Personal tools

Difference between revisions of "FF:406-44C5"

From FANTOM5_SSTAR

Jump to: navigation, search
Line 1: Line 1:
 
{{f5samples
 
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000926,UBERON:0000949,UBERON:0001062,UBERON:0002050,UBERON:0002100,UBERON:0002342,UBERON:0002346,UBERON:0002368,UBERON:0002369,UBERON:0002417,UBERON:0002530,UBERON:0002532,UBERON:0003075,UBERON:0004120,UBERON:0004121,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005423,UBERON:0006598,UBERON:0007284
+
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002369,UBERON:0002100,UBERON:0000483,UBERON:0002530,UBERON:0000926,UBERON:0000479,UBERON:0002346,UBERON:0002368,UBERON:0004121,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0009569,UBERON:0005291,UBERON:0005177,UBERON:0003104,UBERON:0005172,UBERON:0006858,UBERON:0005256,UBERON:0006598,UBERON:0005157,UBERON:0005173,UBERON:0002532,UBERON:0000924,UBERON:0002417,UBERON:0000949,UBERON:0000916,UBERON:0003075,UBERON:0002342,UBERON:0009142,UBERON:0003064,UBERON:0006601,UBERON:0006603,UBERON:0005062,UBERON:0007284
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_disease_facet=
 
|ancestors_in_disease_facet=

Revision as of 09:26, 8 June 2012


Name:adrenal gland, embryo E14
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueadrenal gland
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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs11038

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0365
1002 0.499
1003 --0.0446
1004 0
1005 --0.138
1006 0.0695
1007 --0.00314
1008 0
1009 0.0289
101 0.0858
1010 0
1011 0.0475
1012 0
1013 --0.117
1014 0.315
1015 0.161
1016 0.287
1017 0
1018 0
1019 0
102 0
1020 0
1021 --0.0487
1022 --0.0545
1023 0
1024 0.00214
1025 0.0717
1026 0.0108
1027 0.0695
1028 0
1029 --0.0535
103 0.37
1030 0
1031 0.365
1032 --0.017
1033 0.0653
1034 0
1035 0
1036 0.128
1037 0
1038 --0.0567
1039 0.00745
104 0
1040 --0.0023
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
no result for this sample


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: CNhs11038

Jaspar motif P-value
MA0002.2 0.00393
MA0003.1 0.83
MA0004.1 0.434
MA0006.1 0.371
MA0007.1 0.925
MA0009.1 0.0835
MA0014.1 0.518
MA0017.1 5.92242e-4
MA0018.2 0.921
MA0019.1 0.82
MA0024.1 2.86489e-9
MA0025.1 0.0869
MA0027.1 3.1015e-4
MA0028.1 0.553
MA0029.1 0.00353
MA0030.1 0.00292
MA0031.1 0.0024
MA0035.2 0.0355
MA0038.1 0.0549
MA0039.2 0.215
MA0040.1 0.0292
MA0041.1 0.145
MA0042.1 0.258
MA0043.1 0.788
MA0046.1 9.68521e-5
MA0047.2 1.40509e-4
MA0048.1 0.0032
MA0050.1 1.34247e-5
MA0051.1 1.09077e-7
MA0052.1 5.18523e-5
MA0055.1 0.0126
MA0057.1 0.115
MA0058.1 0.71
MA0059.1 0.464
MA0060.1 8.56563e-10
MA0061.1 0.275
MA0062.2 0.375
MA0065.2 0.00197
MA0066.1 0.0629
MA0067.1 0.284
MA0068.1 0.427
MA0069.1 0.363
MA0070.1 0.254
MA0071.1 0.246
MA0072.1 0.322
MA0073.1 0.966
MA0074.1 0.743
MA0076.1 0.635
MA0077.1 0.125
MA0078.1 0.77
MA0079.2 0.807
MA0080.2 1.52226e-7
MA0081.1 0.454
MA0083.1 0.843
MA0084.1 0.331
MA0087.1 0.238
MA0088.1 0.838
MA0090.1 0.353
MA0091.1 0.643
MA0092.1 0.785
MA0093.1 0.451
MA0099.2 0.0406
MA0100.1 0.824
MA0101.1 0.45
MA0102.2 0.0122
MA0103.1 3.57053e-6
MA0104.2 0.666
MA0105.1 0.678
MA0106.1 0.241
MA0107.1 0.127
MA0108.2 0.827
MA0111.1 0.571
MA0112.2 0.0038
MA0113.1 0.626
MA0114.1 0.00246
MA0115.1 0.195
MA0116.1 0.786
MA0117.1 0.456
MA0119.1 0.777
MA0122.1 0.71
MA0124.1 0.412
MA0125.1 0.0458
MA0131.1 0.914
MA0135.1 0.762
MA0136.1 6.81303e-5
MA0137.2 0.0224
MA0138.2 0.0463
MA0139.1 0.128
MA0140.1 1.22867e-4
MA0141.1 0.776
MA0142.1 0.707
MA0143.1 0.0729
MA0144.1 0.155
MA0145.1 0.0357
MA0146.1 0.706
MA0147.1 0.615
MA0148.1 0.00479
MA0149.1 0.12
MA0150.1 0.0453
MA0152.1 0.797
MA0153.1 2.92312e-5
MA0154.1 0.109
MA0155.1 0.899
MA0156.1 0.00226
MA0157.1 0.00539
MA0159.1 0.0105
MA0160.1 0.178
MA0162.1 0.746
MA0163.1 0.367
MA0164.1 0.844
MA0258.1 0.00479
MA0259.1 0.728



