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FF:13003-139B6

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Name:TSt-4/DLL1 feeder cells, biol_rep3
Species:Mouse (Mus musculus)
Library ID:CNhs13409
Sample type:time courses
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexNA
ageNA
cell typeunclassifiable
cell lineNA
companyNA
collaborationTomokatsu Ikawa (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005644
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13409 CAGE DRX008910 DRR009784
Accession ID Mm9

Library idBAMCTSS
CNhs13409 DRZ001209 DRZ002592
Accession ID Mm10

Library idBAMCTSS
CNhs13409 DRZ012559 DRZ013942
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
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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

CNhs13409

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 -0.0749
1002 -0.0941
1003 -0.175
1004 0
1005 -0.182
1006 -0.387
1007 0.859
1008 0
1009 1.089
101 -0.386
1010 0
1011 -0.337
1012 0
1013 0
1014 -0.0874
1015 0.0708
1016 1.098
1017 0
1018 0
1019 0
102 0
1020 0
1021 -0.0487
1022 -0.124
1023 0
1024 -0.307
1025 -0.0611
1026 0
1027 -0.048
1028 0.909
1029 -0.176
103 0
1030 0
1031 0.282
1032 -0.343
1033 -0.0752
1034 0
1035 0
1036 -0.57
1037 0
1038 0.993
1039 -0.146
104 0
1040 1.043
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: CNhs13409
Jaspar motif P-value
MA0002.2 7.6061e-5
MA0003.1 0.716
MA0004.1 0.791
MA0006.1 0.429
MA0007.1 0.503
MA0009.1 0.674
MA0014.1 0.712
MA0017.1 0.521
MA0018.2 0.0211
MA0019.1 0.849
MA0024.1 0.0224
MA0025.1 0.649
MA0027.1 0.523
MA0028.1 6.53286e-8
MA0029.1 0.824
MA0030.1 0.548
MA0031.1 0.918
MA0035.2 0.77
MA0038.1 0.0039
MA0039.2 8.96027e-5
MA0040.1 0.734
MA0041.1 0.271
MA0042.1 0.604
MA0043.1 0.0143
MA0046.1 0.194
MA0047.2 0.41
MA0048.1 0.401
MA0050.1 0.0233
MA0051.1 0.0226
MA0052.1 0.953
MA0055.1 0.333
MA0057.1 0.792
MA0058.1 0.954
MA0059.1 0.519
MA0060.1 1.99934e-15
MA0061.1 0.0483
MA0062.2 2.26006e-10
MA0065.2 0.12
MA0066.1 0.00777
MA0067.1 0.483
MA0068.1 0.87
MA0069.1 0.492
MA0070.1 0.175
MA0071.1 0.0867
MA0072.1 0.0412
MA0073.1 0.979
MA0074.1 0.234
MA0076.1 2.16229e-6
MA0077.1 0.619
MA0078.1 0.0127
MA0079.2 0.0741
MA0080.2 0.479
MA0081.1 0.0971
MA0083.1 0.096
MA0084.1 0.454
MA0087.1 0.415
MA0088.1 0.112
MA0090.1 0.00855
MA0091.1 0.0576
MA0092.1 0.112
MA0093.1 0.972
MA0099.2 0.023
MA0100.1 0.376
MA0101.1 0.738
MA0102.2 0.92
MA0103.1 0.754
MA0104.2 0.448
MA0105.1 0.0023
MA0106.1 0.0574
MA0107.1 0.373
MA0108.2 0.00111
MA0111.1 0.49
MA0112.2 6.68407e-5
MA0113.1 0.223
MA0114.1 0.574
MA0115.1 0.596
MA0116.1 0.0299
MA0117.1 0.455
MA0119.1 0.021
MA0122.1 0.691
MA0124.1 0.517
MA0125.1 0.0249
MA0131.1 0.0205
MA0135.1 0.054
MA0136.1 0.0319
MA0137.2 0.106
MA0138.2 0.101
MA0139.1 0.324
MA0140.1 0.888
MA0141.1 0.0127
MA0142.1 0.579
MA0143.1 0.00788
MA0144.1 0.751
MA0145.1 0.056
MA0146.1 0.448
MA0147.1 0.598
MA0148.1 0.137
MA0149.1 0.384
MA0150.1 0.038
MA0152.1 0.784
MA0153.1 0.443
MA0154.1 0.00298
MA0155.1 0.705
MA0156.1 0.0106
MA0157.1 0.31
MA0159.1 0.143
MA0160.1 0.0524
MA0162.1 0.36
MA0163.1 0.078
MA0164.1 0.689
MA0258.1 1.39765e-4
MA0259.1 0.456



