Personal tools

FF:684-20A8

From FANTOM5_SSTAR

Revision as of 13:43, 10 August 2017 by Autoedit (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Name:liver, neonate N06
Species:Mouse (Mus musculus)
Library ID:CNhs11101
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
tissueliver
dev stage6 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  SAMD00005319
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11101 CAGE DRX009024 DRR009898
Accession ID Mm9

Library idBAMCTSS
CNhs11101 DRZ001323 DRZ002706
Accession ID Mm10

Library idBAMCTSS
CNhs11101 DRZ012673 DRZ014056
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

CNhs11101

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.659
1002 0.161
1003 0.3
1004 0
1005 0.348
1006 0.0455
1007 0.13
1008 0
1009 0.197
101 0.0375
1010 0
1011 --0.108
1012 0.49
1013 0.273
1014 0.387
1015 --0.172
1016 --0.0783
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.289
1023 0
1024 0.0799
1025 0.428
1026 0
1027 0
1028 0
1029 0.949
103 0.387
1030 0.588
1031 0.241
1032 --0.246
1033 0
1034 0.739
1035 0
1036 0.0388
1037 0
1038 0.205
1039 0.324
104 0
1040 --0.121
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: CNhs11101

Jaspar motif P-value
MA0002.2 0.645
MA0003.1 0.406
MA0004.1 0.953
MA0006.1 0.373
MA0007.1 0.362
MA0009.1 0.336
MA0014.1 0.575
MA0017.1 7.18432e-8
MA0018.2 1.0695e-7
MA0019.1 0.82
MA0024.1 0.363
MA0025.1 0.126
MA0027.1 0.887
MA0028.1 0.038
MA0029.1 0.879
MA0030.1 0.805
MA0031.1 0.964
MA0035.2 0.481
MA0038.1 0.0173
MA0039.2 0.00762
MA0040.1 0.38
MA0041.1 0.134
MA0042.1 0.461
MA0043.1 5.94727e-4
MA0046.1 2.32812e-12
MA0047.2 0.127
MA0048.1 0.0732
MA0050.1 0.237
MA0051.1 0.655
MA0052.1 0.00279
MA0055.1 0.695
MA0057.1 0.883
MA0058.1 0.944
MA0059.1 0.0724
MA0060.1 4.25377e-8
MA0061.1 0.247
MA0062.2 4.27898e-4
MA0065.2 3.98505e-5
MA0066.1 0.0118
MA0067.1 0.146
MA0068.1 0.541
MA0069.1 0.214
MA0070.1 0.627
MA0071.1 0.0246
MA0072.1 0.068
MA0073.1 0.693
MA0074.1 0.327
MA0076.1 0.0064
MA0077.1 0.0226
MA0078.1 0.947
MA0079.2 0.0343
MA0080.2 0.0126
MA0081.1 0.212
MA0083.1 0.132
MA0084.1 0.485
MA0087.1 0.164
MA0088.1 0.471
MA0090.1 0.947
MA0091.1 0.262
MA0092.1 0.102
MA0093.1 0.972
MA0099.2 0.0411
MA0100.1 0.477
MA0101.1 0.865
MA0102.2 0.995
MA0103.1 0.393
MA0104.2 0.805
MA0105.1 8.28206e-6
MA0106.1 0.081
MA0107.1 0.944
MA0108.2 4.21709e-7
MA0111.1 0.497
MA0112.2 2.179e-6
MA0113.1 0.372
MA0114.1 6.7835e-8
MA0115.1 1.39818e-4
MA0116.1 0.0157
MA0117.1 0.968
MA0119.1 0.022
MA0122.1 0.0475
MA0124.1 0.913
MA0125.1 0.347
MA0131.1 0.672
MA0135.1 0.00165
MA0136.1 4.73062e-6
MA0137.2 0.227
MA0138.2 0.908
MA0139.1 0.46
MA0140.1 0.0771
MA0141.1 7.50605e-4
MA0142.1 0.732
MA0143.1 0.183
MA0144.1 0.75
MA0145.1 0.745
MA0146.1 0.917
MA0147.1 0.949
MA0148.1 0.00679
MA0149.1 0.0599
MA0150.1 0.448
MA0152.1 0.371
MA0153.1 7.7018e-11
MA0154.1 0.0061
MA0155.1 0.722
MA0156.1 0.00565
MA0157.1 0.35
MA0159.1 0.0117
MA0160.1 0.0677
MA0162.1 0.457
MA0163.1 4.6319e-5
MA0164.1 0.428
MA0258.1 0.0021
MA0259.1 0.819



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: CNhs11101

Novel motif P-value
1 0.0685
10 0.054
100 0.686
101 0.717
102 0.442
103 0.00299
104 0.801
105 0.543
106 0.0181
107 0.00981
108 0.715
109 0.321
11 0.171
110 0.0608
111 0.0404
112 0.0198
113 0.662
114 0.0384
115 0.398
116 0.928
117 0.0162
118 0.179
119 0.162
12 0.669
120 0.967
121 0.276
122 0.723
123 0.87
124 0.0659
125 0.909
126 0.187
127 0.606
128 0.00727
129 0.325
13 0.0106
130 0.788
131 0.495
132 0.735
133 0.0565
134 0.592
135 0.837
136 0.423
137 0.56
138 0.425
139 0.247
14 0.802
140 0.00168
141 0.145
142 0.0932
143 0.29
144 0.611
145 0.0448
146 0.993
147 0.676
148 0.85
149 0.597
15 0.228
150 0.0933
151 0.635
152 0.845
153 0.0993
154 0.147
155 0.787
156 0.598
157 0.973
158 0.924
159 0.018
160 0.0536
161 0.694
162 0.918
163 0.581
164 0.0896
165 0.95
166 0.952
167 0.0509
168 0.856
169 0.0191
17 0.0903
18 0.244
19 0.0503
2 0.924
20 0.293
21 0.951
22 0.282
23 0.163
24 0.96
25 0.891
26 7.86695e-4
27 0.715
28 0.618
29 0.156
3 0.0182
30 0.433
31 0.31
32 0.0479
33 0.589
34 0.483
35 0.125
36 0.22
37 0.103
38 0.577
39 0.326
4 0.639
40 0.86
41 0.559
42 0.19
43 0.0307
44 0.0788
45 0.643
46 0.033
47 0.48
48 0.34
49 0.0456
5 0.0848
50 0.686
51 0.416
52 0.656
53 0.465
54 0.445
55 0.957
56 0.319
57 0.174
58 0.698
59 0.233
6 0.697
60 0.155
61 0.171
62 0.297
63 0.236
64 0.495
65 0.39
66 0.298
67 0.866
68 0.0339
69 0.578
7 0.25
70 0.167
71 0.0274
72 0.98
73 0.443
74 0.501
75 0.0316
76 0.265
77 0.396
78 0.041
79 0.49
8 0.0256
80 0.789
81 0.759
82 0.105
83 0.88
84 0.437
85 0.0301
86 0.244
87 0.0261
88 0.593
89 0.508
9 0.632
90 0.0249
91 0.0273
92 0.0439
93 0.94
94 0.252
95 0.858
96 0.154
97 0.209
98 0.365
99 0.266



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: CNhs11101


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)
0002107 (liver)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
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)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000312 (mouse neonate N6 sample)
0011403 (mouse liver- neonate N06 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:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)