.566
109 0.0631
11 0.357
110 0.729
111 0.598
112 0.0759
113 0.0584
114 0.965
115 0.675
116 0.357
117 0.0189
118 0.866
119 0.289
12 0.691
120 0.547
121 0.142
122 0.984
123 0.0339
124 0.0146
125 0.512
126 0.00707
127 0.216
128 0.185
129 0.462
13 1.08586e-5
130 0.629
131 0.625
132 0.784
133 0.477
134 0.954
135 0.0616
136 2.79329e-4
137 0.739
138 0.316
139 0.524
14 0.89
140 0.665
141 0.804
142 0.652
143 0.0602
144 0.0259
145 0.226
146 0.25
147 0.814
148 0.882
149 0.431
15 0.353
150 0.497
151 0.437
152 0.0052
153 0.345
154 0.558
155 0.658
156 0.0522
157 0.348
158 0.43
159 0.884
160 0.2
161 0.798
162 0.624
163 0.143
164 0.247
165 0.289
166 0.407
167 0.942
168 0.692
169 0.225
17 0.0579
18 0.379
19 0.832
2 0.863
20 0.238
21 0.577
22 0.497
23 0.856
24 0.636
25 0.548
26 0.0271
27 0.751
28 0.403
29 0.106
3 0.59
30 0.327
31 0.558
32 0.916
33 0.252
34 0.849
35 0.773
36 0.894
37 0.0808
38 0.655
39 0.543
4 0.194
40 0.257
41 0.146
42 0.804
43 0.96
44 0.554
45 0.298
46 0.656
47 0.796
48 0.414
49 0.726
5 0.783
50 0.557
51 0.909
52 0.138
53 0.362
54 0.587
55 0.609
56 0.786
57 0.406
58 0.512
59 0.632
6 0.966
60 0.0317
61 0.326
62 0.47
63 0.257
64 0.927
65 0.547
66 0.514
67 0.394
68 0.331
69 0.473
7 0.088
70 0.135
71 0.684
72 0.347
73 0.00457
74 0.351
75 0.0246
76 0.941
77 0.0632
78 0.0413
79 0.645
8 0.765
80 0.886
81 0.463
82 0.765
83 0.944
84 0.0798
85 0.406
86 0.133
87 3.85332e-4
88 0.202
89 0.606
9 0.809
90 0.992
91 0.35
92 0.489
93 0.142
94 0.503
95 6.11299e-5
96 0.828
97 0.754
98 0.775
99 0.91



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: CNhs13236


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)