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FF:751-24B9

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Name:liver, neonate N10
Species:Mouse (Mus musculus)
Library ID:CNhs11115
Sample type:developmental
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stage10 days neonate
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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  SAMD00005395
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11115 CAGE DRX009026 DRR009900
Accession ID Mm9

Library idBAMCTSS
CNhs11115 DRZ001325 DRZ002708
Accession ID Mm10

Library idBAMCTSS
CNhs11115 DRZ012675 DRZ014058
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

CNhs11115

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0235
1001 0.148
1002 --0.0388
1003 --0.00256
1004 0
1005 0.0791
1006 0.021
1007 --0.0614
1008 0
1009 0.0272
101 --0.0232
1010 0
1011 --0.168
1012 0
1013 0.39
1014 0.00534
1015 --0.166
1016 0.0251
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.193
1023 0
1024 0
1025 0.617
1026 0
1027 0
1028 0
1029 0.0278
103 0
1030 0.118
1031 --0.0163
1032 --0.177
1033 0
1034 0.647
1035 0
1036 0.0301
1037 0
1038 --0.0566
1039 0.487
104 0
1040 --0.152
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: CNhs11115

Jaspar motif P-value
MA0002.2 0.134
MA0003.1 0.364
MA0004.1 0.942
MA0006.1 0.197
MA0007.1 0.489
MA0009.1 0.552
MA0014.1 0.55
MA0017.1 3.28214e-20
MA0018.2 8.29836e-7
MA0019.1 0.505
MA0024.1 0.145
MA0025.1 0.319
MA0027.1 0.421
MA0028.1 0.935
MA0029.1 0.35
MA0030.1 0.03
MA0031.1 0.049
MA0035.2 0.314
MA0038.1 0.736
MA0039.2 0.704
MA0040.1 0.496
MA0041.1 0.195
MA0042.1 0.539
MA0043.1 0.0337
MA0046.1 4.63389e-77
MA0047.2 4.37195e-7
MA0048.1 0.297
MA0050.1 0.00242
MA0051.1 0.00973
MA0052.1 0.0805
MA0055.1 0.346
MA0057.1 0.842
MA0058.1 0.811
MA0059.1 0.286
MA0060.1 0.00381
MA0061.1 0.332
MA0062.2 0.735
MA0065.2 4.75763e-14
MA0066.1 0.0133
MA0067.1 0.027
MA0068.1 0.247
MA0069.1 0.271
MA0070.1 0.296
MA0071.1 6.03811e-4
MA0072.1 1.29276e-4
MA0073.1 0.575
MA0074.1 0.308
MA0076.1 0.553
MA0077.1 0.0179
MA0078.1 0.531
MA0079.2 0.321
MA0080.2 0.181
MA0081.1 0.837
MA0083.1 0.271
MA0084.1 0.434
MA0087.1 0.233
MA0088.1 0.579
MA0090.1 0.503
MA0091.1 0.884
MA0092.1 0.0518
MA0093.1 0.932
MA0099.2 0.198
MA0100.1 0.274
MA0101.1 0.784
MA0102.2 0.326
MA0103.1 0.31
MA0104.2 0.559
MA0105.1 0.0321
MA0106.1 0.0517
MA0107.1 0.98
MA0108.2 0.051
MA0111.1 0.86
MA0112.2 1.37527e-6
MA0113.1 0.531
MA0114.1 2.4388e-20
MA0115.1 4.61353e-10
MA0116.1 0.0841
MA0117.1 0.918
MA0119.1 0.00558
MA0122.1 0.401
MA0124.1 0.505
MA0125.1 0.882
MA0131.1 0.921
MA0135.1 0.57
MA0136.1 0.88
MA0137.2 0.331
MA0138.2 0.381
MA0139.1 0.0692
MA0140.1 0.336
MA0141.1 1.67293e-5
MA0142.1 0.211
MA0143.1 0.127
MA0144.1 0.549
MA0145.1 0.13
MA0146.1 0.201
MA0147.1 0.674
MA0148.1 9.56357e-11
MA0149.1 0.049
MA0150.1 0.0849
MA0152.1 0.271
MA0153.1 3.21055e-51
MA0154.1 0.0592
MA0155.1 0.374
MA0156.1 0.911
MA0157.1 0.0211
MA0159.1 2.43601e-4
MA0160.1 0.00134
MA0162.1 0.493
MA0163.1 3.50784e-5
MA0164.1 0.956
MA0258.1 0.00436
MA0259.1 0.368



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: CNhs11115

Novel motif P-value
1 0.128
10 0.143
100 0.66
101 0.986
102 0.0928
103 0.0156
104 0.555
105 0.827
106 0.0403
107 0.0387
108 0.383
109 0.0684
11 0.113
110 0.0424
111 0.0782
112 0.00567
113 0.899
114 0.0371
115 0.861
116 0.905
117 0.0793
118 0.188
119 0.0979
12 0.593
120 0.562
121 0.767
122 0.606
123 0.289
124 0.409
125 0.277
126 0.336
127 0.55
128 0.0286
129 0.638
13 8.1832e-5
130 0.617
131 0.157
132 0.494
133 0.503
134 0.816
135 0.476
136 0.387
137 0.976
138 0.217
139 0.852
14 0.409
140 0.0187
141 0.383
142 0.363
143 0.843
144 0.749
145 0.0481
146 0.383
147 0.449
148 0.592
149 0.712
15 0.177
150 0.227
151 0.551
152 0.142
153 0.115
154 0.479
155 0.988
156 0.271
157 0.298
158 0.343
159 0.701
160 0.147
161 0.868
162 0.523
163 0.828
164 0.17
165 0.34
166 0.235
167 0.226
168 0.571
169 8.91765e-4
17 0.0707
18 0.899
19 0.014
2 0.751
20 0.493
21 0.477
22 0.131
23 0.327
24 0.254
25 0.745
26 2.42e-4
27 0.725
28 0.452
29 0.391
3 0.0436
30 0.911
31 0.4
32 0.19
33 0.298
34 0.864
35 0.887
36 0.0755
37 0.0618
38 0.269
39 0.287
4 0.803
40 0.197
41 0.505
42 0.276
43 0.0577
44 0.249
45 0.659
46 0.092
47 0.384
48 0.21
49 0.0589
5 0.124
50 0.531
51 0.319
52 0.291
53 0.726
54 0.336
55 0.583
56 0.435
57 0.742
58 0.315
59 0.214
6 0.979
60 0.134
61 0.193
62 0.172
63 0.125
64 0.593
65 0.233
66 0.802
67 0.87
68 0.208
69 0.684
7 0.142
70 0.164
71 0.0408
72 0.753
73 0.148
74 0.762
75 0.055
76 0.995
77 0.46
78 0.0203
79 0.797
8 0.0119
80 0.637
81 0.607
82 0.0553
83 0.974
84 0.961
85 0.0589
86 0.144
87 0.569
88 0.663
89 0.0304
9 0.5
90 0.15
91 0.222
92 0.194
93 0.28
94 0.934
95 0.396
96 0.163
97 0.812
98 0.361
99 0.0558



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: CNhs11115


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0002107 (liver)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000305 (mouse neonate N10 sample)
0011416 (mouse liver- neonate N10 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

UBERON:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)