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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005022
 
|DRA_sample_Accession=CAGE@SAMD00005022
|accession_numbers=CAGE;DRX009065;DRR009939;DRZ001364;DRZ002747
+
|accession_numbers=CAGE;DRX009065;DRR009939;DRZ001364;DRZ002747;DRZ012714;DRZ014097
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001264,UBERON:0002100,UBERON:0000479,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002323,UBERON:0005177,UBERON:0000464,UBERON:0004458,UBERON:0000949
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001264,UBERON:0002100,UBERON:0000479,UBERON:0000466,UBERON:0002075,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0002553,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002323,UBERON:0005177,UBERON:0000464,UBERON:0004458,UBERON:0000949
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_cell_lineage_facet=
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|library_id=CNhs11182
 
|library_id=CNhs11182
 
|library_id_phase_based=2:CNhs11182
 
|library_id_phase_based=2:CNhs11182
 +
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1548
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1548
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pancreas%252c%2520neonate%2520N30.CNhs11182.1548-44H5.mm10.nobarcode.bam
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pancreas%252c%2520neonate%2520N30.CNhs11182.1548-44H5.mm10.nobarcode.bam
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pancreas%252c%2520neonate%2520N30.CNhs11182.1548-44H5.mm10.nobarcode.ctss.bed.gz
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/pancreas%252c%2520neonate%2520N30.CNhs11182.1548-44H5.mm10.nobarcode.ctss.bed.gz

Latest revision as of 13:21, 10 August 2017


Name:pancreas, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11182
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
tissuepancreas
dev stage30 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  SAMD00005022
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11182 CAGE DRX009065 DRR009939
Accession ID Mm9

Library idBAMCTSS
CNhs11182 DRZ001364 DRZ002747
Accession ID Mm10

Library idBAMCTSS
CNhs11182 DRZ012714 DRZ014097
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

CNhs11182

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0233
1002 --0.0941
1003 --0.123
1004 0
1005 0
1006 --0.0539
1007 0.128
1008 0
1009 0.0481
101 --0.0247
1010 0
1011 --0.269
1012 0
1013 0.628
1014 --0.0874
1015 --0.294
1016 --0.286
1017 0
1018 0.0162
1019 0
102 0
1020 0
1021 0.243
1022 0.736
1023 0
1024 0
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.148
103 --0.0317
1030 0
1031 --0.178
1032 0.134
1033 0
1034 1.235
1035 0
1036 --0.183
1037 0
1038 0.202
1039 0.267
104 0
1040 --0.11
1041 0.308



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: CNhs11182

Jaspar motif P-value
MA0002.2 0.307
MA0003.1 0.587
MA0004.1 0.269
MA0006.1 0.142
MA0007.1 0.408
MA0009.1 0.711
MA0014.1 0.273
MA0017.1 0.232
MA0018.2 0.00566
MA0019.1 0.754
MA0024.1 0.00292
MA0025.1 0.158
MA0027.1 0.81
MA0028.1 0.807
MA0029.1 0.889
MA0030.1 0.942
MA0031.1 0.51
MA0035.2 0.0919
MA0038.1 0.343
MA0039.2 0.0415
MA0040.1 0.753
MA0041.1 0.173
MA0042.1 0.532
MA0043.1 0.0645
MA0046.1 1.31132e-8
MA0047.2 2.22179e-4
MA0048.1 0.838
MA0050.1 0.564
MA0051.1 0.409
MA0052.1 0.00129
MA0055.1 0.435
MA0057.1 0.135
MA0058.1 0.318
MA0059.1 0.0105
MA0060.1 7.5109e-4
MA0061.1 0.815
MA0062.2 0.902
MA0065.2 0.0396
MA0066.1 0.47
MA0067.1 0.0688
MA0068.1 0.165
MA0069.1 0.552
MA0070.1 0.807
MA0071.1 0.204
MA0072.1 0.0898
MA0073.1 0.368
MA0074.1 0.134
MA0076.1 0.643
MA0077.1 0.732
MA0078.1 0.608
MA0079.2 0.225
MA0080.2 0.905
MA0081.1 0.499
MA0083.1 0.00411
MA0084.1 0.42
MA0087.1 0.112
MA0088.1 0.104
MA0090.1 0.0647
MA0091.1 0.00164
MA0092.1 0.19
MA0093.1 0.264
MA0099.2 0.853
MA0100.1 0.0513
MA0101.1 0.983
MA0102.2 0.0779
MA0103.1 5.97306e-6
MA0104.2 0.337
MA0105.1 0.854
MA0106.1 0.135
MA0107.1 0.438
MA0108.2 0.134
MA0111.1 0.706
MA0112.2 6.03656e-4
MA0113.1 0.857
MA0114.1 0.201
MA0115.1 0.802
MA0116.1 0.62
MA0117.1 0.383
MA0119.1 0.63
MA0122.1 0.83
MA0124.1 0.356
MA0125.1 0.377
MA0131.1 0.751
MA0135.1 0.49
MA0136.1 0.11
MA0137.2 0.0022
MA0138.2 0.498
MA0139.1 0.292
MA0140.1 0.0199
MA0141.1 0.0131
MA0142.1 0.888
MA0143.1 0.845
MA0144.1 0.0181
MA0145.1 0.0217
MA0146.1 0.0508
MA0147.1 0.117
MA0148.1 2.54975e-5
MA0149.1 0.0194
MA0150.1 0.286
MA0152.1 0.845
MA0153.1 2.68906e-4
MA0154.1 0.0332
MA0155.1 0.376
MA0156.1 0.868
MA0157.1 0.132
MA0159.1 0.0921
MA0160.1 0.113
MA0162.1 0.52
MA0163.1 0.0659
MA0164.1 0.43
MA0258.1 0.0177
MA0259.1 0.78



