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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005400
 
|DRA_sample_Accession=CAGE@SAMD00005400
|accession_numbers=CAGE;DRX009099;DRR009973;DRZ001398;DRZ002781
+
|accession_numbers=CAGE;DRX009099;DRR009973;DRZ001398;DRZ002781;DRZ012748;DRZ014131
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000945,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010039,UBERON:0010317,UBERON:0001555,UBERON:0005409,UBERON:0001041
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000945,UBERON:0000479,UBERON:0001007,UBERON:0004119,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0004921,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010039,UBERON:0010317,UBERON:0001555,UBERON:0005409,UBERON:0001041
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_cell_lineage_facet=
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|library_id=CNhs11134
 
|library_id=CNhs11134
 
|library_id_phase_based=2:CNhs11134
 
|library_id_phase_based=2:CNhs11134
 +
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;1386
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;1386
 +
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N30.CNhs11134.1386-42I1.mm10.nobarcode.bam
 +
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N30.CNhs11134.1386-42I1.mm10.nobarcode.ctss.bed.gz
 +
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N30.CNhs11134.1386-42I1.mm9.nobarcode.bam
 +
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N30.CNhs11134.1386-42I1.mm9.ctss.bed.gz
 +
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/stomach%252c%2520neonate%2520N30.CNhs11134.1386-42I1.mm9.nobarcode.rdna.fa.gz
 
|name=stomach, neonate N30
 
|name=stomach, neonate N30
 
|namespace=FANTOM5
 
|namespace=FANTOM5

Latest revision as of 13:16, 10 August 2017


Name:stomach, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11134
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
tissuestomach
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  SAMD00005400
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11134 CAGE DRX009099 DRR009973
Accession ID Mm9

Library idBAMCTSS
CNhs11134 DRZ001398 DRZ002781
Accession ID Mm10

Library idBAMCTSS
CNhs11134 DRZ012748 DRZ014131
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

CNhs11134

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0859
1001 0.0905
1002 0.00605
1003 --0.0798
1004 0
1005 0.25
1006 0
1007 0.0383
1008 0
1009 0.0207
101 --0.13
1010 0
1011 --0.108
1012 0.0835
1013 0.199
1014 --0.0874
1015 --0.376
1016 --0.191
1017 0
1018 0.586
1019 0
102 0
1020 0
1021 --0.0231
1022 0.111
1023 0
1024 0
1025 0.686
1026 0
1027 0
1028 0
1029 0.375
103 0.12
1030 0
1031 --0.185
1032 0.67
1033 0
1034 0.131
1035 0.0624
1036 --0.139
1037 0
1038 0.0428
1039 0.16
104 0.983
1040 --0.0865
1041 0.1



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: CNhs11134

Jaspar motif P-value
MA0002.2 0.643
MA0003.1 0.226
MA0004.1 0.443
MA0006.1 0.0373
MA0007.1 0.939
MA0009.1 0.121
MA0014.1 0.319
MA0017.1 4.28203e-10
MA0018.2 0.155
MA0019.1 0.642
MA0024.1 5.5036e-4
MA0025.1 0.519
MA0027.1 0.493
MA0028.1 0.618
MA0029.1 0.614
MA0030.1 0.425
MA0031.1 0.0265
MA0035.2 0.76
MA0038.1 0.912
MA0039.2 7.88581e-5
MA0040.1 0.0211
MA0041.1 0.357
MA0042.1 0.665
MA0043.1 0.921
MA0046.1 3.29615e-27
MA0047.2 5.95022e-5
MA0048.1 0.999
MA0050.1 7.70974e-4
MA0051.1 7.03903e-4
MA0052.1 0.00583
MA0055.1 0.35
MA0057.1 0.14
MA0058.1 0.33
MA0059.1 0.0996
MA0060.1 0.0497
MA0061.1 0.454
MA0062.2 0.742
MA0065.2 2.29829e-9
MA0066.1 0.568
MA0067.1 0.316
MA0068.1 0.814
MA0069.1 0.663
MA0070.1 0.211
MA0071.1 0.447
MA0072.1 0.949
MA0073.1 0.617
MA0074.1 0.526
MA0076.1 0.413
MA0077.1 0.395
MA0078.1 0.223
MA0079.2 0.918
MA0080.2 9.7886e-4
MA0081.1 0.244
MA0083.1 0.0227
MA0084.1 0.0774
MA0087.1 0.563
MA0088.1 0.993
MA0090.1 0.27
MA0091.1 0.707
MA0092.1 0.93
MA0093.1 0.469
MA0099.2 2.92515e-4
MA0100.1 0.159
MA0101.1 0.957
MA0102.2 0.198
MA0103.1 1.1132e-5
MA0104.2 0.0196
MA0105.1 0.775
MA0106.1 0.166
MA0107.1 0.735
MA0108.2 0.534
MA0111.1 0.557
MA0112.2 2.98904e-4
MA0113.1 0.267
MA0114.1 1.69505e-18
MA0115.1 1.00757e-4
MA0116.1 0.501
MA0117.1 0.865
MA0119.1 0.00698
MA0122.1 0.77
MA0124.1 0.339
MA0125.1 0.307
MA0131.1 0.538
MA0135.1 0.0922
MA0136.1 0.0012
MA0137.2 0.819
MA0138.2 0.295
MA0139.1 0.098
MA0140.1 0.122
MA0141.1 0.0343
MA0142.1 0.103
MA0143.1 0.0229
MA0144.1 0.257
MA0145.1 0.00228
MA0146.1 0.486
MA0147.1 0.022
MA0148.1 1.83387e-5
MA0149.1 0.0401
MA0150.1 0.198
MA0152.1 0.192
MA0153.1 5.1708e-18
MA0154.1 0.124
MA0155.1 0.97
MA0156.1 0.0111
MA0157.1 0.0223
MA0159.1 0.0244
MA0160.1 0.12
MA0162.1 0.59
MA0163.1 0.683
MA0164.1 0.803
MA0258.1 0.0554
MA0259.1 0.0584



