Personal tools

FF:12229-129F6

From FANTOM5_SSTAR

Jump to: navigation, search


Name:Lgr5 positive intestinal stem cells, pool2
Species:Mouse (Mus musculus)
Library ID:CNhs12556
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  SAMD00005032
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12556 CAGE DRX008770 DRR009642
Accession ID Mm9

Library idBAMCTSS
CNhs12556 DRZ001067 DRZ002452
Accession ID Mm10

Library idBAMCTSS
CNhs12556 DRZ012417 DRZ013802
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

CNhs12556

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 -0.123
1004 0
1005 0.108
1006 -0.2
1007 -0.204
1008 1.787
1009 -0.19
101 0.128
1010 0
1011 -0.255
1012 0
1013 0.0769
1014 -0.0874
1015 -0.236
1016 -0.465
1017 0
1018 0.5
1019 0
102 0
1020 0
1021 0
1022 0.125
1023 0
1024 -0.14
1025 -0.0611
1026 0
1027 -0.048
1028 0
1029 -0.176
103 -0.0887
1030 0
1031 -0.93
1032 0.415
1033 0.26
1034 0
1035 0
1036 0.387
1037 0
1038 -0.158
1039 0.193
104 0
1040 -0.936
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: CNhs12556
Jaspar motif P-value
MA0002.2 0.176
MA0003.1 0.739
MA0004.1 0.0466
MA0006.1 0.906
MA0007.1 0.106
MA0009.1 0.266
MA0014.1 0.123
MA0017.1 1.2258e-14
MA0018.2 0.0243
MA0019.1 0.647
MA0024.1 1.45434e-4
MA0025.1 0.126
MA0027.1 0.262
MA0028.1 3.36025e-7
MA0029.1 0.123
MA0030.1 0.923
MA0031.1 0.547
MA0035.2 5.7974e-4
MA0038.1 0.483
MA0039.2 0.00477
MA0040.1 0.0352
MA0041.1 0.179
MA0042.1 0.364
MA0043.1 0.0122
MA0046.1 6.47713e-38
MA0047.2 0.00318
MA0048.1 0.0238
MA0050.1 0.0319
MA0051.1 0.0233
MA0052.1 0.00304
MA0055.1 4.85488e-4
MA0057.1 0.207
MA0058.1 0.0422
MA0059.1 7.03105e-4
MA0060.1 2.08378e-4
MA0061.1 0.32
MA0062.2 4.0465e-9
MA0065.2 2.38691e-7
MA0066.1 0.499
MA0067.1 0.791
MA0068.1 0.641
MA0069.1 0.349
MA0070.1 0.425
MA0071.1 0.0154
MA0072.1 0.626
MA0073.1 0.958
MA0074.1 0.514
MA0076.1 2.22101e-6
MA0077.1 0.359
MA0078.1 0.173
MA0079.2 0.105
MA0080.2 0.00282
MA0081.1 0.962
MA0083.1 0.00464
MA0084.1 0.0702
MA0087.1 0.0927
MA0088.1 0.00983
MA0090.1 0.845
MA0091.1 0.704
MA0092.1 0.556
MA0093.1 0.0526
MA0099.2 0.0896
MA0100.1 0.116
MA0101.1 0.0736
MA0102.2 0.521
MA0103.1 4.44e-6
MA0104.2 0.0138
MA0105.1 0.0718
MA0106.1 0.294
MA0107.1 0.248
MA0108.2 0.818
MA0111.1 0.832
MA0112.2 0.0178
MA0113.1 0.09
MA0114.1 7.01781e-16
MA0115.1 2.28165e-9
MA0116.1 0.0589
MA0117.1 0.954
MA0119.1 0.224
MA0122.1 0.399
MA0124.1 0.685
MA0125.1 0.186
MA0131.1 0.167
MA0135.1 0.725
MA0136.1 1.1514e-9
MA0137.2 2.29938e-5
MA0138.2 0.25
MA0139.1 0.0776
MA0140.1 0.208
MA0141.1 1.51017e-5
MA0142.1 0.151
MA0143.1 0.457
MA0144.1 0.00436
MA0145.1 0.558
MA0146.1 0.33
MA0147.1 0.00257
MA0148.1 0.00193
MA0149.1 0.00401
MA0150.1 0.323
MA0152.1 0.262
MA0153.1 8.25846e-29
MA0154.1 0.52
MA0155.1 0.71
MA0156.1 3.15287e-6
MA0157.1 0.93
MA0159.1 5.253e-4
MA0160.1 1.47013e-4
MA0162.1 0.652
MA0163.1 0.00542
MA0164.1 0.981
MA0258.1 0.0796
MA0259.1 0.115



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: CNhs12556
Novel motif P-value
1 0.195
10 0.0393
100 0.34
101 0.426
102 0.816
103 0.127
104 0.897
105 0.435
106 0.306
107 0.742
108 0.617
109 0.0164
11 0.155
110 0.105
111 0.113
112 0.0688
113 0.0915
114 0.932
115 0.615
116 0.523
117 0.017
118 0.397
119 0.61
12 1
120 0.842
121 0.527
122 0.572
123 0.0149
124 0.0264
125 0.0379
126 0.00424
127 0.429
128 0.815
129 0.593
13 2.22926e-6
130 0.408
131 0.678
132 0.658
133 0.751
134 0.468
135 0.085
136 0.015
137 0.707
138 0.277
139 0.711
14 0.842
140 0.414
141 0.849
142 0.755
143 0.105
144 0.0322
145 0.0149
146 0.314
147 0.824
148 0.719
149 0.382
15 0.179
150 0.469
151 0.861
152 0.519
153 0.798
154 0.73
155 0.756
156 0.177
157 0.467
158 0.443
159 0.748
160 0.565
161 0.268
162 0.377
163 0.727
164 0.036
165 0.115
166 0.512
167 0.206
168 0.814
169 0.0843
17 0.128
18 0.38
19 0.851
2 0.362
20 0.119
21 0.895
22 0.877
23 0.311
24 0.0725
25 0.166
26 6.30996e-4
27 0.912
28 0.995
29 0.00184
3 0.255
30 0.831
31 0.54
32 0.699
33 0.042
34 0.662
35 0.625
36 0.117
37 0.185
38 0.493
39 0.367
4 0.366
40 0.069
41 0.181
42 0.693
43 0.792
44 0.437
45 0.918
46 0.201
47 0.371
48 0.187
49 0.614
5 0.817
50 0.982
51 0.805
52 0.677
53 0.491
54 0.96
55 0.393
56 0.888
57 0.696
58 0.238
59 0.944
6 0.422
60 0.169
61 0.246
62 0.204
63 0.293
64 0.473
65 0.5
66 0.446
67 0.977
68 0.975
69 0.347
7 0.02
70 0.0561
71 0.0168
72 0.335
73 0.0925
74 0.933
75 0.0102
76 0.362
77 0.496
78 0.032
79 0.442
8 0.0725
80 0.757
81 0.814
82 0.77
83 0.268
84 0.767
85 0.574
86 0.425
87 0.014
88 0.502
89 0.681
9 0.675
90 0.0197
91 0.264
92 0.642
93 0.154
94 0.878
95 0.0021
96 0.332
97 0.914
98 0.305
99 0.421



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: CNhs12556


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)