Personal tools

FF:457-17C6

From FANTOM5_SSTAR

Jump to: navigation, search


Name:heart, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs11021
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
tissueheart
dev stage16 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  SAMD00005268
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11021 CAGE DRX008976 DRR009850
Accession ID Mm9

Library idBAMCTSS
CNhs11021 DRZ001275 DRZ002658
Accession ID Mm10

Library idBAMCTSS
CNhs11021 DRZ012625 DRZ014008
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11021

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0.248
100 0
1000 0.304
1001 0.297
1002 0.412
1003 0.0211
1004 0
1005 -0.151
1006 0.279
1007 0.0272
1008 0
1009 0.104
101 -0.0179
1010 0
1011 -0.0231
1012 0.117
1013 -0.207
1014 0.563
1015 0.0448
1016 0.109
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.455
1023 0
1024 0.158
1025 0.048
1026 0
1027 0
1028 0.0623
1029 0.186
103 0.201
1030 0
1031 0.255
1032 0.0264
1033 -0.00419
1034 0
1035 0.611
1036 -0.0614
1037 0
1038 0.0704
1039 0.172
104 0
1040 0.102
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: CNhs11021
Jaspar motif P-value
MA0002.2 0.0159
MA0003.1 0.283
MA0004.1 0.233
MA0006.1 0.942
MA0007.1 0.397
MA0009.1 0.932
MA0014.1 0.54
MA0017.1 0.00392
MA0018.2 0.0119
MA0019.1 0.298
MA0024.1 0.0196
MA0025.1 0.081
MA0027.1 0.183
MA0028.1 0.365
MA0029.1 0.484
MA0030.1 0.0421
MA0031.1 0.0389
MA0035.2 0.377
MA0038.1 0.8
MA0039.2 0.0151
MA0040.1 0.0532
MA0041.1 0.148
MA0042.1 0.284
MA0043.1 0.0578
MA0046.1 6.52461e-18
MA0047.2 0.0173
MA0048.1 0.00235
MA0050.1 2.84269e-4
MA0051.1 0.00541
MA0052.1 5.30868e-22
MA0055.1 6.61484e-4
MA0057.1 0.938
MA0058.1 0.305
MA0059.1 0.943
MA0060.1 0.243
MA0061.1 0.485
MA0062.2 1.33677e-5
MA0065.2 0.279
MA0066.1 0.959
MA0067.1 0.343
MA0068.1 0.333
MA0069.1 0.156
MA0070.1 0.566
MA0071.1 0.658
MA0072.1 0.127
MA0073.1 0.853
MA0074.1 0.582
MA0076.1 0.0149
MA0077.1 0.647
MA0078.1 0.49
MA0079.2 0.228
MA0080.2 0.00221
MA0081.1 0.726
MA0083.1 1.50926e-14
MA0084.1 0.947
MA0087.1 0.64
MA0088.1 0.54
MA0090.1 0.00296
MA0091.1 0.472
MA0092.1 0.76
MA0093.1 0.234
MA0099.2 1.38797e-7
MA0100.1 0.562
MA0101.1 0.116
MA0102.2 0.0106
MA0103.1 1.45106e-5
MA0104.2 0.668
MA0105.1 0.0726
MA0106.1 0.638
MA0107.1 0.109
MA0108.2 0.892
MA0111.1 0.525
MA0112.2 0.0268
MA0113.1 0.471
MA0114.1 3.71219e-4
MA0115.1 0.499
MA0116.1 0.857
MA0117.1 0.562
MA0119.1 0.0305
MA0122.1 0.998
MA0124.1 0.319
MA0125.1 0.596
MA0131.1 0.396
MA0135.1 0.0393
MA0136.1 5.40156e-4
MA0137.2 0.00984
MA0138.2 0.481
MA0139.1 0.52
MA0140.1 0.154
MA0141.1 8.13072e-6
MA0142.1 0.269
MA0143.1 0.905
MA0144.1 0.21
MA0145.1 0.217
MA0146.1 0.894
MA0147.1 0.618
MA0148.1 0.0636
MA0149.1 0.151
MA0150.1 0.00162
MA0152.1 0.624
MA0153.1 2.47191e-11
MA0154.1 0.249
MA0155.1 0.239
MA0156.1 1.90176e-7
MA0157.1 0.163
MA0159.1 0.0374
MA0160.1 0.127
MA0162.1 0.119
MA0163.1 0.0805
MA0164.1 0.421
MA0258.1 0.478
MA0259.1 0.256



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: CNhs11021
Novel motif P-value
1 0.515
10 0.615
100 0.839
101 0.914
102 0.695
103 0.835
104 0.988
105 0.677
106 0.793
107 0.692
108 0.964
109 0.501
11 0.704
110 0.0544
111 0.476
112 0.361
113 0.416
114 0.958
115 0.963
116 0.521
117 0.326
118 0.389
119 0.639
12 0.514
120 0.247
121 0.449
122 0.133
123 0.09
124 0.728
125 0.748
126 0.905
127 0.201
128 0.309
129 0.879
13 1.60022e-4
130 0.288
131 0.357
132 0.834
133 0.244
134 0.661
135 0.792
136 0.0247
137 0.576
138 0.14
139 0.88
14 0.89
140 0.337
141 0.732
142 0.698
143 0.559
144 0.0774
145 0.135
146 0.383
147 0.748
148 0.858
149 0.506
15 0.352
150 0.178
151 0.185
152 0.491
153 0.89
154 0.831
155 0.343
156 0.00799
157 0.705
158 0.498
159 0.0329
160 0.0725
161 0.561
162 0.603
163 0.804
164 0.598
165 0.163
166 0.454
167 0.925
168 0.49
169 0.00661
17 0.928
18 0.201
19 0.157
2 0.281
20 0.177
21 0.954
22 0.347
23 0.214
24 0.41
25 0.553
26 0.00838
27 0.21
28 0.22
29 0.482
3 0.683
30 0.0291
31 0.779
32 0.708
33 0.141
34 0.937
35 0.558
36 0.124
37 0.108
38 0.407
39 0.941
4 0.452
40 0.00322
41 0.789
42 0.779
43 0.57
44 0.788
45 0.038
46 0.744
47 0.986
48 0.954
49 0.379
5 0.47
50 0.31
51 0.85
52 0.922
53 0.446
54 0.665
55 0.152
56 0.882
57 0.186
58 0.653
59 0.232
6 0.137
60 0.96
61 0.629
62 0.497
63 0.539
64 0.731
65 0.344
66 0.434
67 0.625
68 0.455
69 0.47
7 0.232
70 0.101
71 0.0083
72 0.0883
73 0.644
74 0.395
75 0.796
76 0.501
77 0.728
78 0.379
79 0.591
8 0.699
80 0.0186
81 0.726
82 0.792
83 0.848
84 0.835
85 0.631
86 0.69
87 4.92412e-6
88 0.377
89 0.344
9 0.615
90 0.647
91 0.0974
92 0.883
93 0.331
94 0.152
95 0.658
96 0.352
97 0.161
98 0.549
99 0.712



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: CNhs11021


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)
0007100 (primary circulatory organ)
0000948 (heart)
0000479 (tissue)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0010317 (germ layer / neural crest derived structure)
0004535 (cardiovascular system)
0001009 (circulatory 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)
0000299 (mouse embryonic day 16 sample)
0011356 (mouse heart- embryo E16 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:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0004140 (primary heart field)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)