Personal tools

FF:413-26A8

From FANTOM5_SSTAR

Jump to: navigation, search


Name:forelimb, embryo E14
Species:Mouse (Mus musculus)
Library ID:CNhs10577
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
tissueforelimb
dev stage14 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  SAMD00005821
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10577 CAGE DRX008966 DRR009840
Accession ID Mm9

Library idBAMCTSS
CNhs10577 DRZ001265 DRZ002648
Accession ID Mm10

Library idBAMCTSS
CNhs10577 DRZ012615 DRZ013998
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

CNhs10577

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0275
1002 0.1
1003 0.208
1004 0
1005 0
1006 --0.0589
1007 0.0577
1008 0
1009 --0.00941
101 0.0717
1010 0
1011 0
1012 0
1013 --0.126
1014 0.319
1015 0.3
1016 0.386
1017 0
1018 0.321
1019 0
102 0
1020 0
1021 0.158
1022 0
1023 0
1024 --0.0337
1025 0
1026 0.0566
1027 0.0374
1028 0
1029 --0.0899
103 0.321
1030 0
1031 0.357
1032 --0.0243
1033 0.0109
1034 0
1035 0
1036 0.14
1037 0
1038 --0.00817
1039 --0.129
104 0
1040 0.101
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: CNhs10577

Jaspar motif P-value
MA0002.2 0.00477
MA0003.1 0.727
MA0004.1 0.959
MA0006.1 0.684
MA0007.1 0.278
MA0009.1 0.265
MA0014.1 0.155
MA0017.1 1.88791e-8
MA0018.2 0.728
MA0019.1 0.663
MA0024.1 2.87209e-4
MA0025.1 0.264
MA0027.1 0.107
MA0028.1 0.968
MA0029.1 0.617
MA0030.1 0.0476
MA0031.1 0.0257
MA0035.2 4.46668e-5
MA0038.1 0.201
MA0039.2 0.248
MA0040.1 0.0898
MA0041.1 0.697
MA0042.1 0.269
MA0043.1 0.21
MA0046.1 2.90481e-21
MA0047.2 0.00189
MA0048.1 0.465
MA0050.1 2.87925e-5
MA0051.1 4.26837e-4
MA0052.1 7.17367e-4
MA0055.1 0.272
MA0057.1 0.271
MA0058.1 0.874
MA0059.1 0.586
MA0060.1 7.66799e-7
MA0061.1 0.267
MA0062.2 0.2
MA0065.2 8.18238e-5
MA0066.1 0.0908
MA0067.1 0.0944
MA0068.1 0.268
MA0069.1 0.933
MA0070.1 0.487
MA0071.1 0.0141
MA0072.1 0.00727
MA0073.1 0.954
MA0074.1 0.782
MA0076.1 0.849
MA0077.1 0.171
MA0078.1 0.708
MA0079.2 0.0965
MA0080.2 2.11135e-9
MA0081.1 0.282
MA0083.1 0.231
MA0084.1 0.329
MA0087.1 0.947
MA0088.1 0.389
MA0090.1 0.188
MA0091.1 0.823
MA0092.1 0.814
MA0093.1 0.865
MA0099.2 0.0127
MA0100.1 0.562
MA0101.1 0.451
MA0102.2 0.239
MA0103.1 0.00262
MA0104.2 0.967
MA0105.1 0.147
MA0106.1 0.426
MA0107.1 0.236
MA0108.2 9.94962e-4
MA0111.1 0.142
MA0112.2 1.92679e-5
MA0113.1 0.177
MA0114.1 1.10185e-6
MA0115.1 0.00474
MA0116.1 0.00402
MA0117.1 0.0914
MA0119.1 0.0787
MA0122.1 0.696
MA0124.1 0.448
MA0125.1 0.201
MA0131.1 0.433
MA0135.1 0.325
MA0136.1 1.01077e-6
MA0137.2 0.2
MA0138.2 1.94066e-4
MA0139.1 0.00184
MA0140.1 4.91067e-5
MA0141.1 1.33398e-4
MA0142.1 0.521
MA0143.1 0.109
MA0144.1 0.39
MA0145.1 0.243
MA0146.1 0.977
MA0147.1 0.99
MA0148.1 4.49569e-5
MA0149.1 0.00252
MA0150.1 1.81337e-4
MA0152.1 0.118
MA0153.1 4.6595e-18
MA0154.1 4.57562e-4
MA0155.1 0.319
MA0156.1 0.00182
MA0157.1 0.263
MA0159.1 0.00617
MA0160.1 0.00191
MA0162.1 0.992
MA0163.1 0.291
MA0164.1 0.688
MA0258.1 2.42242e-4
MA0259.1 0.888



