Personal tools

FF:1377-27I3

From FANTOM5_SSTAR

Jump to: navigation, search


Name:adrenal gland, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11223
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
tissueadrenal gland
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  SAMD00005199
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11223 CAGE DRX008933 DRR009807
Accession ID Mm9

Library idBAMCTSS
CNhs11223 DRZ001232 DRZ002615
Accession ID Mm10

Library idBAMCTSS
CNhs11223 DRZ012582 DRZ013965
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sample
Ranked 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 sample
Ranked 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

CNhs11223

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.138
1001 0.161
1002 0.0514
1003 -0.0159
1004 0
1005 0
1006 0.0845
1007 -0.0437
1008 0
1009 0.269
101 -0.0793
1010 0
1011 -0.00857
1012 8.764537e-4
1013 0.141
1014 -0.0874
1015 -0.149
1016 0.00282
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0514
1022 0.274
1023 0
1024 0.177
1025 0
1026 0
1027 0
1028 0
1029 -0.0379
103 0
1030 0
1031 -0.0421
1032 0.0574
1033 -0.0151
1034 0.0514
1035 0
1036 -0.348
1037 0
1038 -0.0542
1039 0.501
104 0
1040 -0.032
1041 0.63



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs11223
Jaspar motif P-value
MA0002.2 0.606
MA0003.1 0.312
MA0004.1 0.104
MA0006.1 0.122
MA0007.1 0.264
MA0009.1 0.366
MA0014.1 0.075
MA0017.1 0.00623
MA0018.2 0.545
MA0019.1 0.526
MA0024.1 0.0134
MA0025.1 0.00498
MA0027.1 0.102
MA0028.1 0.493
MA0029.1 0.0119
MA0030.1 0.506
MA0031.1 0.22
MA0035.2 0.864
MA0038.1 0.0575
MA0039.2 0.00485
MA0040.1 0.974
MA0041.1 0.271
MA0042.1 0.71
MA0043.1 0.419
MA0046.1 0.476
MA0047.2 0.723
MA0048.1 0.494
MA0050.1 0.00258
MA0051.1 0.00107
MA0052.1 0.408
MA0055.1 0.425
MA0057.1 0.935
MA0058.1 0.218
MA0059.1 0.0571
MA0060.1 0.212
MA0061.1 0.604
MA0062.2 0.883
MA0065.2 2.22947e-7
MA0066.1 0.578
MA0067.1 0.883
MA0068.1 0.498
MA0069.1 0.0598
MA0070.1 0.0252
MA0071.1 5.52998e-5
MA0072.1 0.00373
MA0073.1 0.769
MA0074.1 0.996
MA0076.1 0.348
MA0077.1 0.994
MA0078.1 0.142
MA0079.2 0.0414
MA0080.2 0.00585
MA0081.1 0.815
MA0083.1 0.727
MA0084.1 0.604
MA0087.1 0.849
MA0088.1 0.455
MA0090.1 0.865
MA0091.1 0.262
MA0092.1 0.968
MA0093.1 0.17
MA0099.2 0.197
MA0100.1 0.205
MA0101.1 0.85
MA0102.2 0.8
MA0103.1 1.62727e-5
MA0104.2 0.0523
MA0105.1 0.0245
MA0106.1 0.695
MA0107.1 0.918
MA0108.2 0.0676
MA0111.1 0.355
MA0112.2 0.0673
MA0113.1 0.812
MA0114.1 4.03915e-6
MA0115.1 0.732
MA0116.1 0.52
MA0117.1 0.818
MA0119.1 0.0256
MA0122.1 0.732
MA0124.1 0.785
MA0125.1 0.448
MA0131.1 0.613
MA0135.1 0.487
MA0136.1 0.0576
MA0137.2 0.704
MA0138.2 0.179
MA0139.1 0.992
MA0140.1 0.903
MA0141.1 1.12831e-8
MA0142.1 0.00911
MA0143.1 0.819
MA0144.1 0.804
MA0145.1 0.186
MA0146.1 0.00268
MA0147.1 0.0408
MA0148.1 0.503
MA0149.1 0.0935
MA0150.1 0.0123
MA0152.1 0.995
MA0153.1 0.131
MA0154.1 0.288
MA0155.1 0.891
MA0156.1 0.469
MA0157.1 0.625
MA0159.1 0.714
MA0160.1 1.30517e-7
MA0162.1 0.488
MA0163.1 0.596
MA0164.1 0.345
MA0258.1 0.0504
MA0259.1 0.0441



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs11223
Novel motif P-value
1 0.298
10 0.639
100 0.18
101 0.971
102 0.786
103 0.747
104 0.809
105 0.739
106 0.255
107 0.725
108 0.0811
109 0.243
11 0.152
110 0.284
111 0.399
112 0.46
113 0.951
114 0.815
115 0.119
116 0.353
117 0.463
118 0.948
119 0.613
12 0.683
120 0.0117
121 0.137
122 0.96
123 0.261
124 0.383
125 0.711
126 0.23
127 0.245
128 0.169
129 0.543
13 0.0957
130 0.496
131 0.18
132 0.978
133 0.787
134 0.638
135 0.144
136 0.0161
137 0.812
138 0.194
139 0.281
14 0.278
140 0.0679
141 0.926
142 0.65
143 0.614
144 0.805
145 0.839
146 0.27
147 0.786
148 0.253
149 0.0136
15 0.69
150 0.387
151 0.464
152 0.00446
153 0.803
154 0.31
155 0.917
156 6.46565e-4
157 0.43
158 0.724
159 0.907
160 0.423
161 0.669
162 0.795
163 0.828
164 0.746
165 0.996
166 0.448
167 0.0656
168 0.847
169 0.0257
17 0.153
18 0.961
19 0.251
2 0.24
20 0.303
21 0.956
22 0.0153
23 0.186
24 0.158
25 0.738
26 0.672
27 0.922
28 0.866
29 0.385
3 0.755
30 0.588
31 0.705
32 0.583
33 0.36
34 0.673
35 0.427
36 0.232
37 0.247
38 0.18
39 0.237
4 0.903
40 0.659
41 0.094
42 0.626
43 0.921
44 0.258
45 0.693
46 0.176
47 0.505
48 0.306
49 0.463
5 0.788
50 0.392
51 0.864
52 0.984
53 0.679
54 0.664
55 0.0073
56 0.667
57 0.621
58 0.318
59 0.728
6 0.986
60 0.784
61 0.815
62 0.148
63 0.22
64 0.397
65 0.784
66 0.863
67 0.257
68 0.9
69 0.393
7 0.853
70 0.356
71 0.0453
72 0.744
73 0.0031
74 0.952
75 0.944
76 0.263
77 0.402
78 0.389
79 0.623
8 0.639
80 0.28
81 0.538
82 0.0909
83 5.40063e-4
84 0.101
85 0.51
86 0.551
87 0.0153
88 0.432
89 0.637
9 0.49
90 0.51
91 0.00198
92 0.732
93 0.887
94 0.151
95 0.0026
96 0.94
97 0.328
98 0.334
99 0.447



de novo motifs identified by HOMER in promoters active in this sample
Summary:The result of HOMER in this sample is shown.
Analyst:NA

library id: CNhs11223


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)
0002369 (adrenal gland)
0002100 (trunk)
0000479 (tissue)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0005172 (abdomen element)
0002530 (gland)
0006858 (adrenal/interrenal gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0000916 (abdomen)

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)
0011466 (mouse adrenal gland - 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:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)