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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005134
 
|DRA_sample_Accession=CAGE@SAMD00005134
|accession_numbers=CAGE;DRX008984;DRR009858;DRZ001283;DRZ002666
+
|accession_numbers=CAGE;DRX008984;DRR009858;DRZ001283;DRZ002666;DRZ012633;DRZ014016
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007100,UBERON:0000948,UBERON:0000479,UBERON:0010314,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0010317,UBERON:0004535,UBERON:0001009
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007100,UBERON:0000948,UBERON:0000479,UBERON:0010314,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0010317,UBERON:0004535,UBERON:0001009
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_cell_lineage_facet=
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|microRNAs=
 
|microRNAs=
 
|microRNAs_nn=
 
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;1351
+
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1351
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;1351
+
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1351
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520neonate%2520N25.CNhs11196.1351-25D3.mm10.nobarcode.bam  
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520neonate%2520N25.CNhs11196.1351-25D3.mm10.nobarcode.bam  
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520neonate%2520N25.CNhs11196.1351-25D3.mm10.nobarcode.ctss.bed.gz  
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520neonate%2520N25.CNhs11196.1351-25D3.mm10.nobarcode.ctss.bed.gz  

Latest revision as of 13:12, 10 August 2017


Name:heart, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11196
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 stage25 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  SAMD00005134
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11196 CAGE DRX008984 DRR009858
Accession ID Mm9

Library idBAMCTSS
CNhs11196 DRZ001283 DRZ002666
Accession ID Mm10

Library idBAMCTSS
CNhs11196 DRZ012633 DRZ014016
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

CNhs11196

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0.854
100 0
1000 0.812
1001 0.701
1002 0.0754
1003 0.18
1004 0
1005 0
1006 0.575
1007 --0.151
1008 0
1009 0.25
101 --0.0446
1010 0
1011 0
1012 0.0862
1013 --0.0775
1014 --0.00116
1015 --0.256
1016 0.0121
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.717
1023 0
1024 0.458
1025 0
1026 0.0862
1027 0.0252
1028 0
1029 0.0978
103 0.0637
1030 0
1031 --0.0306
1032 0.132
1033 0
1034 0
1035 0.404
1036 --0.307
1037 0
1038 0.0914
1039 0.641
104 0
1040 0.219
1041 0.322



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: CNhs11196

Jaspar motif P-value
MA0002.2 0.731
MA0003.1 0.277
MA0004.1 0.0746
MA0006.1 0.205
MA0007.1 0.985
MA0009.1 0.862
MA0014.1 0.634
MA0017.1 0.68
MA0018.2 0.0981
MA0019.1 0.167
MA0024.1 4.37417e-4
MA0025.1 0.486
MA0027.1 0.398
MA0028.1 0.0257
MA0029.1 0.802
MA0030.1 0.162
MA0031.1 0.457
MA0035.2 3.31506e-5
MA0038.1 0.613
MA0039.2 0.676
MA0040.1 0.254
MA0041.1 0.387
MA0042.1 0.435
MA0043.1 0.133
MA0046.1 1.50793e-15
MA0047.2 0.68
MA0048.1 0.722
MA0050.1 0.0355
MA0051.1 0.0257
MA0052.1 1.50826e-51
MA0055.1 0.464
MA0057.1 0.591
MA0058.1 0.0445
MA0059.1 0.159
MA0060.1 2.58092e-11
MA0061.1 0.517
MA0062.2 4.46631e-5
MA0065.2 0.00727
MA0066.1 0.834
MA0067.1 0.403
MA0068.1 0.855
MA0069.1 0.184
MA0070.1 0.943
MA0071.1 0.00983
MA0072.1 0.657
MA0073.1 0.859
MA0074.1 0.201
MA0076.1 0.00193
MA0077.1 0.835
MA0078.1 0.701
MA0079.2 0.77
MA0080.2 0.237
MA0081.1 0.848
MA0083.1 7.71115e-11
MA0084.1 0.5
MA0087.1 0.529
MA0088.1 0.707
MA0090.1 1.45143e-4
MA0091.1 0.492
MA0092.1 0.412
MA0093.1 0.058
MA0099.2 0.333
MA0100.1 0.0182
MA0101.1 0.938
MA0102.2 0.225
MA0103.1 0.00541
MA0104.2 0.0534
MA0105.1 0.376
MA0106.1 0.351
MA0107.1 0.576
MA0108.2 0.377
MA0111.1 0.783
MA0112.2 1.44568e-6
MA0113.1 0.334
MA0114.1 0.934
MA0115.1 0.185
MA0116.1 0.755
MA0117.1 0.547
MA0119.1 0.124
MA0122.1 0.0331
MA0124.1 0.759
MA0125.1 0.247
MA0131.1 0.167
MA0135.1 0.141
MA0136.1 0.00454
MA0137.2 0.265
MA0138.2 0.00631
MA0139.1 0.688
MA0140.1 0.00186
MA0141.1 3.73787e-9
MA0142.1 0.363
MA0143.1 0.172
MA0144.1 0.508
MA0145.1 0.0498
MA0146.1 0.0631
MA0147.1 0.115
MA0148.1 0.761
MA0149.1 0.863
MA0150.1 0.0537
MA0152.1 0.215
MA0153.1 5.20794e-10
MA0154.1 0.0134
MA0155.1 0.283
MA0156.1 0.0429
MA0157.1 0.89
MA0159.1 9.35272e-6
MA0160.1 1.86427e-5
MA0162.1 0.0834
MA0163.1 0.11
MA0164.1 0.298
MA0258.1 0.00165
MA0259.1 0.205



