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FF:1345-25G2

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Name:liver, neonate N03
Species:Mouse (Mus musculus)
Library ID:CNhs11123
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 stage3 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  SAMD00004696
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11123 CAGE DRX009023 DRR009897
Accession ID Mm9

Library idBAMCTSS
CNhs11123 DRZ001322 DRZ002705
Accession ID Mm10

Library idBAMCTSS
CNhs11123 DRZ012672 DRZ014055
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

CNhs11123

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.105
1002 0.00541
1003 0.0184
1004 0
1005 0.105
1006 -0.0097
1007 -0.11
1008 0
1009 -0.0946
101 0.0438
1010 0
1011 -0.147
1012 0
1013 0.26
1014 0.0203
1015 -0.156
1016 -0.272
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0362
1022 0.137
1023 0
1024 0.116
1025 0.322
1026 0
1027 0
1028 0
1029 0.199
103 -0.0138
1030 0.105
1031 -0.251
1032 -0.232
1033 0
1034 0.66
1035 0
1036 0.202
1037 0
1038 -0.244
1039 0.405
104 0
1040 -0.333
1041 0



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: CNhs11123
Jaspar motif P-value
MA0002.2 0.0362
MA0003.1 0.415
MA0004.1 0.7
MA0006.1 0.299
MA0007.1 0.662
MA0009.1 0.276
MA0014.1 0.341
MA0017.1 4.96926e-16
MA0018.2 1.18045e-5
MA0019.1 0.301
MA0024.1 0.71
MA0025.1 0.68
MA0027.1 0.999
MA0028.1 0.661
MA0029.1 0.0957
MA0030.1 0.285
MA0031.1 0.358
MA0035.2 1.29992e-6
MA0038.1 0.188
MA0039.2 0.584
MA0040.1 0.482
MA0041.1 0.312
MA0042.1 0.67
MA0043.1 0.0176
MA0046.1 3.96894e-56
MA0047.2 3.96348e-5
MA0048.1 0.208
MA0050.1 0.0595
MA0051.1 0.192
MA0052.1 0.00372
MA0055.1 0.368
MA0057.1 0.662
MA0058.1 0.603
MA0059.1 0.0897
MA0060.1 0.0815
MA0061.1 0.216
MA0062.2 0.891
MA0065.2 2.24468e-9
MA0066.1 0.0156
MA0067.1 0.0986
MA0068.1 0.708
MA0069.1 0.168
MA0070.1 0.78
MA0071.1 0.00169
MA0072.1 0.00184
MA0073.1 0.737
MA0074.1 0.297
MA0076.1 0.796
MA0077.1 0.0319
MA0078.1 0.754
MA0079.2 0.145
MA0080.2 0.208
MA0081.1 0.957
MA0083.1 0.132
MA0084.1 0.171
MA0087.1 0.0502
MA0088.1 0.31
MA0090.1 0.956
MA0091.1 0.455
MA0092.1 0.105
MA0093.1 0.736
MA0099.2 0.61
MA0100.1 0.897
MA0101.1 0.793
MA0102.2 0.317
MA0103.1 0.294
MA0104.2 0.759
MA0105.1 9.60218e-4
MA0106.1 0.0834
MA0107.1 0.93
MA0108.2 0.165
MA0111.1 0.966
MA0112.2 4.60811e-6
MA0113.1 0.39
MA0114.1 1.34213e-14
MA0115.1 4.77723e-10
MA0116.1 0.00791
MA0117.1 0.986
MA0119.1 0.00628
MA0122.1 0.329
MA0124.1 0.643
MA0125.1 0.893
MA0131.1 0.898
MA0135.1 0.157
MA0136.1 0.853
MA0137.2 0.48
MA0138.2 0.712
MA0139.1 0.0734
MA0140.1 7.39085e-13
MA0141.1 2.55471e-5
MA0142.1 0.32
MA0143.1 0.127
MA0144.1 0.569
MA0145.1 0.317
MA0146.1 0.251
MA0147.1 0.625
MA0148.1 2.097e-7
MA0149.1 0.0343
MA0150.1 0.0401
MA0152.1 0.864
MA0153.1 6.80349e-43
MA0154.1 0.0185
MA0155.1 0.526
MA0156.1 0.894
MA0157.1 0.313
MA0159.1 0.00283
MA0160.1 0.00359
MA0162.1 0.351
MA0163.1 2.40476e-5
MA0164.1 0.714
MA0258.1 0.00506
MA0259.1 0.864



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: CNhs11123
Novel motif P-value
1 0.0727
10 0.111
100 0.54
101 0.985
102 0.216
103 0.00503
104 0.732
105 0.935
106 0.0549
107 0.0418
108 0.554
109 0.0229
11 0.0722
110 0.0588
111 0.0232
112 0.00535
113 0.813
114 0.0586
115 0.924
116 0.677
117 0.0209
118 0.177
119 0.0919
12 0.716
120 0.563
121 0.766
122 0.633
123 0.234
124 0.287
125 0.828
126 0.136
127 0.581
128 0.0381
129 0.38
13 6.43339e-4
130 0.667
131 0.42
132 0.867
133 0.158
134 0.392
135 0.529
136 0.605
137 0.46
138 0.393
139 0.469
14 0.705
140 0.0279
141 0.787
142 0.182
143 0.459
144 0.853
145 0.0308
146 0.352
147 0.587
148 0.661
149 0.728
15 0.118
150 0.176
151 0.452
152 0.216
153 0.276
154 0.657
155 0.528
156 0.113
157 0.826
158 0.867
159 0.992
160 0.138
161 0.833
162 0.643
163 0.478
164 0.0362
165 0.339
166 0.674
167 0.108
168 0.56
169 0.00171
17 0.0716
18 0.458
19 0.0392
2 0.995
20 0.426
21 0.992
22 0.222
23 0.425
24 0.237
25 0.737
26 1.00678e-4
27 0.713
28 0.503
29 0.077
3 0.0221
30 0.992
31 0.38
32 0.154
33 0.259
34 0.899
35 0.588
36 0.0216
37 0.0742
38 0.383
39 0.305
4 0.599
40 0.161
41 0.776
42 0.16
43 0.0725
44 0.0793
45 0.855
46 0.0646
47 0.209
48 0.148
49 0.0605
5 0.13
50 0.571
51 0.344
52 0.372
53 0.867
54 0.338
55 0.542
56 0.344
57 0.447
58 0.372
59 0.214
6 0.885
60 0.155
61 0.228
62 0.119
63 0.124
64 0.444
65 0.247
66 0.889
67 0.496
68 0.183
69 0.577
7 0.131
70 0.167
71 0.0259
72 0.627
73 0.145
74 0.599
75 0.047
76 0.755
77 0.441
78 0.0213
79 0.934
8 0.00754
80 0.263
81 0.664
82 0.0972
83 0.867
84 0.866
85 0.107
86 0.261
87 0.76
88 0.845
89 0.191
9 0.594
90 0.0785
91 0.146
92 0.157
93 0.324
94 0.693
95 0.175
96 0.13
97 0.644
98 0.239
99 0.118



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: CNhs11123


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)
0000311 (mouse neonate N3 sample)
0011484 (mouse liver- neonate N03 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)