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FF:433-16D7

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Name:liver, embryo E15
Species:Mouse (Mus musculus)
Library ID:CNhs10520
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stage15 days embryo
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  DRS008881
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10520 CAGE DRX009018 DRR009892
Accession ID Mm9

Library idBAMCTSS
CNhs10520 DRZ001317 DRZ002700
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs10520

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 7.556884e-4
1002 --0.0941
1003 --0.0538
1004 0
1005 0.0413
1006 --0.132
1007 --0.0756
1008 0
1009 --0.0699
101 0.107
1010 0
1011 --0.0397
1012 0
1013 --0.00524
1014 0
1015 --0.0727
1016 --0.183
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0149
1022 --0.0682
1023 0
1024 --0.001
1025 0.206
1026 0
1027 --0.048
1028 0
1029 --0.0989
103 --0.0617
1030 0
1031 --0.234
1032 --0.177
1033 --0.0333
1034 0.0802
1035 0
1036 0.185
1037 0
1038 --0.218
1039 --0.0391
104 0
1040 --0.263
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: CNhs10520

Jaspar motif P-value
MA0002.2 0.0163
MA0003.1 0.511
MA0004.1 0.431
MA0006.1 0.306
MA0007.1 0.711
MA0009.1 0.169
MA0014.1 0.622
MA0017.1 5.53939e-12
MA0018.2 0.00141
MA0019.1 0.429
MA0024.1 8.37023e-9
MA0025.1 0.963
MA0027.1 0.897
MA0028.1 0.0127
MA0029.1 0.0379
MA0030.1 0.13
MA0031.1 0.603
MA0035.2 1.53258e-30
MA0038.1 0.368
MA0039.2 0.00993
MA0040.1 0.0651
MA0041.1 0.109
MA0042.1 0.425
MA0043.1 0.165
MA0046.1 1.99157e-44
MA0047.2 4.22322e-4
MA0048.1 0.0904
MA0050.1 0.888
MA0051.1 0.632
MA0052.1 4.75691e-4
MA0055.1 0.0524
MA0057.1 0.554
MA0058.1 0.306
MA0059.1 0.104
MA0060.1 3.03632e-9
MA0061.1 0.174
MA0062.2 4.03045e-4
MA0065.2 2.49641e-6
MA0066.1 0.0292
MA0067.1 0.237
MA0068.1 0.35
MA0069.1 0.0428
MA0070.1 0.558
MA0071.1 0.124
MA0072.1 0.0656
MA0073.1 0.764
MA0074.1 0.577
MA0076.1 0.0361
MA0077.1 0.329
MA0078.1 0.57
MA0079.2 0.176
MA0080.2 9.96336e-5
MA0081.1 0.251
MA0083.1 0.461
MA0084.1 0.135
MA0087.1 0.0193
MA0088.1 0.0261
MA0090.1 0.478
MA0091.1 0.419
MA0092.1 0.62
MA0093.1 0.427
MA0099.2 0.576
MA0100.1 0.0315
MA0101.1 0.417
MA0102.2 0.0966
MA0103.1 0.986
MA0104.2 0.438
MA0105.1 0.00262
MA0106.1 0.747
MA0107.1 0.793
MA0108.2 0.206
MA0111.1 0.926
MA0112.2 0.00739
MA0113.1 0.363
MA0114.1 1.71665e-10
MA0115.1 4.53376e-6
MA0116.1 0.00305
MA0117.1 0.774
MA0119.1 0.0341
MA0122.1 0.333
MA0124.1 0.624
MA0125.1 0.632
MA0131.1 0.507
MA0135.1 0.62
MA0136.1 1.20849e-4
MA0137.2 0.555
MA0138.2 0.045
MA0139.1 0.316
MA0140.1 2.69631e-65
MA0141.1 0.0679
MA0142.1 0.163
MA0143.1 0.213
MA0144.1 0.634
MA0145.1 0.974
MA0146.1 0.0597
MA0147.1 0.359
MA0148.1 3.56979e-6
MA0149.1 0.0156
MA0150.1 3.00529e-4
MA0152.1 0.524
MA0153.1 2.79903e-35
MA0154.1 0.056
MA0155.1 0.67
MA0156.1 8.60813e-4
MA0157.1 0.895
MA0159.1 0.0303
MA0160.1 0.0246
MA0162.1 0.478
MA0163.1 2.46622e-5
MA0164.1 0.571
MA0258.1 0.227
MA0259.1 0.614



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: CNhs10520

Novel motif P-value
1 0.118
10 0.0933
100 0.299
101 0.715
102 0.602
103 0.0227
104 0.918
105 0.722
106 0.423
107 0.561
108 0.483
109 0.0104
11 0.113
110 0.116
111 0.0182
112 0.0151
113 0.699
114 0.657
115 0.712
116 0.985
117 0.00202
118 0.0464
119 0.0869
12 0.9
120 0.92
121 0.2
122 0.892
123 0.0863
124 0.642
125 0.755
126 0.116
127 0.253
128 0.154
129 0.953
13 3.39724e-5
130 0.428
131 0.0789
132 0.0552
133 0.941
134 0.227
135 0.476
136 0.187
137 0.228
138 0.99
139 0.86
14 0.851
140 0.626
141 0.307
142 0.127
143 0.354
144 0.94
145 0.0183
146 0.284
147 0.871
148 0.435
149 0.837
15 0.0191
150 0.215
151 0.478
152 0.645
153 0.845
154 0.446
155 0.578
156 0.0739
157 0.859
158 0.257
159 0.776
160 0.325
161 0.186
162 0.902
163 0.758
164 0.00281
165 0.291
166 0.444
167 0.265
168 0.682
169 0.0236
17 0.423
18 0.575
19 0.193
2 0.679
20 0.0893
21 0.764
22 0.391
23 0.864
24 0.446
25 0.296
26 4.79882e-4
27 0.657
28 0.336
29 0.0183
3 0.0211
30 0.892
31 0.916
32 0.553
33 0.101
34 0.702
35 0.708
36 0.0253
37 0.233
38 0.602
39 0.908
4 0.493
40 0.073
41 0.638
42 0.0474
43 0.085
44 0.702
45 0.916
46 0.135
47 0.104
48 0.137
49 0.0649
5 0.0824
50 0.778
51 0.521
52 0.659
53 0.954
54 0.547
55 0.277
56 0.597
57 0.641
58 0.595
59 0.347
6 0.972
60 0.236
61 0.461
62 0.115
63 0.336
64 0.498
65 0.546
66 0.121
67 0.348
68 0.53
69 0.762
7 0.0198
70 0.663
71 0.0169
72 0.409
73 0.298
74 0.411
75 0.0527
76 0.817
77 0.943
78 0.0017
79 0.525
8 0.0096
80 0.0401
81 0.78
82 0.939
83 0.405
84 0.961
85 0.669
86 0.225
87 0.0481
88 0.841
89 0.699
9 0.689
90 0.161
91 0.323
92 0.571
93 0.81
94 0.377
95 0.0608
96 0.0833
97 0.644
98 0.247
99 0.716



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: CNhs10520


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)
0000922 (embryo)
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)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000298 (mouse embryonic day 15 sample)
0011349 (mouse liver- embryo E15 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)