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: CNhs11182

Novel motif P-value
1 0.06
10 0.153
100 0.523
101 0.722
102 0.432
103 0.0428
104 0.436
105 0.802
106 0.0256
107 0.216
108 0.899
109 0.0556
11 0.0793
110 0.0788
111 0.0258
112 0.164
113 0.561
114 0.119
115 0.865
116 0.205
117 0.171
118 0.908
119 0.027
12 0.614
120 0.975
121 0.52
122 0.186
123 0.718
124 0.87
125 0.327
126 0.0324
127 0.44
128 0.0115
129 0.253
13 0.00918
130 0.9
131 0.35
132 0.871
133 0.0952
134 0.781
135 0.424
136 0.145
137 0.169
138 0.106
139 0.427
14 0.725
140 0.132
141 0.508
142 0.289
143 0.278
144 0.445
145 0.0393
146 0.399
147 0.526
148 0.221
149 0.191
15 0.278
150 0.298
151 0.42
152 0.00421
153 0.689
154 0.982
155 0.19
156 0.698
157 0.181
158 0.175
159 0.631
160 0.229
161 0.454
162 0.714
163 0.688
164 0.0546
165 0.0595
166 0.149
167 0.709
168 0.726
169 0.0328
17 0.0317
18 0.725
19 0.0893
2 0.4
20 0.833
21 0.842
22 0.314
23 0.525
24 0.101
25 0.862
26 0.0112
27 0.609
28 0.77
29 0.256
3 0.198
30 0.913
31 0.289
32 0.295
33 0.626
34 0.917
35 0.309
36 0.46
37 0.0602
38 0.48
39 0.437
4 0.13
40 0.682
41 0.515
42 0.194
43 0.386
44 0.36
45 0.716
46 0.104
47 0.368
48 0.251
49 0.215
5 0.269
50 0.715
51 0.607
52 0.292
53 0.833
54 0.735
55 0.0386
56 0.467
57 0.651
58 0.356
59 0.0337
6 0.9
60 0.103
61 0.254
62 0.278
63 0.101
64 0.442
65 0.152
66 0.253
67 0.856
68 0.886
69 0.226
7 0.129
70 0.0661
71 0.0137
72 0.341
73 0.00777
74 0.632
75 0.276
76 0.918
77 0.063
78 0.192
79 0.0535
8 0.0686
80 0.882
81 0.378
82 0.148
83 0.696
84 0.892
85 0.0342
86 0.11
87 0.0278
88 0.951
89 0.659
9 0.712
90 0.02
91 0.408
92 0.131
93 0.166
94 0.867
95 0.388
96 0.327
97 0.00766
98 0.777
99 0.673



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: CNhs11182


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)
0001264 (pancreas)
0002100 (trunk)
0000479 (tissue)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002323 (body cavity)
0005177 (trunk region element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0000949 (endocrine system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011255 (mouse pancreas- neonate N30 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

FF:0000294 (mouse embryonic day 11 sample)