Personal tools

FF:639-21E3

From FANTOM5_SSTAR

Jump to: navigation, search


Name:heart, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11213
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 stage0 day 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  SAMD00005147
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11213 CAGE DRX008979 DRR009853
Accession ID Mm9

Library idBAMCTSS
CNhs11213 DRZ001278 DRZ002661
Accession ID Mm10

Library idBAMCTSS
CNhs11213 DRZ012628 DRZ014011
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

CNhs11213

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0.458
100 0
1000 0.208
1001 0.435
1002 0.24
1003 --0.0122
1004 0
1005 --0.0575
1006 0.395
1007 0.0651
1008 0
1009 0.173
101 --0.0248
1010 0
1011 --0.0164
1012 0.0799
1013 --0.2
1014 0.451
1015 --0.0108
1016 0.159
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0817
1022 0.756
1023 0
1024 0.259
1025 0
1026 0
1027 0
1028 0.048
1029 0.204
103 0.13
1030 0
1031 0.185
1032 0.0948
1033 --0.0273
1034 0
1035 0.618
1036 --0.185
1037 0
1038 0.193
1039 0.386
104 0
1040 0.164
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: CNhs11213

Jaspar motif P-value
MA0002.2 0.034
MA0003.1 0.733
MA0004.1 0.206
MA0006.1 0.414
MA0007.1 0.941
MA0009.1 0.757
MA0014.1 0.652
MA0017.1 0.0309
MA0018.2 0.173
MA0019.1 0.808
MA0024.1 0.164
MA0025.1 0.455
MA0027.1 0.643
MA0028.1 0.0757
MA0029.1 0.953
MA0030.1 0.633
MA0031.1 0.854
MA0035.2 0.237
MA0038.1 0.458
MA0039.2 0.0441
MA0040.1 0.227
MA0041.1 0.478
MA0042.1 0.623
MA0043.1 0.225
MA0046.1 2.29514e-15
MA0047.2 0.818
MA0048.1 0.0873
MA0050.1 0.0872
MA0051.1 0.145
MA0052.1 9.60146e-27
MA0055.1 0.00528
MA0057.1 0.793
MA0058.1 0.234
MA0059.1 0.18
MA0060.1 0.0012
MA0061.1 0.178
MA0062.2 2.41688e-5
MA0065.2 0.819
MA0066.1 0.781
MA0067.1 0.845
MA0068.1 0.247
MA0069.1 0.321
MA0070.1 0.995
MA0071.1 0.438
MA0072.1 0.587
MA0073.1 0.946
MA0074.1 0.446
MA0076.1 0.015
MA0077.1 0.976
MA0078.1 0.95
MA0079.2 0.397
MA0080.2 0.0117
MA0081.1 0.936
MA0083.1 4.14744e-13
MA0084.1 0.97
MA0087.1 0.388
MA0088.1 0.09
MA0090.1 2.97719e-4
MA0091.1 0.965
MA0092.1 0.372
MA0093.1 0.195
MA0099.2 2.95202e-4
MA0100.1 0.585
MA0101.1 0.349
MA0102.2 0.0205
MA0103.1 3.41365e-5
MA0104.2 0.0749
MA0105.1 0.241
MA0106.1 0.805
MA0107.1 0.453
MA0108.2 0.979
MA0111.1 0.582
MA0112.2 0.0204
MA0113.1 0.325
MA0114.1 0.00154
MA0115.1 0.601
MA0116.1 0.0556
MA0117.1 0.836
MA0119.1 0.12
MA0122.1 0.583
MA0124.1 0.705
MA0125.1 0.443
MA0131.1 0.809
MA0135.1 0.29
MA0136.1 0.00412
MA0137.2 0.129
MA0138.2 0.922
MA0139.1 0.136
MA0140.1 0.156
MA0141.1 9.63969e-8
MA0142.1 0.086
MA0143.1 0.595
MA0144.1 0.852
MA0145.1 0.6
MA0146.1 0.27
MA0147.1 0.071
MA0148.1 0.655
MA0149.1 0.299
MA0150.1 0.225
MA0152.1 0.108
MA0153.1 1.96848e-11
MA0154.1 0.553
MA0155.1 0.354
MA0156.1 3.94118e-4
MA0157.1 0.615
MA0159.1 0.0086
MA0160.1 0.00472
MA0162.1 0.268
MA0163.1 0.823
MA0164.1 0.401
MA0258.1 0.121
MA0259.1 0.363



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: CNhs11213

Novel motif P-value
1 0.434
10 0.644
100 0.689
101 0.367
102 0.79
103 0.722
104 0.547
105 0.481
106 0.283
107 0.198
108 0.876
109 0.662
11 0.895
110 0.274
111 0.323
112 0.393
113 0.391
114 0.295
115 0.957
116 0.255
117 0.729
118 0.412
119 0.489
12 0.944
120 0.261
121 0.59
122 0.438
123 0.251
124 0.445
125 0.919
126 0.614
127 0.138
128 0.72
129 0.637
13 5.41498e-4
130 0.269
131 0.413
132 0.985
133 0.473
134 0.975
135 0.808
136 0.0563
137 0.3
138 0.133
139 0.572
14 0.89
140 0.548
141 0.424
142 0.857
143 0.43
144 0.131
145 0.129
146 0.665
147 0.749
148 0.992
149 0.404
15 0.677
150 0.188
151 0.36
152 0.248
153 0.922
154 0.582
155 0.126
156 5.13022e-36
157 0.755
158 0.105
159 0.0158
160 0.289
161 0.354
162 0.813
163 0.552
164 0.256
165 0.04
166 0.55
167 0.769
168 0.705
169 0.00493
17 0.59
18 0.039
19 0.228
2 0.665
20 0.198
21 0.399
22 0.309
23 0.0448
24 0.497
25 0.613
26 0.0831
27 0.271
28 0.341
29 0.369
3 0.895
30 0.0869
31 0.816
32 0.412
33 0.235
34 0.472
35 0.263
36 0.0893
37 0.0745
38 0.105
39 0.993
4 0.478
40 0.00554
41 0.993
42 0.549
43 0.581
44 0.996
45 0.256
46 0.917
47 0.748
48 0.923
49 0.371
5 0.13
50 0.626
51 0.892
52 0.6
53 0.421
54 0.976
55 0.232
56 0.972
57 0.426
58 0.91
59 0.153
6 0.0459
60 0.437
61 0.721
62 0.531
63 0.435
64 0.521
65 0.0461
66 0.367
67 0.951
68 0.67
69 0.23
7 0.223
70 0.168
71 0.302
72 0.107
73 0.112
74 0.944
75 0.294
76 0.461
77 0.915
78 0.0875
79 0.497
8 0.889
80 0.0309
81 0.447
82 0.705
83 0.989
84 0.442
85 0.157
86 0.768
87 2.81429e-6
88 0.376
89 0.105
9 0.38
90 0.906
91 0.242
92 0.463
93 0.292
94 0.865
95 0.187
96 0.485
97 0.217
98 0.714
99 0.342



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: CNhs11213


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)
0000304 (mouse neonate N0 sample)
0011393 (mouse heart- neonate N00 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)