Personal tools

FF:480-44A6

From FANTOM5_SSTAR

Jump to: navigation, search


Name:lung, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs10605
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
tissuelung
dev stage17 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  SAMD00004965
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10605 CAGE DRX009035 DRR009909
Accession ID Mm9

Library idBAMCTSS
CNhs10605 DRZ001334 DRZ002717
Accession ID Mm10

Library idBAMCTSS
CNhs10605 DRZ012684 DRZ014067
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

CNhs10605

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.0528
1002 --0.0818
1003 0.0942
1004 0
1005 0.0652
1006 0
1007 0.0934
1008 0
1009 0.169
101 --0.0221
1010 0
1011 0.045
1012 0
1013 --0.0819
1014 0.177
1015 0.0347
1016 0.25
1017 0
1018 0.108
1019 0
102 0
1020 0
1021 0
1022 0.0673
1023 0
1024 0.337
1025 1.211
1026 0
1027 0
1028 0
1029 0.203
103 0.0673
1030 0
1031 0.492
1032 --0.0204
1033 0
1034 0
1035 0.0673
1036 --0.0187
1037 0
1038 0.373
1039 0.0209
104 0
1040 0.313
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: CNhs10605

Jaspar motif P-value
MA0002.2 0.0446
MA0003.1 0.117
MA0004.1 0.171
MA0006.1 0.201
MA0007.1 0.337
MA0009.1 0.673
MA0014.1 0.789
MA0017.1 2.35709e-6
MA0018.2 0.216
MA0019.1 0.468
MA0024.1 0.00484
MA0025.1 0.402
MA0027.1 0.445
MA0028.1 0.839
MA0029.1 0.768
MA0030.1 0.0822
MA0031.1 0.115
MA0035.2 0.0188
MA0038.1 0.187
MA0039.2 0.013
MA0040.1 0.607
MA0041.1 0.693
MA0042.1 0.463
MA0043.1 0.316
MA0046.1 1.93014e-5
MA0047.2 7.53659e-7
MA0048.1 0.526
MA0050.1 0.623
MA0051.1 0.855
MA0052.1 0.135
MA0055.1 0.0351
MA0057.1 0.899
MA0058.1 0.103
MA0059.1 0.00225
MA0060.1 4.00437e-4
MA0061.1 0.531
MA0062.2 0.848
MA0065.2 0.00125
MA0066.1 0.0104
MA0067.1 0.273
MA0068.1 0.729
MA0069.1 0.805
MA0070.1 0.266
MA0071.1 0.0137
MA0072.1 0.0845
MA0073.1 0.623
MA0074.1 0.137
MA0076.1 0.798
MA0077.1 0.843
MA0078.1 0.0288
MA0079.2 0.0216
MA0080.2 0.418
MA0081.1 0.505
MA0083.1 5.71507e-4
MA0084.1 0.774
MA0087.1 0.969
MA0088.1 0.589
MA0090.1 0.00417
MA0091.1 0.178
MA0092.1 0.671
MA0093.1 0.212
MA0099.2 0.0307
MA0100.1 0.754
MA0101.1 0.846
MA0102.2 0.32
MA0103.1 0.208
MA0104.2 0.00299
MA0105.1 0.00169
MA0106.1 0.67
MA0107.1 0.391
MA0108.2 0.613
MA0111.1 0.628
MA0112.2 7.93069e-4
MA0113.1 0.959
MA0114.1 3.04359e-6
MA0115.1 0.00194
MA0116.1 0.0156
MA0117.1 0.0232
MA0119.1 0.681
MA0122.1 0.193
MA0124.1 0.291
MA0125.1 0.506
MA0131.1 0.746
MA0135.1 0.22
MA0136.1 0.816
MA0137.2 0.84
MA0138.2 0.00523
MA0139.1 0.856
MA0140.1 0.148
MA0141.1 4.77937e-6
MA0142.1 0.162
MA0143.1 0.801
MA0144.1 0.982
MA0145.1 0.0641
MA0146.1 0.5
MA0147.1 6.52325e-4
MA0148.1 9.28319e-5
MA0149.1 0.232
MA0150.1 1.23925e-4
MA0152.1 0.876
MA0153.1 3.77621e-4
MA0154.1 0.193
MA0155.1 0.187
MA0156.1 0.0515
MA0157.1 0.457
MA0159.1 0.00269
MA0160.1 0.00267
MA0162.1 0.6
MA0163.1 0.0138
MA0164.1 0.335
MA0258.1 9.62163e-5
MA0259.1 0.378



