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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005872
 
|DRA_sample_Accession=CAGE@SAMD00005872
|accession_numbers=CAGE;DRX008762;DRR009634;DRZ001059;DRZ002444
+
|accession_numbers=CAGE;DRX008762;DRR009634;DRZ001059;DRZ002444;DRZ012409;DRZ013794
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000160,UBERON:0000483,UBERON:0001242,UBERON:0000479,UBERON:0001007,UBERON:0000344,UBERON:0000064,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0005911,UBERON:0004923,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0000060,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0000490,UBERON:0001262,UBERON:0004786,UBERON:0000485,UBERON:0003350,UBERON:0003929,UBERON:0004808,UBERON:0001277,UBERON:0010317,UBERON:0001555,UBERON:0005409
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000160,UBERON:0000483,UBERON:0001242,UBERON:0000479,UBERON:0001007,UBERON:0000344,UBERON:0000064,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0005911,UBERON:0004923,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0000060,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0000490,UBERON:0001262,UBERON:0004786,UBERON:0000485,UBERON:0003350,UBERON:0003929,UBERON:0004808,UBERON:0001277,UBERON:0010317,UBERON:0001555,UBERON:0005409
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000075,CL:0000066,CL:0002371,CL:0002563,CL:0000255,CL:0000239,CL:0000677,CL:0000212,CL:0002076,CL:0002251,CL:0000584
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000075,CL:0000066,CL:0002371,CL:0002563,CL:0000255,CL:0000239,CL:0000677,CL:0000212,CL:0002076,CL:0002251,CL:0000584

Latest revision as of 12:20, 10 August 2017


Name:CD326+ enterocyte isolated from mice, treated with RANKL, day03, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs13242
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_Ep+_a
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005872
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13242 CAGE DRX008762 DRR009634
Accession ID Mm9

Library idBAMCTSS
CNhs13242 DRZ001059 DRZ002444
Accession ID Mm10

Library idBAMCTSS
CNhs13242 DRZ012409 DRZ013794
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

CNhs13242

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0706
1002 --0.116
1003 --0.156
1004 0
1005 0.943
1006 --0.42
1007 0.217
1008 1.06
1009 --0.19
101 --0.409
1010 0
1011 --0.337
1012 0
1013 0.419
1014 --0.0874
1015 --0.364
1016 --0.465
1017 0
1018 0.579
1019 0
102 0
1020 0
1021 0
1022 0
1023 0
1024 --0.307
1025 0
1026 0
1027 --0.048
1028 0
1029 --0.176
103 --0.0848
1030 0
1031 --0.781
1032 1.094
1033 0
1034 0
1035 0
1036 --0.183
1037 0
1038 0.157
1039 0.0126
104 0
1040 --0.376
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: CNhs13242

Jaspar motif P-value
MA0002.2 0.0181
MA0003.1 0.377
MA0004.1 0.718
MA0006.1 0.0454
MA0007.1 0.277
MA0009.1 0.152
MA0014.1 0.05
MA0017.1 5.43916e-34
MA0018.2 0.0267
MA0019.1 0.0258
MA0024.1 2.55729e-5
MA0025.1 0.248
MA0027.1 0.676
MA0028.1 0.0377
MA0029.1 0.892
MA0030.1 0.345
MA0031.1 0.201
MA0035.2 3.27086e-6
MA0038.1 0.686
MA0039.2 7.2344e-6
MA0040.1 0.178
MA0041.1 0.22
MA0042.1 0.271
MA0043.1 0.11
MA0046.1 4.40257e-51
MA0047.2 0.0328
MA0048.1 0.276
MA0050.1 1.69843e-4
MA0051.1 1.06129e-6
MA0052.1 0.957
MA0055.1 0.239
MA0057.1 0.053
MA0058.1 0.817
MA0059.1 0.391
MA0060.1 0.841
MA0061.1 0.00179
MA0062.2 4.08608e-5
MA0065.2 6.59578e-17
MA0066.1 0.124
MA0067.1 0.375
MA0068.1 0.11
MA0069.1 0.899
MA0070.1 0.384
MA0071.1 0.0472
MA0072.1 0.827
MA0073.1 0.912
MA0074.1 0.369
MA0076.1 0.0857
MA0077.1 0.46
MA0078.1 0.806
MA0079.2 0.0769
MA0080.2 9.02861e-5
MA0081.1 0.89
MA0083.1 0.697
MA0084.1 0.192
MA0087.1 0.278
MA0088.1 0.748
MA0090.1 0.319
MA0091.1 0.0398
MA0092.1 0.708
MA0093.1 0.756
MA0099.2 1.49328e-14
MA0100.1 0.793
MA0101.1 2.48815e-6
MA0102.2 0.836
MA0103.1 2.31916e-6
MA0104.2 0.0729
MA0105.1 0.479
MA0106.1 0.615
MA0107.1 1.04385e-6
MA0108.2 3.0289e-4
MA0111.1 0.357
MA0112.2 0.0174
MA0113.1 0.939
MA0114.1 3.31427e-42
MA0115.1 6.66596e-18
MA0116.1 0.905
MA0117.1 0.137
MA0119.1 0.0959
MA0122.1 0.935
MA0124.1 0.667
MA0125.1 0.852
MA0131.1 0.628
MA0135.1 0.177
MA0136.1 4.58941e-8
MA0137.2 0.0226
MA0138.2 0.975
MA0139.1 0.338
MA0140.1 0.0849
MA0141.1 1.85482e-7
MA0142.1 0.0154
MA0143.1 0.11
MA0144.1 0.00171
MA0145.1 0.00394
MA0146.1 0.0882
MA0147.1 0.0679
MA0148.1 0.048
MA0149.1 0.0411
MA0150.1 0.00367
MA0152.1 0.178
MA0153.1 1.35869e-42
MA0154.1 0.103
MA0155.1 0.776
MA0156.1 1.43499e-5
MA0157.1 0.908
MA0159.1 8.89128e-4
MA0160.1 1.73404e-6
MA0162.1 0.91
MA0163.1 0.735
MA0164.1 0.799
MA0258.1 0.133
MA0259.1 0.467



