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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005990
 
|DRA_sample_Accession=CAGE@SAMD00005990
|accession_numbers=CAGE;DRX008973;DRR009847;DRZ001272;DRZ002655
+
|accession_numbers=CAGE;DRX008973;DRR009847;DRZ001272;DRZ002655;DRZ012622;DRZ014005
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,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:0000922,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=

Latest revision as of 13:29, 10 August 2017


Name:heart, embryo E13
Species:Mouse (Mus musculus)
Library ID:CNhs11013
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 stage13 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  SAMD00005990
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11013 CAGE DRX008973 DRR009847
Accession ID Mm9

Library idBAMCTSS
CNhs11013 DRZ001272 DRZ002655
Accession ID Mm10

Library idBAMCTSS
CNhs11013 DRZ012622 DRZ014005
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

CNhs11013

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0.134
100 0
1000 0.0719
1001 0.205
1002 0.523
1003 --0.0681
1004 0
1005 --0.0967
1006 0.164
1007 0.0238
1008 0
1009 0.13
101 0.033
1010 0
1011 --0.019
1012 0
1013 --0.236
1014 0.54
1015 0.171
1016 0.089
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0719
1022 0.301
1023 0
1024 0.0719
1025 0
1026 0
1027 --0.048
1028 0
1029 0.171
103 0.0719
1030 0
1031 0.324
1032 0.00398
1033 0.024
1034 0
1035 0.387
1036 0.0388
1037 0
1038 0.0124
1039 0.0898
104 0
1040 0.0667
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: CNhs11013

Jaspar motif P-value
MA0002.2 0.00472
MA0003.1 0.693
MA0004.1 0.807
MA0006.1 0.924
MA0007.1 0.147
MA0009.1 0.926
MA0014.1 0.803
MA0017.1 0.00216
MA0018.2 0.893
MA0019.1 0.654
MA0024.1 9.06794e-5
MA0025.1 0.151
MA0027.1 0.0215
MA0028.1 0.158
MA0029.1 0.405
MA0030.1 0.011
MA0031.1 0.0183
MA0035.2 0.118
MA0038.1 0.99
MA0039.2 0.0214
MA0040.1 0.0252
MA0041.1 0.171
MA0042.1 0.228
MA0043.1 0.924
MA0046.1 2.72163e-21
MA0047.2 0.00336
MA0048.1 0.0134
MA0050.1 4.25139e-6
MA0051.1 0.0021
MA0052.1 5.87717e-21
MA0055.1 9.18486e-5
MA0057.1 0.653
MA0058.1 0.788
MA0059.1 0.266
MA0060.1 0.135
MA0061.1 0.197
MA0062.2 0.327
MA0065.2 0.081
MA0066.1 0.637
MA0067.1 0.59
MA0068.1 0.386
MA0069.1 0.274
MA0070.1 0.793
MA0071.1 0.909
MA0072.1 0.109
MA0073.1 0.984
MA0074.1 0.605
MA0076.1 0.868
MA0077.1 0.917
MA0078.1 0.228
MA0079.2 0.527
MA0080.2 0.00393
MA0081.1 0.795
MA0083.1 3.18368e-16
MA0084.1 0.78
MA0087.1 0.786
MA0088.1 0.336
MA0090.1 0.00285
MA0091.1 0.946
MA0092.1 0.907
MA0093.1 0.858
MA0099.2 9.25482e-7
MA0100.1 0.867
MA0101.1 0.238
MA0102.2 0.00318
MA0103.1 5.66736e-6
MA0104.2 0.669
MA0105.1 0.439
MA0106.1 0.883
MA0107.1 0.102
MA0108.2 0.613
MA0111.1 0.333
MA0112.2 0.57
MA0113.1 0.893
MA0114.1 3.0006e-5
MA0115.1 0.886
MA0116.1 0.402
MA0117.1 0.434
MA0119.1 0.187
MA0122.1 0.864
MA0124.1 0.512
MA0125.1 0.879
MA0131.1 0.409
MA0135.1 0.369
MA0136.1 0.00841
MA0137.2 0.0541
MA0138.2 0.0152
MA0139.1 0.337
MA0140.1 0.0411
MA0141.1 0.00914
MA0142.1 0.21
MA0143.1 0.715
MA0144.1 0.28
MA0145.1 0.174
MA0146.1 0.927
MA0147.1 0.643
MA0148.1 0.0117
MA0149.1 0.0973
MA0150.1 0.00486
MA0152.1 0.947
MA0153.1 2.9713e-13
MA0154.1 0.656
MA0155.1 0.174
MA0156.1 3.7647e-4
MA0157.1 0.0654
MA0159.1 0.0939
MA0160.1 0.366
MA0162.1 0.292
MA0163.1 0.0393
MA0164.1 0.569
MA0258.1 0.372
MA0259.1 0.263



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: CNhs11013

Novel motif P-value
1 0.573
10 0.825
100 0.866
101 0.949
102 0.773
103 0.201
104 0.871
105 0.942
106 0.176
107 0.571
108 0.839
109 0.762
11 0.388
110 0.233
111 0.728
112 0.378
113 0.348
114 0.554
115 0.892
116 0.533
117 0.157
118 0.521
119 0.176
12 0.42
120 0.204
121 0.655
122 0.21
123 0.0155
124 0.564
125 0.672
126 0.915
127 0.285
128 0.0376
129 0.369
13 0.00121
130 0.322
131 0.671
132 0.582
133 0.646
134 0.682
135 0.899
136 0.0665
137 0.713
138 0.0819
139 0.821
14 0.424
140 0.9
141 0.191
142 0.645
143 0.735
144 0.0607
145 0.2
146 0.205
147 0.842
148 0.545
149 0.631
15 0.203
150 0.511
151 0.122
152 0.626
153 0.438
154 0.604
155 0.424
156 0.207
157 0.975
158 0.826
159 0.274
160 0.324
161 0.902
162 0.947
163 0.42
164 0.761
165 0.19
166 0.831
167 0.861
168 0.75
169 0.0989
17 0.524
18 0.314
19 0.58
2 0.258
20 0.111
21 0.69
22 0.784
23 0.089
24 0.451
25 0.566
26 0.0232
27 0.147
28 0.339
29 0.312
3 0.782
30 0.0477
31 0.613
32 0.402
33 0.189
34 0.784
35 0.457
36 0.191
37 0.243
38 0.205
39 0.33
4 0.808
40 0.00386
41 0.897
42 0.597
43 0.534
44 0.563
45 0.045
46 0.878
47 0.697
48 0.639
49 0.58
5 0.774
50 0.478
51 0.875
52 0.489
53 0.576
54 0.626
55 0.262
56 0.734
57 0.413
58 0.624
59 0.338
6 0.193
60 0.445
61 0.308
62 0.423
63 0.825
64 0.599
65 0.151
66 0.747
67 0.867
68 0.42
69 0.235
7 0.836
70 0.0126
71 0.0184
72 0.101
73 0.433
74 0.653
75 0.534
76 0.548
77 0.453
78 0.876
79 0.171
8 0.94
80 0.0161
81 0.5
82 0.677
83 0.819
84 0.593
85 0.559
86 0.943
87 0.00133
88 0.267
89 0.32
9 0.957
90 0.943
91 0.214
92 0.401
93 0.261
94 0.36
95 0.27
96 0.419
97 0.131
98 0.0946
99 0.531



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: CNhs11013


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)
0000293 (mouse embryonic day 13 sample)
0011327 (mouse heart- embryo E13 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)