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: CNhs13409
Novel motif P-value
1 0.177
10 0.588
100 0.861
101 0.719
102 0.617
103 0.318
104 0.424
105 0.0432
106 9.14521e-4
107 0.00227
108 0.702
109 0.941
11 0.173
110 0.15
111 0.442
112 0.0823
113 0.667
114 0.0363
115 0.205
116 0.857
117 0.417
118 0.626
119 0.347
12 0.972
120 0.607
121 0.875
122 0.689
123 0.355
124 0.898
125 0.0387
126 0.173
127 0.32
128 0.00548
129 0.167
13 0.684
130 0.672
131 0.311
132 0.285
133 0.977
134 0.839
135 0.469
136 0.112
137 0.493
138 0.458
139 0.0235
14 0.667
140 0.031
141 0.141
142 0.909
143 0.0056
144 0.502
145 0.174
146 0.959
147 0.585
148 0.104
149 0.0892
15 0.148
150 0.0544
151 0.305
152 0.221
153 0.0979
154 0.706
155 0.917
156 0.766
157 0.24
158 0.0798
159 0.71
160 0.146
161 0.277
162 0.516
163 0.333
164 0.421
165 0.195
166 0.403
167 0.999
168 0.901
169 0.0316
17 0.0953
18 0.109
19 0.0754
2 0.476
20 0.827
21 0.207
22 0.101
23 0.00559
24 0.933
25 0.98
26 0.0388
27 0.669
28 0.812
29 0.488
3 0.171
30 0.982
31 0.413
32 0.41
33 0.836
34 0.461
35 0.0729
36 0.691
37 0.31
38 0.294
39 0.458
4 0.459
40 0.816
41 0.0814
42 0.323
43 0.142
44 0.551
45 0.483
46 0.047
47 0.697
48 0.734
49 0.104
5 0.134
50 0.843
51 0.363
52 0.2
53 0.57
54 0.461
55 0.508
56 0.708
57 0.179
58 0.509
59 0.0666
6 0.97
60 0.0783
61 0.579
62 0.217
63 0.204
64 0.372
65 0.129
66 0.206
67 0.755
68 0.0443
69 0.421
7 0.389
70 0.0235
71 0.129
72 0.86
73 0.32
74 0.617
75 0.283
76 0.331
77 0.106
78 0.362
79 0.935
8 0.152
80 0.487
81 0.402
82 0.0216
83 0.96
84 0.13
85 0.134
86 0.761
87 0.341
88 0.751
89 0.158
9 0.359
90 0.0846
91 0.0315
92 0.0252
93 0.00745
94 0.00709
95 0.172
96 0.199
97 0.532
98 0.39
99 0.668



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: CNhs13409


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)
0000066 (epithelial cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0002076 (endo-epithelial cell)
0002293 (epithelial cell of thymus)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002370 (thymus)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000077 (mixed endoderm/mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002368 (endocrine gland)
0004177 (hemopoietic organ)
0005057 (immune organ)
0002530 (gland)
0005058 (hemolymphoid system gland)
0010317 (germ layer / neural crest derived structure)
0000153 (anterior region of body)
0002390 (hematopoietic system)
0000949 (endocrine system)
0002193 (hemolymphoid system)
0002405 (immune system)
0009113 (thymic region)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000343 (control treatment sample)
0000350 (experimentally modified sample)
0011508 (mouse TSt-4/DLL1 feeder cells 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)