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: CNhs13242

Novel motif P-value
1 0.306
10 0.556
100 0.818
101 0.852
102 0.848
103 0.945
104 0.646
105 0.114
106 0.0171
107 0.162
108 0.411
109 0.109
11 0.261
110 0.584
111 0.202
112 0.045
113 0.255
114 0.278
115 0.501
116 0.0746
117 0.089
118 0.713
119 0.158
12 0.656
120 0.526
121 0.265
122 0.601
123 0.0899
124 0.279
125 0.648
126 0.102
127 0.164
128 0.138
129 0.291
13 1.87764e-5
130 0.639
131 0.949
132 0.586
133 0.416
134 0.793
135 0.112
136 0.00993
137 0.765
138 0.231
139 0.251
14 0.69
140 0.73
141 0.292
142 0.655
143 0.119
144 0.252
145 0.236
146 0.231
147 0.744
148 0.995
149 0.902
15 0.221
150 0.327
151 0.947
152 0.0201
153 0.582
154 0.556
155 0.37
156 0.163
157 0.325
158 0.465
159 0.697
160 0.394
161 0.801
162 0.745
163 0.057
164 0.247
165 0.261
166 0.709
167 0.786
168 0.965
169 0.0904
17 0.0322
18 0.801
19 0.413
2 0.58
20 0.317
21 0.93
22 0.211
23 0.223
24 0.805
25 0.472
26 0.0257
27 0.634
28 0.22
29 0.314
3 0.306
30 0.217
31 0.899
32 0.484
33 0.225
34 0.92
35 0.876
36 0.647
37 0.0237
38 0.534
39 0.448
4 0.394
40 0.391
41 0.219
42 0.861
43 0.438
44 0.264
45 0.223
46 0.65
47 0.691
48 0.39
49 0.534
5 0.977
50 0.355
51 0.697
52 0.106
53 0.483
54 0.342
55 0.438
56 0.668
57 0.506
58 0.314
59 0.218
6 0.724
60 0.0214
61 0.64
62 0.282
63 0.147
64 0.914
65 0.396
66 0.682
67 0.398
68 0.0496
69 0.94
7 0.0651
70 0.0165
71 0.423
72 0.359
73 0.0132
74 0.708
75 0.0413
76 0.987
77 0.0494
78 0.0219
79 0.682
8 0.936
80 0.958
81 0.945
82 0.0711
83 0.703
84 0.0341
85 0.126
86 0.0945
87 0.0057
88 0.207
89 0.627
9 0.986
90 0.938
91 0.902
92 0.704
93 0.262
94 0.407
95 0.0054
96 0.897
97 0.855
98 0.594
99 0.634



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: CNhs13242


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)
0011113 (mouse CD326-positive enterocyte isolated from mice- treated with RANKL- day03 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

CL:0000223 (endodermal cell)