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FF:12971-138H1

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Name:TSt-4/DLL1 feeder cells, biol_rep1
Species:Mouse (Mus musculus)
Library ID:CNhs13407
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  SAMD00005333
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13407 CAGE DRX008908 DRR009782
Accession ID Mm9

Library idBAMCTSS
CNhs13407 DRZ001207 DRZ002590
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

CNhs13407

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0668
1002 0.361
1003 --0.102
1004 0
1005 0
1006 --0.143
1007 0.315
1008 0
1009 0.882
101 --0.0812
1010 0
1011 --0.337
1012 0
1013 0.115
1014 --0.0874
1015 --0.00444
1016 0.405
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 --0.124
1023 0
1024 --0.307
1025 0
1026 0
1027 --0.048
1028 0.359
1029 --0.115
103 0.321
1030 0
1031 0.0949
1032 --0.184
1033 --0.0752
1034 0
1035 0
1036 0.0168
1037 0
1038 0.554
1039 0.0102
104 0
1040 0.883
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: CNhs13407

Jaspar motif P-value
MA0002.2 1.92641e-4
MA0003.1 0.765
MA0004.1 0.59
MA0006.1 0.207
MA0007.1 0.594
MA0009.1 0.304
MA0014.1 0.246
MA0017.1 0.123
MA0018.2 0.72
MA0019.1 0.999
MA0024.1 0.00964
MA0025.1 0.925
MA0027.1 0.495
MA0028.1 0.805
MA0029.1 0.543
MA0030.1 0.579
MA0031.1 0.845
MA0035.2 6.39194e-4
MA0038.1 0.116
MA0039.2 0.148
MA0040.1 0.991
MA0041.1 0.755
MA0042.1 0.493
MA0043.1 0.441
MA0046.1 3.71484e-5
MA0047.2 0.844
MA0048.1 0.00485
MA0050.1 0.0156
MA0051.1 0.0222
MA0052.1 1.71128e-4
MA0055.1 0.148
MA0057.1 0.502
MA0058.1 0.441
MA0059.1 0.796
MA0060.1 8.48182e-5
MA0061.1 0.0759
MA0062.2 0.709
MA0065.2 0.841
MA0066.1 0.291
MA0067.1 0.165
MA0068.1 0.164
MA0069.1 0.57
MA0070.1 0.2
MA0071.1 0.5
MA0072.1 0.22
MA0073.1 0.591
MA0074.1 0.797
MA0076.1 0.843
MA0077.1 0.246
MA0078.1 0.00548
MA0079.2 0.147
MA0080.2 0.961
MA0081.1 0.238
MA0083.1 0.00462
MA0084.1 0.182
MA0087.1 0.682
MA0088.1 0.00544
MA0090.1 1.98238e-5
MA0091.1 0.23
MA0092.1 0.257
MA0093.1 0.676
MA0099.2 3.4467e-4
MA0100.1 0.0839
MA0101.1 0.294
MA0102.2 0.00734
MA0103.1 1.60612e-6
MA0104.2 0.188
MA0105.1 0.0186
MA0106.1 3.06164e-6
MA0107.1 0.215
MA0108.2 1.97756e-4
MA0111.1 0.518
MA0112.2 0.179
MA0113.1 0.833
MA0114.1 0.0752
MA0115.1 0.199
MA0116.1 0.303
MA0117.1 0.494
MA0119.1 0.0103
MA0122.1 0.635
MA0124.1 0.238
MA0125.1 0.0967
MA0131.1 0.868
MA0135.1 0.181
MA0136.1 0.254
MA0137.2 0.183
MA0138.2 0.00463
MA0139.1 0.623
MA0140.1 0.00195
MA0141.1 0.448
MA0142.1 0.906
MA0143.1 0.029
MA0144.1 0.0892
MA0145.1 0.17
MA0146.1 0.0481
MA0147.1 0.169
MA0148.1 0.852
MA0149.1 0.379
MA0150.1 0.0395
MA0152.1 0.664
MA0153.1 5.37938e-4
MA0154.1 0.0673
MA0155.1 0.849
MA0156.1 0.832
MA0157.1 0.0727
MA0159.1 0.794
MA0160.1 0.609
MA0162.1 0.0942
MA0163.1 0.342
MA0164.1 0.977
MA0258.1 0.294
MA0259.1 0.969



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: CNhs13407

Novel motif P-value
1 0.185
10 0.0374
100 0.448
101 0.675
102 0.356
103 0.428
104 0.92
105 0.222
106 0.198
107 0.25
108 0.897
109 0.228
11 0.214
110 0.0308
111 0.513
112 0.5
113 0.428
114 0.173
115 0.456
116 0.244
117 0.00158
118 0.705
119 0.894
12 0.257
120 0.353
121 0.89
122 0.909
123 0.652
124 0.206
125 0.146
126 0.494
127 0.105
128 0.183
129 0.0692
13 0.428
130 0.792
131 0.186
132 0.795
133 0.802
134 0.75
135 0.216
136 0.168
137 0.252
138 0.516
139 0.737
14 0.951
140 0.877
141 0.283
142 0.72
143 0.0503
144 0.0368
145 0.112
146 0.922
147 0.432
148 0.819
149 0.273
15 0.392
150 0.0511
151 0.921
152 0.191
153 0.678
154 0.401
155 0.609
156 0.0635
157 0.564
158 0.851
159 0.125
160 0.721
161 0.249
162 0.924
163 0.56
164 0.0092
165 0.884
166 0.526
167 0.465
168 0.49
169 0.0132
17 0.174
18 0.207
19 0.169
2 0.755
20 0.124
21 0.0435
22 0.147
23 0.609
24 0.583
25 0.895
26 0.00495
27 0.451
28 0.891
29 0.0823
3 0.0448
30 0.554
31 0.439
32 0.888
33 0.816
34 0.743
35 0.664
36 0.415
37 0.0622
38 0.315
39 0.212
4 0.197
40 0.69
41 0.155
42 0.264
43 0.118
44 0.485
45 0.71
46 0.156
47 0.306
48 0.693
49 0.196
5 0.247
50 0.875
51 0.626
52 0.705
53 0.689
54 0.973
55 0.294
56 0.575
57 0.0217
58 0.816
59 0.0978
6 0.763
60 0.151
61 0.492
62 0.435
63 0.557
64 0.788
65 0.635
66 0.291
67 0.441
68 0.44
69 0.175
7 0.125
70 0.0274
71 0.00407
72 0.561
73 0.0404
74 0.21
75 0.0424
76 0.408
77 0.173
78 0.0409
79 0.362
8 0.6
80 0.171
81 0.203
82 0.138
83 0.25
84 0.645
85 0.185
86 0.52
87 0.171
88 0.613
89 0.427
9 0.494
90 0.00158
91 0.0442
92 0.21
93 0.00574
94 0.123
95 0.932
96 0.575
97 0.128
98 0.264
99 0.944



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: CNhs13407


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)