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FF:12230-129F7

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Name:Lgr5 positive intestinal stem cells, pool3
Species:Mouse (Mus musculus)
Library ID:CNhs12557
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
sexfemale
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  SAMD00005546
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12557 CAGE DRX008771 DRR009643
Accession ID Mm9

Library idBAMCTSS
CNhs12557 DRZ001068 DRZ002453
Accession ID Mm10

Library idBAMCTSS
CNhs12557 DRZ012418 DRZ013803
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

CNhs12557

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 --0.143
1004 0
1005 0.0807
1006 --0.147
1007 --0.125
1008 1.102
1009 --0.19
101 0.128
1010 0
1011 --0.188
1012 0
1013 0.021
1014 --0.0874
1015 --0.164
1016 --0.465
1017 0
1018 0.259
1019 0
102 0
1020 0
1021 0
1022 0.111
1023 0
1024 --0.14
1025 --0.00846
1026 0
1027 --0.048
1028 0
1029 --0.176
103 --0.0887
1030 0
1031 -1.044
1032 0.317
1033 0.436
1034 0
1035 0
1036 0.494
1037 0
1038 --0.101
1039 0.177
104 0
1040 --0.711
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: CNhs12557

Jaspar motif P-value
MA0002.2 0.446
MA0003.1 0.845
MA0004.1 0.00816
MA0006.1 0.943
MA0007.1 0.101
MA0009.1 0.232
MA0014.1 0.0715
MA0017.1 2.29387e-12
MA0018.2 1.5081e-6
MA0019.1 0.608
MA0024.1 4.29108e-6
MA0025.1 0.0145
MA0027.1 0.152
MA0028.1 5.33992e-9
MA0029.1 0.166
MA0030.1 0.351
MA0031.1 0.142
MA0035.2 3.97469e-4
MA0038.1 0.11
MA0039.2 9.44534e-5
MA0040.1 0.0404
MA0041.1 0.157
MA0042.1 0.437
MA0043.1 2.92303e-6
MA0046.1 1.73143e-42
MA0047.2 4.19068e-4
MA0048.1 0.00723
MA0050.1 0.00743
MA0051.1 0.00513
MA0052.1 0.327
MA0055.1 1.02517e-4
MA0057.1 0.185
MA0058.1 0.00712
MA0059.1 8.90678e-4
MA0060.1 5.88688e-11
MA0061.1 0.34
MA0062.2 2.24426e-11
MA0065.2 3.50076e-6
MA0066.1 0.996
MA0067.1 0.154
MA0068.1 0.816
MA0069.1 0.459
MA0070.1 0.644
MA0071.1 0.0642
MA0072.1 0.662
MA0073.1 0.99
MA0074.1 0.801
MA0076.1 4.75925e-8
MA0077.1 0.219
MA0078.1 0.257
MA0079.2 0.334
MA0080.2 0.00215
MA0081.1 0.715
MA0083.1 0.584
MA0084.1 0.0311
MA0087.1 0.171
MA0088.1 0.0288
MA0090.1 0.991
MA0091.1 0.174
MA0092.1 0.198
MA0093.1 0.00962
MA0099.2 0.0411
MA0100.1 0.134
MA0101.1 0.0267
MA0102.2 0.645
MA0103.1 5.82553e-6
MA0104.2 0.00918
MA0105.1 0.376
MA0106.1 0.459
MA0107.1 0.087
MA0108.2 0.0137
MA0111.1 0.486
MA0112.2 0.217
MA0113.1 0.44
MA0114.1 3.58103e-15
MA0115.1 3.72874e-8
MA0116.1 0.216
MA0117.1 0.736
MA0119.1 0.606
MA0122.1 0.225
MA0124.1 0.54
MA0125.1 0.594
MA0131.1 0.101
MA0135.1 0.41
MA0136.1 1.07295e-9
MA0137.2 1.19763e-4
MA0138.2 0.0505
MA0139.1 0.141
MA0140.1 0.327
MA0141.1 6.68314e-4
MA0142.1 0.0675
MA0143.1 0.109
MA0144.1 0.011
MA0145.1 0.712
MA0146.1 0.314
MA0147.1 0.00209
MA0148.1 0.00101
MA0149.1 0.00909
MA0150.1 0.305
MA0152.1 0.342
MA0153.1 9.95202e-31
MA0154.1 0.823
MA0155.1 0.451
MA0156.1 6.5807e-7
MA0157.1 0.746
MA0159.1 0.00361
MA0160.1 3.93888e-4
MA0162.1 0.947
MA0163.1 0.0603
MA0164.1 0.767
MA0258.1 0.385
MA0259.1 0.0898



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: CNhs12557

Novel motif P-value
1 0.437
10 0.0671
100 0.33
101 0.169
102 0.952
103 0.681
104 0.953
105 0.481
106 0.413
107 0.754
108 0.683
109 0.0564
11 0.339
110 0.146
111 0.223
112 0.16
113 0.0646
114 0.444
115 0.471
116 0.961
117 0.0144
118 0.642
119 0.987
12 0.903
120 0.624
121 0.344
122 0.879
123 0.0103
124 0.072
125 0.0235
126 0.00724
127 0.532
128 0.946
129 0.915
13 2.53855e-7
130 0.422
131 0.939
132 0.539
133 0.265
134 0.388
135 0.0424
136 0.00552
137 0.462
138 0.396
139 0.346
14 0.714
140 0.614
141 0.208
142 0.763
143 0.0578
144 0.0104
145 0.0132
146 0.309
147 0.566
148 0.28
149 0.208
15 0.41
150 0.475
151 0.584
152 0.464
153 0.815
154 0.589
155 0.948
156 0.39
157 0.441
158 0.309
159 0.745
160 0.879
161 0.689
162 0.113
163 0.682
164 0.189
165 0.188
166 0.529
167 0.214
168 0.92
169 0.235
17 0.187
18 0.179
19 0.628
2 0.206
20 0.0743
21 0.795
22 0.931
23 0.31
24 0.146
25 0.153
26 0.00235
27 0.828
28 0.894
29 0.00681
3 0.483
30 0.826
31 0.324
32 0.263
33 0.075
34 0.437
35 0.815
36 0.15
37 0.322
38 0.696
39 0.656
4 0.457
40 0.0536
41 0.254
42 0.85
43 0.648
44 0.88
45 0.86
46 0.409
47 0.705
48 0.336
49 0.844
5 0.76
50 0.864
51 0.825
52 0.732
53 0.414
54 0.959
55 0.935
56 0.967
57 0.706
58 0.293
59 0.648
6 0.64
60 0.179
61 0.279
62 0.286
63 0.555
64 0.735
65 0.839
66 0.324
67 0.559
68 0.761
69 0.143
7 0.0196
70 0.258
71 0.0363
72 0.464
73 0.0544
74 0.697
75 0.0164
76 0.57
77 0.772
78 0.0489
79 0.961
8 0.358
80 0.674
81 0.425
82 0.643
83 0.438
84 0.668
85 0.952
86 0.369
87 0.00396
88 0.5
89 0.978
9 0.708
90 0.164
91 0.0199
92 0.0898
93 0.111
94 0.427
95 8.47968e-4
96 0.456
97 0.939
98 0.634
99 0.753



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: CNhs12557


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)
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)