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: CNhs10577

Novel motif P-value
1 0.0375
10 0.208
100 0.834
101 0.68
102 0.584
103 0.0189
104 0.55
105 0.765
106 0.0311
107 0.2
108 0.77
109 0.275
11 0.206
110 0.282
111 0.00935
112 0.0157
113 0.485
114 0.00765
115 0.722
116 0.922
117 0.284
118 0.358
119 0.0295
12 0.551
120 0.759
121 0.466
122 0.863
123 0.108
124 0.232
125 0.141
126 0.232
127 0.0639
128 0.0674
129 0.0899
13 0.796
130 0.189
131 0.919
132 0.502
133 0.71
134 0.769
135 0.736
136 0.55
137 0.766
138 0.688
139 0.00175
14 0.275
140 0.105
141 0.388
142 0.81
143 0.584
144 0.531
145 0.308
146 0.426
147 0.334
148 0.16
149 0.511
15 0.0534
150 0.702
151 0.0112
152 0.48
153 0.142
154 0.647
155 0.784
156 4.74515e-4
157 0.173
158 0.16
159 0.0592
160 0.921
161 0.288
162 0.822
163 0.0431
164 0.25
165 0.18
166 0.157
167 0.313
168 0.728
169 0.183
17 0.171
18 0.222
19 0.267
2 0.645
20 0.902
21 0.802
22 0.64
23 0.217
24 0.79
25 0.232
26 0.664
27 0.513
28 0.192
29 0.286
3 0.158
30 0.669
31 0.379
32 0.412
33 0.632
34 0.966
35 0.0313
36 0.165
37 0.189
38 0.345
39 0.796
4 0.49
40 0.321
41 0.507
42 0.398
43 0.114
44 0.0628
45 0.846
46 0.292
47 0.122
48 0.13
49 0.062
5 0.118
50 0.501
51 0.6
52 0.438
53 0.751
54 0.397
55 0.824
56 0.389
57 0.463
58 0.217
59 0.433
6 0.471
60 0.19
61 0.451
62 0.0588
63 0.354
64 0.408
65 0.229
66 0.491
67 0.731
68 0.00457
69 0.47
7 0.261
70 0.00304
71 0.251
72 0.465
73 0.554
74 0.413
75 0.0782
76 0.892
77 0.272
78 0.569
79 0.764
8 0.0966
80 0.0639
81 0.435
82 0.113
83 0.492
84 0.54
85 0.019
86 0.758
87 0.625
88 0.891
89 0.511
9 0.834
90 0.028
91 0.652
92 0.114
93 0.364
94 0.677
95 0.335
96 0.243
97 0.701
98 0.208
99 0.95



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: CNhs10577


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)
0002102 (forelimb)
0000479 (tissue)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)
0004708 (paired limb/fin)
0002101 (limb)
0004710 (pectoral appendage)
0010317 (germ layer / neural crest derived structure)
0010707 (appendage girdle complex)
0000153 (anterior region of body)
0010708 (pectoral complex)

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)
0000296 (mouse embryonic day 14 sample)
0011342 (mouse forelimb- embryo E14 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:0005417 (forelimb bud)
UBERON:0005733 (limb field)
UBERON:0005732 (limb/fin field)
UBERON:0005729 (forelimb/pectoral fin field)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)