Personal tools

FF:1368-26H1

From FANTOM5_SSTAR

Jump to: navigation, search


Name:liver, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11198
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 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  SAMD00004760
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11198 CAGE DRX009028 DRR009902
Accession ID Mm9

Library idBAMCTSS
CNhs11198 DRZ001327 DRZ002710
Accession ID Mm10

Library idBAMCTSS
CNhs11198 DRZ012677 DRZ014060
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

CNhs11198

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.162
1001 0.116
1002 --0.116
1003 0.0278
1004 0
1005 0.00294
1006 0.107
1007 --0.0939
1008 0
1009 0.0434
101 0.00851
1010 0
1011 --0.182
1012 0
1013 0.496
1014 --0.0874
1015 --0.37
1016 --0.362
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.116
1022 0.523
1023 0
1024 0
1025 0.235
1026 0
1027 0
1028 0
1029 --0.0428
103 --0.0563
1030 0
1031 --0.217
1032 --0.268
1033 0
1034 0.862
1035 0
1036 --0.208
1037 0
1038 --0.191
1039 0.718
104 0
1040 --0.141
1041 0.0717



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: CNhs11198

Jaspar motif P-value
MA0002.2 0.316
MA0003.1 0.517
MA0004.1 0.657
MA0006.1 0.236
MA0007.1 0.268
MA0009.1 0.629
MA0014.1 0.263
MA0017.1 3.06405e-24
MA0018.2 7.55013e-5
MA0019.1 0.572
MA0024.1 0.0625
MA0025.1 0.181
MA0027.1 0.687
MA0028.1 0.429
MA0029.1 0.483
MA0030.1 0.0144
MA0031.1 0.00237
MA0035.2 0.0432
MA0038.1 0.324
MA0039.2 0.248
MA0040.1 0.589
MA0041.1 0.826
MA0042.1 0.997
MA0043.1 0.23
MA0046.1 1.42394e-103
MA0047.2 2.78536e-8
MA0048.1 0.341
MA0050.1 0.00401
MA0051.1 0.00288
MA0052.1 0.97
MA0055.1 0.213
MA0057.1 0.531
MA0058.1 0.441
MA0059.1 0.135
MA0060.1 0.889
MA0061.1 0.527
MA0062.2 0.842
MA0065.2 1.71533e-16
MA0066.1 0.0397
MA0067.1 0.0905
MA0068.1 0.287
MA0069.1 0.0737
MA0070.1 0.2
MA0071.1 2.32266e-5
MA0072.1 1.85889e-6
MA0073.1 0.907
MA0074.1 0.306
MA0076.1 0.967
MA0077.1 0.0275
MA0078.1 0.586
MA0079.2 0.281
MA0080.2 0.332
MA0081.1 0.536
MA0083.1 0.0841
MA0084.1 0.444
MA0087.1 0.255
MA0088.1 0.203
MA0090.1 0.436
MA0091.1 0.844
MA0092.1 0.196
MA0093.1 0.665
MA0099.2 0.559
MA0100.1 0.364
MA0101.1 0.844
MA0102.2 0.158
MA0103.1 0.181
MA0104.2 0.933
MA0105.1 0.086
MA0106.1 0.0333
MA0107.1 0.758
MA0108.2 0.0968
MA0111.1 0.697
MA0112.2 8.34929e-6
MA0113.1 0.432
MA0114.1 1.72291e-24
MA0115.1 4.96652e-12
MA0116.1 0.0996
MA0117.1 0.717
MA0119.1 0.00825
MA0122.1 0.577
MA0124.1 0.562
MA0125.1 0.612
MA0131.1 0.87
MA0135.1 0.621
MA0136.1 0.156
MA0137.2 0.0558
MA0138.2 0.377
MA0139.1 0.152
MA0140.1 0.546
MA0141.1 1.22638e-7
MA0142.1 0.0921
MA0143.1 0.213
MA0144.1 0.29
MA0145.1 0.0654
MA0146.1 0.153
MA0147.1 0.829
MA0148.1 6.03629e-11
MA0149.1 0.00896
MA0150.1 0.00301
MA0152.1 0.573
MA0153.1 4.45591e-68
MA0154.1 0.129
MA0155.1 0.65
MA0156.1 0.534
MA0157.1 0.00113
MA0159.1 2.42461e-4
MA0160.1 8.98409e-6
MA0162.1 0.314
MA0163.1 0.00276
MA0164.1 0.805
MA0258.1 0.00115
MA0259.1 0.606



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: CNhs11198

Novel motif P-value
1 0.0758
10 0.178
100 0.581
101 0.952
102 0.125
103 0.011
104 0.669
105 0.421
106 0.132
107 0.12
108 0.388
109 0.0515
11 0.0726
110 0.0276
111 0.0482
112 0.0142
113 0.965
114 0.0477
115 0.557
116 0.894
117 0.0688
118 0.541
119 0.0758
12 0.637
120 0.388
121 0.432
122 0.351
123 0.126
124 0.805
125 0.196
126 0.302
127 0.879
128 0.151
129 0.598
13 2.2796e-5
130 0.875
131 0.184
132 0.57
133 0.593
134 0.56
135 0.599
136 0.376
137 0.955
138 0.406
139 0.825
14 0.417
140 0.179
141 0.43
142 0.197
143 0.995
144 0.634
145 0.0615
146 0.322
147 0.456
148 0.231
149 0.301
15 0.178
150 0.248
151 0.666
152 0.148
153 0.251
154 0.711
155 0.938
156 0.114
157 0.471
158 0.593
159 0.413
160 0.169
161 0.718
162 0.65
163 0.242
164 0.0645
165 0.351
166 0.137
167 0.412
168 0.691
169 6.09801e-4
17 0.0591
18 0.822
19 0.036
2 0.899
20 0.455
21 0.39
22 0.122
23 0.405
24 0.224
25 0.57
26 0.00338
27 0.87
28 0.492
29 0.247
3 0.0612
30 0.86
31 0.363
32 0.239
33 0.224
34 0.844
35 0.483
36 0.0646
37 0.0638
38 0.262
39 0.25
4 0.809
40 0.11
41 0.898
42 0.384
43 0.113
44 0.0429
45 0.675
46 0.135
47 0.34
48 0.135
49 0.092
5 0.127
50 0.602
51 0.295
52 0.4
53 0.581
54 0.404
55 0.535
56 0.505
57 0.972
58 0.292
59 0.255
6 0.81
60 0.203
61 0.265
62 0.136
63 0.0955
64 0.52
65 0.196
66 0.926
67 0.844
68 0.443
69 0.945
7 0.14
70 0.0922
71 0.0439
72 0.798
73 0.0886
74 0.545
75 0.0264
76 0.682
77 0.423
78 0.00948
79 0.996
8 0.0122
80 0.502
81 0.638
82 0.0428
83 0.477
84 0.398
85 0.0349
86 0.163
87 0.144
88 0.768
89 0.0752
9 0.804
90 0.0748
91 0.382
92 0.384
93 0.089
94 0.964
95 0.184
96 0.281
97 0.324
98 0.627
99 0.092



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: CNhs11198


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)
0000309 (mouse neonate N25 sample)
0011485 (mouse liver- 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: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)