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FF:12987-138I8

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Name:TSt-4/DLL1 feeder cells, biol_rep2
Species:Mouse (Mus musculus)
Library ID:CNhs13408
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  SAMD00005409
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13408 CAGE DRX008909 DRR009783
Accession ID Mm9

Library idBAMCTSS
CNhs13408 DRZ001208 DRZ002591
Accession ID Mm10

Library idBAMCTSS
CNhs13408 DRZ012558 DRZ013941
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 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

CNhs13408

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0749
1002 0
1003 --0.175
1004 0
1005 --0.154
1006 --0.183
1007 0.742
1008 0
1009 0.938
101 --0.108
1010 0
1011 --0.337
1012 0
1013 --0.0976
1014 --0.0874
1015 0.0647
1016 0.854
1017 0
1018 0
1019 0
102 0
1020 0
1021 --0.0487
1022 --0.124
1023 0
1024 --0.307
1025 0
1026 0
1027 --0.048
1028 0
1029 --0.176
103 0
1030 0
1031 0.255
1032 --0.353
1033 --0.0752
1034 0
1035 0
1036 --0.38
1037 0
1038 1.081
1039 --0.026
104 0
1040 1.017
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: CNhs13408

Jaspar motif P-value
MA0002.2 0.00278
MA0003.1 0.927
MA0004.1 0.357
MA0006.1 0.269
MA0007.1 0.93
MA0009.1 0.578
MA0014.1 0.85
MA0017.1 0.124
MA0018.2 0.0615
MA0019.1 0.946
MA0024.1 0.00322
MA0025.1 0.693
MA0027.1 0.351
MA0028.1 1.02974e-6
MA0029.1 0.983
MA0030.1 0.665
MA0031.1 0.72
MA0035.2 0.131
MA0038.1 0.00596
MA0039.2 4.21121e-4
MA0040.1 0.964
MA0041.1 0.646
MA0042.1 0.564
MA0043.1 0.374
MA0046.1 3.13162e-5
MA0047.2 0.985
MA0048.1 0.0309
MA0050.1 0.661
MA0051.1 0.229
MA0052.1 0.426
MA0055.1 0.882
MA0057.1 0.909
MA0058.1 0.463
MA0059.1 0.556
MA0060.1 1.64422e-11
MA0061.1 0.0658
MA0062.2 1.96907e-6
MA0065.2 0.243
MA0066.1 0.0895
MA0067.1 0.975
MA0068.1 0.757
MA0069.1 0.992
MA0070.1 0.708
MA0071.1 0.05
MA0072.1 0.00447
MA0073.1 0.526
MA0074.1 0.284
MA0076.1 6.13196e-5
MA0077.1 0.242
MA0078.1 9.37614e-4
MA0079.2 0.413
MA0080.2 0.135
MA0081.1 0.116
MA0083.1 3.61076e-4
MA0084.1 0.778
MA0087.1 0.804
MA0088.1 0.655
MA0090.1 8.76044e-5
MA0091.1 0.336
MA0092.1 0.141
MA0093.1 0.545
MA0099.2 0.0074
MA0100.1 0.11
MA0101.1 0.499
MA0102.2 0.264
MA0103.1 1.51952e-4
MA0104.2 0.103
MA0105.1 0.658
MA0106.1 0.00506
MA0107.1 0.178
MA0108.2 9.98286e-6
MA0111.1 0.983
MA0112.2 0.773
MA0113.1 0.944
MA0114.1 0.0287
MA0115.1 0.449
MA0116.1 0.308
MA0117.1 0.115
MA0119.1 0.0496
MA0122.1 0.547
MA0124.1 0.867
MA0125.1 0.00627
MA0131.1 0.0391
MA0135.1 0.273
MA0136.1 0.0851
MA0137.2 0.322
MA0138.2 0.0118
MA0139.1 0.207
MA0140.1 0.205
MA0141.1 0.141
MA0142.1 0.322
MA0143.1 0.00637
MA0144.1 0.405
MA0145.1 0.425
MA0146.1 0.263
MA0147.1 0.0494
MA0148.1 0.718
MA0149.1 0.488
MA0150.1 0.00485
MA0152.1 0.613
MA0153.1 9.93577e-5
MA0154.1 0.204
MA0155.1 0.688
MA0156.1 0.0234
MA0157.1 0.256
MA0159.1 0.369
MA0160.1 0.0521
MA0162.1 0.904
MA0163.1 0.344
MA0164.1 0.779
MA0258.1 0.0809
MA0259.1 0.59



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: CNhs13408

Novel motif P-value
1 0.399
10 0.857
100 0.28
101 0.79
102 0.359
103 0.636
104 0.754
105 0.129
106 0.00402
107 0.00199
108 0.675
109 0.563
11 0.34
110 0.211
111 0.228
112 0.299
113 0.77
114 0.0175
115 0.107
116 0.978
117 0.872
118 0.734
119 0.855
12 0.764
120 0.823
121 0.617
122 0.79
123 0.877
124 0.282
125 0.0194
126 0.407
127 0.208
128 0.0279
129 0.0817
13 0.431
130 0.735
131 0.355
132 0.426
133 0.766
134 0.908
135 0.306
136 0.121
137 0.653
138 0.427
139 0.594
14 0.979
140 0.688
141 0.469
142 0.523
143 0.0695
144 0.0843
145 0.11
146 0.885
147 0.339
148 0.493
149 0.288
15 0.36
150 0.0407
151 0.432
152 0.63
153 0.286
154 0.369
155 0.726
156 0.821
157 0.637
158 0.112
159 0.915
160 0.909
161 0.193
162 0.528
163 0.654
164 0.0924
165 0.405
166 0.833
167 0.576
168 0.548
169 0.191
17 0.131
18 0.072
19 0.0751
2 0.663
20 0.357
21 0.104
22 0.103
23 0.0148
24 0.915
25 0.633
26 0.0041
27 0.918
28 0.753
29 0.87
3 0.634
30 0.689
31 0.962
32 0.856
33 0.593
34 0.505
35 0.476
36 0.204
37 0.786
38 0.23
39 0.49
4 0.414
40 0.139
41 0.0375
42 0.492
43 0.0912
44 0.988
45 0.411
46 0.0462
47 0.707
48 0.908
49 0.0891
5 0.197
50 0.879
51 0.381
52 0.271
53 0.654
54 0.404
55 0.275
56 0.587
57 0.236
58 0.462
59 0.073
6 0.815
60 0.0361
61 0.836
62 0.206
63 0.507
64 0.837
65 0.389
66 0.129
67 0.579
68 0.156
69 0.368
7 0.186
70 0.0483
71 0.176
72 0.888
73 0.805
74 0.982
75 0.474
76 0.53
77 0.338
78 0.144
79 0.839
8 0.694
80 0.759
81 0.541
82 0.16
83 0.215
84 0.0614
85 0.405
86 0.6
87 0.293
88 0.813
89 0.705
9 0.36
90 0.121
91 0.272
92 0.00628
93 6.79852e-5
94 0.171
95 0.00355
96 0.165
97 0.0721
98 0.953
99 0.7



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: CNhs13408


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)
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)