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FF:12228-129F5

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Name:Lgr5 positive intestinal stem cells, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs12555
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
strainNA
tissuesmall intestine
dev stageNA
sexmale
ageNA
cell typestem cell
cell lineNA
companyNA
collaborationMarc van de Wetering
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005052
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12555 CAGE DRX008769 DRR009641
Accession ID Mm9

Library idBAMCTSS
CNhs12555 DRZ001066 DRZ002451
Accession ID Mm10

Library idBAMCTSS
CNhs12555 DRZ012416 DRZ013801
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

CNhs12555

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 -0.0355
1001 -0.0668
1002 -0.116
1003 -0.109
1004 0
1005 0.11
1006 -0.143
1007 -0.0809
1008 0.883
1009 -0.19
101 0.13
1010 0
1011 -0.298
1012 0
1013 -0.136
1014 -0.0874
1015 -0.143
1016 -0.426
1017 0
1018 0.437
1019 0
102 0
1020 0
1021 0
1022 0.218
1023 0
1024 -0.172
1025 0
1026 0
1027 -0.048
1028 0
1029 -0.176
103 -0.0887
1030 0
1031 -1.033
1032 0.431
1033 0.575
1034 0
1035 0
1036 0.452
1037 0
1038 -0.12
1039 0.103
104 0
1040 -0.811
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: CNhs12555
Jaspar motif P-value
MA0002.2 0.368
MA0003.1 0.798
MA0004.1 0.0111
MA0006.1 0.962
MA0007.1 0.141
MA0009.1 0.172
MA0014.1 0.0615
MA0017.1 2.12026e-13
MA0018.2 1.46134e-5
MA0019.1 0.625
MA0024.1 4.53992e-5
MA0025.1 0.025
MA0027.1 0.224
MA0028.1 1.80788e-9
MA0029.1 0.12
MA0030.1 0.389
MA0031.1 0.109
MA0035.2 6.67734e-4
MA0038.1 0.174
MA0039.2 1.31569e-4
MA0040.1 0.123
MA0041.1 0.135
MA0042.1 0.436
MA0043.1 6.61037e-6
MA0046.1 5.84292e-42
MA0047.2 5.83788e-4
MA0048.1 0.0138
MA0050.1 0.0122
MA0051.1 0.00668
MA0052.1 0.0921
MA0055.1 4.4324e-5
MA0057.1 0.198
MA0058.1 0.00862
MA0059.1 0.00188
MA0060.1 6.38026e-9
MA0061.1 0.156
MA0062.2 1.83612e-12
MA0065.2 1.60445e-6
MA0066.1 0.81
MA0067.1 0.218
MA0068.1 0.923
MA0069.1 0.425
MA0070.1 0.503
MA0071.1 0.0274
MA0072.1 0.672
MA0073.1 0.878
MA0074.1 0.797
MA0076.1 5.82987e-9
MA0077.1 0.279
MA0078.1 0.361
MA0079.2 0.289
MA0080.2 0.00234
MA0081.1 0.862
MA0083.1 0.154
MA0084.1 0.0585
MA0087.1 0.167
MA0088.1 0.0193
MA0090.1 0.595
MA0091.1 0.24
MA0092.1 0.179
MA0093.1 0.0124
MA0099.2 0.0741
MA0100.1 0.073
MA0101.1 0.00875
MA0102.2 0.675
MA0103.1 5.32734e-6
MA0104.2 0.0211
MA0105.1 0.128
MA0106.1 0.43
MA0107.1 0.044
MA0108.2 0.361
MA0111.1 0.464
MA0112.2 0.176
MA0113.1 0.312
MA0114.1 2.09187e-15
MA0115.1 5.01733e-9
MA0116.1 0.082
MA0117.1 0.884
MA0119.1 0.607
MA0122.1 0.238
MA0124.1 0.692
MA0125.1 0.59
MA0131.1 0.0951
MA0135.1 0.436
MA0136.1 3.12593e-11
MA0137.2 9.20984e-5
MA0138.2 0.0748
MA0139.1 0.129
MA0140.1 0.484
MA0141.1 6.27359e-4
MA0142.1 0.108
MA0143.1 0.3
MA0144.1 0.00805
MA0145.1 0.809
MA0146.1 0.154
MA0147.1 0.00744
MA0148.1 8.08488e-4
MA0149.1 0.00797
MA0150.1 0.564
MA0152.1 0.456
MA0153.1 5.83854e-30
MA0154.1 0.88
MA0155.1 0.477
MA0156.1 1.20242e-7
MA0157.1 0.551
MA0159.1 0.00201
MA0160.1 5.42802e-4
MA0162.1 0.955
MA0163.1 0.0156
MA0164.1 0.805
MA0258.1 0.382
MA0259.1 0.136



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: CNhs12555
Novel motif P-value
1 0.42
10 0.0665
100 0.273
101 0.327
102 0.885
103 0.515
104 0.938
105 0.486
106 0.438
107 0.946
108 0.509
109 0.0503
11 0.337
110 0.122
111 0.35
112 0.142
113 0.0526
114 0.52
115 0.395
116 0.829
117 0.0077
118 0.485
119 0.937
12 0.834
120 0.769
121 0.308
122 0.847
123 0.0304
124 0.0304
125 0.105
126 0.00355
127 0.753
128 0.835
129 0.916
13 3.09425e-7
130 0.241
131 0.828
132 0.33
133 0.462
134 0.262
135 0.0712
136 0.00466
137 0.424
138 0.461
139 0.319
14 0.724
140 0.985
141 0.366
142 0.911
143 0.0346
144 0.0176
145 0.0218
146 0.437
147 0.8
148 0.52
149 0.231
15 0.338
150 0.508
151 0.767
152 0.5
153 0.918
154 0.814
155 0.871
156 0.215
157 0.407
158 0.309
159 0.833
160 0.981
161 0.711
162 0.224
163 0.695
164 0.147
165 0.238
166 0.721
167 0.263
168 0.805
169 0.158
17 0.204
18 0.151
19 0.77
2 0.25
20 0.0776
21 0.771
22 0.999
23 0.27
24 0.0885
25 0.127
26 0.00684
27 0.787
28 0.95
29 0.00903
3 0.351
30 0.875
31 0.326
32 0.237
33 0.053
34 0.367
35 0.827
36 0.107
37 0.235
38 0.678
39 0.628
4 0.61
40 0.0615
41 0.239
42 0.767
43 0.802
44 0.979
45 0.851
46 0.437
47 0.598
48 0.276
49 0.897
5 0.849
50 0.985
51 0.856
52 0.782
53 0.495
54 0.978
55 0.705
56 0.936
57 0.742
58 0.285
59 0.732
6 0.572
60 0.198
61 0.305
62 0.261
63 0.5
64 0.645
65 0.909
66 0.337
67 0.694
68 0.661
69 0.176
7 0.0168
70 0.234
71 0.0382
72 0.408
73 0.0721
74 0.525
75 0.0132
76 0.618
77 0.665
78 0.0285
79 0.746
8 0.333
80 0.589
81 0.483
82 0.791
83 0.498
84 0.755
85 0.743
86 0.369
87 0.00428
88 0.52
89 0.975
9 0.693
90 0.104
91 0.0323
92 0.121
93 0.142
94 0.401
95 0.00292
96 0.597
97 0.994
98 0.557
99 0.753



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: CNhs12555


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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002563 (intestinal epithelial cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)
0002250 (intestinal crypt stem cell)

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)
0000079 (mouse Lgr5-positive intestinal epithelial stem 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


CL:0000223 (endodermal cell)