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: CNhs10605

Novel motif P-value
1 0.0706
10 0.127
100 0.483
101 0.926
102 0.993
103 0.139
104 0.791
105 0.811
106 0.737
107 0.703
108 0.858
109 0.254
11 0.126
110 0.34
111 0.0214
112 0.144
113 0.905
114 0.0141
115 0.318
116 0.846
117 0.0284
118 0.442
119 0.13
12 0.468
120 0.104
121 0.312
122 0.853
123 0.569
124 0.684
125 0.991
126 0.998
127 0.397
128 0.517
129 0.321
13 0.113
130 0.00281
131 0.63
132 0.749
133 0.727
134 0.689
135 0.602
136 0.195
137 0.455
138 0.607
139 0.00676
14 0.739
140 0.0278
141 0.262
142 0.22
143 0.257
144 0.395
145 0.478
146 0.989
147 0.378
148 0.069
149 0.53
15 0.123
150 0.331
151 0.131
152 0.0916
153 0.214
154 0.772
155 0.874
156 0.0397
157 0.802
158 0.794
159 0.032
160 0.335
161 0.897
162 0.875
163 0.174
164 0.287
165 0.235
166 0.415
167 0.0162
168 0.947
169 0.869
17 0.214
18 0.00507
19 0.92
2 0.678
20 0.615
21 0.805
22 0.651
23 0.703
24 0.599
25 0.144
26 0.979
27 0.567
28 0.799
29 0.206
3 0.205
30 0.614
31 0.115
32 0.00507
33 0.66
34 0.775
35 0.00257
36 0.234
37 0.8
38 0.836
39 0.619
4 0.74
40 0.909
41 0.39
42 0.489
43 0.14
44 0.0383
45 0.429
46 0.149
47 0.205
48 0.222
49 0.0539
5 0.278
50 0.322
51 0.491
52 0.448
53 0.666
54 0.326
55 0.906
56 0.528
57 0.158
58 0.478
59 0.929
6 0.593
60 0.753
61 0.754
62 0.0968
63 0.75
64 0.2
65 0.474
66 0.941
67 0.941
68 0.0264
69 0.572
7 0.99
70 0.00362
71 0.322
72 0.27
73 0.77
74 0.965
75 0.0333
76 0.627
77 0.708
78 0.257
79 0.833
8 0.0392
80 0.772
81 0.0354
82 0.0821
83 0.114
84 0.51
85 0.129
86 0.723
87 0.378
88 0.766
89 0.439
9 0.624
90 0.00162
91 0.476
92 0.0349
93 0.59
94 0.0201
95 0.772
96 0.0552
97 0.784
98 0.453
99 0.959



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: CNhs10605


FANTOM5 (FF) ontology


Direct parent terms

part_of relathionship
UBERON:0000310 breast

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)
0002048 (lung)
0000310 (breast)
0002100 (trunk)
0000479 (tissue)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0005177 (trunk region element)
0000117 (respiratory tube)
0000171 (respiration organ)
0000464 (anatomical space)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0000065 (respiratory tract)
0000170 (pair of lungs)
0001004 (respiratory system)
0001443 (chest)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

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)
0000300 (mouse embryonic day 17 sample)
0011368 (mouse lung- embryo E17 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:0008947 (respiratory primordium)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)