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: CNhs11038

Novel motif P-value
1 0.0997
10 0.212
100 0.867
101 0.832
102 0.848
103 0.195
104 0.821
105 0.42
106 0.0303
107 0.318
108 0.723
109 0.369
11 0.47
110 0.857
111 0.0317
112 0.258
113 0.319
114 0.045
115 0.733
116 0.795
117 0.393
118 0.467
119 0.0761
12 0.616
120 0.338
121 0.84
122 0.763
123 0.973
124 0.63
125 0.0655
126 0.244
127 0.366
128 0.0271
129 0.107
13 0.183
130 0.438
131 0.814
132 0.336
133 0.285
134 0.319
135 0.533
136 0.755
137 0.858
138 0.368
139 0.0138
14 0.132
140 0.13
141 0.33
142 0.745
143 0.283
144 0.407
145 0.748
146 0.776
147 0.601
148 0.218
149 0.689
15 0.115
150 0.821
151 0.0445
152 0.518
153 0.567
154 0.538
155 0.912
156 2.8089e-7
157 0.158
158 0.087
159 0.0869
160 0.98
161 0.721
162 0.91
163 0.0379
164 0.344
165 0.0814
166 0.589
167 0.476
168 0.535
169 0.166
17 0.204
18 0.778
19 0.816
2 0.938
20 0.865
21 0.641
22 0.604
23 0.234
24 0.739
25 0.298
26 0.481
27 0.528
28 0.0995
29 0.64
3 0.576
30 0.871
31 0.531
32 0.975
33 0.667
34 0.912
35 0.106
36 0.582
37 0.203
38 0.693
39 0.575
4 0.706
40 0.915
41 0.0218
42 0.84
43 0.283
44 0.47
45 0.254
46 0.237
47 0.353
48 0.345
49 0.0961
5 0.142
50 0.533
51 0.64
52 0.334
53 0.898
54 0.409
55 0.225
56 0.689
57 0.854
58 0.0728
59 0.813
6 0.578
60 0.0673
61 0.405
62 0.087
63 0.347
64 0.982
65 0.401
66 0.621
67 0.889
68 0.141
69 0.623
7 0.125
70 3.90236e-4
71 0.416
72 0.486
73 0.212
74 0.512
75 0.425
76 0.922
77 0.426
78 0.313
79 0.28
8 0.852
80 0.15
81 0.544
82 0.272
83 0.57
84 0.114
85 0.0137
86 0.605
87 0.978
88 0.913
89 0.0838
9 0.581
90 0.328
91 0.37
92 0.285
93 0.213
94 0.98
95 0.597
96 0.887
97 0.836
98 0.364
99 0.82



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: CNhs11038


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)
0002369 (adrenal gland)
0002100 (trunk)
0000483 (epithelium)
0002530 (gland)
0000926 (mesoderm)
0000479 (tissue)
0002346 (neurectoderm)
0002368 (endocrine gland)
0004121 (ectoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0000119 (cell layer)
0009569 (subdivision of trunk)
0005291 (embryonic tissue)
0005177 (trunk region element)
0003104 (mesenchyme)
0005172 (abdomen element)
0006858 (adrenal/interrenal gland)
0005256 (trunk mesenchyme)
0006598 (presumptive structure)
0005157 (epithelial fold)
0005173 (abdominal segment element)
0002532 (epiblast (generic))
0000924 (ectoderm)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0000916 (abdomen)
0003075 (neural plate)
0002342 (neural crest)
0009142 (entire embryonic mesenchyme)
0003064 (intermediate mesoderm)
0006601 (presumptive ectoderm)
0006603 (presumptive mesoderm)
0005062 (neural fold)
0007284 (presumptive neural plate)

FF: FANTOM5
NA

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

NA