Personal tools

FF:11849-124I4

From FANTOM5_SSTAR

Jump to: navigation, search


Name:CD326+ enterocyte, pool2
Species:Mouse (Mus musculus)
Library ID:CNhs13197
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 numberCont_Ep+_b
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004678
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13197 CAGE DRX008788 DRR009660
Accession ID Mm9

Library idBAMCTSS
CNhs13197 DRZ001085 DRZ002470
Accession ID Mm10

Library idBAMCTSS
CNhs13197 DRZ012435 DRZ013820
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sample
Ranked 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 sample
Ranked 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

CNhs13197

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 0.0745
1006 -0.317
1007 0.0722
1008 1.448
1009 -0.19
101 -0.51
1010 0
1011 -0.337
1012 0
1013 0.222
1014 -0.0874
1015 -0.584
1016 -0.488
1017 0
1018 0.478
1019 0
102 0
1020 0
1021 0.603
1022 -0.0704
1023 0
1024 -0.307
1025 0
1026 0
1027 -0.048
1028 0
1029 -0.115
103 -0.0887
1030 0
1031 -1.148
1032 0.896
1033 0.12
1034 0
1035 0
1036 0.196
1037 0
1038 0.415
1039 -0.0514
104 0
1040 -0.884
1041 0



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs13197
Jaspar motif P-value
MA0002.2 0.0202
MA0003.1 0.642
MA0004.1 0.61
MA0006.1 0.036
MA0007.1 0.217
MA0009.1 0.12
MA0014.1 0.0535
MA0017.1 8.60242e-40
MA0018.2 0.00727
MA0019.1 0.0886
MA0024.1 1.46652e-4
MA0025.1 0.299
MA0027.1 0.279
MA0028.1 0.237
MA0029.1 0.85
MA0030.1 0.275
MA0031.1 0.0465
MA0035.2 9.7584e-7
MA0038.1 0.513
MA0039.2 1.03939e-4
MA0040.1 0.0917
MA0041.1 0.158
MA0042.1 0.219
MA0043.1 0.338
MA0046.1 6.84917e-49
MA0047.2 0.0409
MA0048.1 0.137
MA0050.1 8.26523e-5
MA0051.1 3.82717e-7
MA0052.1 0.744
MA0055.1 0.167
MA0057.1 0.122
MA0058.1 0.602
MA0059.1 0.489
MA0060.1 0.297
MA0061.1 0.766
MA0062.2 0.0137
MA0065.2 1.09392e-17
MA0066.1 0.193
MA0067.1 0.198
MA0068.1 0.125
MA0069.1 0.758
MA0070.1 0.611
MA0071.1 0.00813
MA0072.1 0.419
MA0073.1 0.813
MA0074.1 0.233
MA0076.1 0.33
MA0077.1 0.431
MA0078.1 0.799
MA0079.2 0.169
MA0080.2 0.0643
MA0081.1 0.451
MA0083.1 0.549
MA0084.1 0.286
MA0087.1 0.357
MA0088.1 0.501
MA0090.1 0.908
MA0091.1 0.0846
MA0092.1 0.914
MA0093.1 0.654
MA0099.2 1.02887e-6
MA0100.1 0.615
MA0101.1 0.595
MA0102.2 0.917
MA0103.1 8.42809e-7
MA0104.2 0.0541
MA0105.1 0.0958
MA0106.1 0.925
MA0107.1 0.678
MA0108.2 0.0425
MA0111.1 0.616
MA0112.2 0.0289
MA0113.1 0.537
MA0114.1 3.00312e-53
MA0115.1 5.07003e-17
MA0116.1 0.0911
MA0117.1 0.0995
MA0119.1 0.0613
MA0122.1 0.564
MA0124.1 0.591
MA0125.1 0.691
MA0131.1 0.845
MA0135.1 0.103
MA0136.1 0.00151
MA0137.2 0.78
MA0138.2 0.658
MA0139.1 0.619
MA0140.1 0.0219
MA0141.1 1.42074e-10
MA0142.1 0.0445
MA0143.1 0.0647
MA0144.1 0.0583
MA0145.1 0.0134
MA0146.1 0.066
MA0147.1 0.0404
MA0148.1 0.0203
MA0149.1 0.0128
MA0150.1 0.0334
MA0152.1 0.0712
MA0153.1 6.62693e-40
MA0154.1 0.606
MA0155.1 0.418
MA0156.1 0.014
MA0157.1 0.474
MA0159.1 8.02461e-4
MA0160.1 1.403e-7
MA0162.1 0.487
MA0163.1 0.417
MA0164.1 0.613
MA0258.1 0.0821
MA0259.1 0.662



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs13197
Novel motif P-value
1 0.284
10 0.498
100 0.569
101 0.804
102 0.69
103 0.807
104 0.823
105 0.338
106 0.0492
107 0.413
108 0.5
109 0.308
11 0.258
110 0.565
111 0.134
112 0.0482
113 0.187
114 0.0731
115 0.575
116 0.328
117 0.07
118 0.61
119 0.263
12 0.654
120 0.943
121 0.43
122 0.813
123 0.0378
124 0.113
125 0.427
126 0.103
127 0.628
128 0.0834
129 0.585
13 1.11912e-5
130 0.605
131 0.996
132 0.411
133 0.228
134 0.608
135 0.0661
136 0.00479
137 0.273
138 0.191
139 0.359
14 0.773
140 0.575
141 0.834
142 0.369
143 0.169
144 0.301
145 0.228
146 0.434
147 0.812
148 0.663
149 0.394
15 0.259
150 0.28
151 0.789
152 0.0641
153 0.574
154 0.671
155 0.323
156 0.145
157 0.477
158 0.332
159 0.572
160 0.325
161 0.831
162 0.851
163 0.12
164 0.256
165 0.948
166 0.443
167 0.837
168 0.739
169 0.198
17 0.0807
18 0.716
19 0.693
2 0.969
20 0.191
21 0.948
22 0.28
23 0.268
24 0.95
25 0.376
26 0.0377
27 0.545
28 0.31
29 0.448
3 0.333
30 0.325
31 0.949
32 0.499
33 0.207
34 0.807
35 0.77
36 0.851
37 0.0184
38 0.692
39 0.434
4 0.497
40 0.3
41 0.226
42 0.737
43 0.749
44 0.441
45 0.357
46 0.636
47 0.925
48 0.555
49 0.479
5 0.99
50 0.808
51 0.832
52 0.134
53 0.285
54 0.456
55 0.358
56 0.801
57 0.486
58 0.402
59 0.544
6 0.908
60 0.0348
61 0.704
62 0.301
63 0.365
64 0.914
65 0.459
66 0.586
67 0.183
68 0.0345
69 0.827
7 0.0496
70 0.0197
71 0.328
72 0.643
73 0.0134
74 0.727
75 0.0674
76 0.753
77 0.168
78 0.014
79 0.794
8 0.996
80 0.867
81 0.804
82 0.2
83 0.657
84 0.0264
85 0.193
86 0.0785
87 0.00975
88 0.303
89 0.738
9 0.665
90 0.822
91 0.719
92 0.939
93 0.174
94 0.279
95 0.0702
96 0.679
97 0.901
98 0.964
99 0.897



de novo motifs identified by HOMER in promoters active in this sample
Summary:The result of HOMER in this sample is shown.
Analyst:NA

library id: CNhs13197


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)
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)
0011149 (mouse CD326-positive enterocyte 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)