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: CNhs11134

Novel motif P-value
1 0.357
10 0.427
100 0.695
101 0.993
102 0.949
103 0.793
104 0.683
105 0.167
106 0.00629
107 0.0549
108 0.866
109 0.072
11 0.49
110 0.331
111 0.686
112 0.117
113 0.455
114 0.267
115 0.731
116 0.657
117 0.728
118 0.962
119 0.136
12 0.493
120 0.869
121 0.399
122 0.403
123 0.331
124 0.707
125 0.494
126 0.0248
127 0.553
128 0.0207
129 0.423
13 2.39791e-4
130 0.849
131 0.00148
132 0.609
133 0.928
134 0.549
135 0.399
136 0.219
137 0.4
138 0.301
139 0.144
14 0.468
140 0.01
141 0.322
142 0.495
143 0.137
144 0.287
145 0.0925
146 0.236
147 0.214
148 0.199
149 0.528
15 0.172
150 0.4
151 0.396
152 0.0186
153 0.61
154 0.399
155 0.602
156 0.0464
157 0.791
158 0.667
159 0.753
160 0.305
161 0.53
162 0.931
163 0.706
164 0.202
165 0.93
166 0.284
167 0.773
168 0.899
169 0.0222
17 0.0218
18 0.0706
19 0.0382
2 0.407
20 0.976
21 0.818
22 0.348
23 0.35
24 0.337
25 0.831
26 0.0284
27 0.941
28 0.498
29 0.587
3 0.467
30 0.4
31 0.779
32 0.318
33 0.242
34 0.66
35 0.665
36 0.805
37 0.0225
38 0.282
39 0.217
4 0.394
40 0.534
41 0.85
42 0.988
43 0.349
44 0.997
45 0.339
46 0.441
47 0.651
48 0.562
49 0.26
5 0.556
50 0.267
51 0.621
52 0.0324
53 0.915
54 0.397
55 0.267
56 0.386
57 0.855
58 0.324
59 0.875
6 0.366
60 0.0206
61 0.0889
62 0.56
63 0.173
64 0.777
65 0.0908
66 0.614
67 0.0504
68 0.209
69 0.482
7 0.099
70 0.089
71 0.357
72 0.645
73 0.0603
74 0.642
75 0.22
76 0.63
77 0.135
78 0.0412
79 0.963
8 0.516
80 0.721
81 0.743
82 0.32
83 0.0721
84 0.365
85 0.062
86 0.223
87 0.746
88 0.831
89 0.218
9 0.76
90 0.529
91 0.663
92 0.509
93 0.385
94 0.621
95 0.165
96 0.948
97 0.619
98 0.537
99 0.103



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: CNhs11134


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)
0000945 (stomach)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010039 (food storage organ)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)
0001041 (foregut)

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)
0011494 (mouse stomach- 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

UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)