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: CNhs11196

Novel motif P-value
1 0.0775
10 0.583
100 0.675
101 0.714
102 0.772
103 0.374
104 0.65
105 0.101
106 0.193
107 0.153
108 0.673
109 0.154
11 0.278
110 0.154
111 0.0173
112 0.597
113 0.666
114 0.0793
115 0.55
116 0.967
117 0.785
118 0.784
119 0.08
12 0.918
120 0.205
121 0.164
122 0.654
123 0.517
124 0.689
125 0.697
126 0.635
127 0.469
128 0.444
129 0.0495
13 0.00142
130 0.791
131 0.868
132 0.767
133 0.575
134 0.609
135 0.812
136 0.48
137 0.551
138 0.115
139 0.078
14 0.149
140 0.311
141 0.439
142 0.917
143 0.461
144 0.453
145 0.409
146 0.631
147 0.501
148 0.345
149 0.00312
15 0.251
150 0.412
151 0.149
152 0.0717
153 0.462
154 0.949
155 0.0551
156 0.178
157 0.874
158 0.0941
159 0.0364
160 0.248
161 0.942
162 0.538
163 0.274
164 0.382
165 3.4078e-4
166 0.214
167 0.905
168 0.0798
169 7.75013e-5
17 0.11
18 0.376
19 0.0348
2 0.592
20 0.746
21 0.326
22 0.028
23 0.323
24 0.833
25 0.721
26 0.0912
27 0.903
28 0.813
29 0.896
3 0.259
30 0.57
31 0.394
32 0.926
33 0.73
34 0.2
35 0.965
36 0.66
37 0.0145
38 0.623
39 0.623
4 0.413
40 0.902
41 0.559
42 0.758
43 0.151
44 0.75
45 0.531
46 0.483
47 0.437
48 0.423
49 0.155
5 0.187
50 0.604
51 0.501
52 0.313
53 0.692
54 0.39
55 0.921
56 0.406
57 0.377
58 0.383
59 0.0266
6 0.179
60 0.181
61 0.602
62 0.342
63 0.0769
64 0.667
65 0.432
66 0.137
67 0.709
68 0.857
69 0.124
7 0.0995
70 0.304
71 0.0659
72 0.904
73 0.0466
74 0.256
75 0.543
76 0.862
77 0.224
78 0.0321
79 0.912
8 0.425
80 0.509
81 0.387
82 0.0874
83 0.283
84 0.21
85 0.00379
86 0.704
87 0.0543
88 0.534
89 0.0445
9 0.129
90 0.442
91 0.331
92 0.129
93 0.77
94 0.499
95 0.246
96 0.481
97 0.372
98 0.245
99 0.736



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: CNhs11196


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000309 (mouse neonate N25 sample)
0011475 (mouse heart- neonate N25 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)