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FF:33-1H6

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Name:stomach, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10503
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 stageadult
sexmale
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  SAMD00005432
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10503 CAGE DRX009090 DRR009964
Accession ID Mm9

Library idBAMCTSS
CNhs10503 DRZ001389 DRZ002772
Accession ID Mm10

Library idBAMCTSS
CNhs10503 DRZ012739 DRZ014122
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

CNhs10503

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.749
1001 0.0714
1002 0.535
1003 0.275
1004 0
1005 0.0941
1006 --0.0864
1007 --0.115
1008 0
1009 0.101
101 --0.105
1010 0
1011 0
1012 0
1013 0.407
1014 0
1015 --0.187
1016 --0.2
1017 0.761
1018 0.683
1019 0
102 0
1020 0
1021 --0.0487
1022 0.549
1023 0
1024 0.0265
1025 0.587
1026 0
1027 0
1028 0
1029 0.316
103 0
1030 0
1031 --0.256
1032 0.285
1033 --0.0665
1034 0.291
1035 0
1036 --0.2
1037 0
1038 0.0249
1039 0.256
104 0
1040 0.035
1041 0.464



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: CNhs10503

Jaspar motif P-value
MA0002.2 0.114
MA0003.1 0.194
MA0004.1 0.961
MA0006.1 0.242
MA0007.1 0.233
MA0009.1 0.116
MA0014.1 0.78
MA0017.1 0.00795
MA0018.2 0.00343
MA0019.1 0.981
MA0024.1 0.0011
MA0025.1 0.0778
MA0027.1 0.643
MA0028.1 0.224
MA0029.1 0.556
MA0030.1 0.971
MA0031.1 0.56
MA0035.2 0.39
MA0038.1 0.15
MA0039.2 0.146
MA0040.1 0.176
MA0041.1 0.233
MA0042.1 0.374
MA0043.1 6.3758e-5
MA0046.1 2.335e-7
MA0047.2 2.07395e-4
MA0048.1 0.913
MA0050.1 0.516
MA0051.1 0.94
MA0052.1 0.899
MA0055.1 0.304
MA0057.1 0.0389
MA0058.1 0.822
MA0059.1 0.488
MA0060.1 8.98166e-9
MA0061.1 0.55
MA0062.2 0.0394
MA0065.2 0.00208
MA0066.1 0.117
MA0067.1 0.515
MA0068.1 0.0538
MA0069.1 0.176
MA0070.1 0.281
MA0071.1 0.97
MA0072.1 0.677
MA0073.1 0.714
MA0074.1 0.148
MA0076.1 0.0729
MA0077.1 0.537
MA0078.1 0.947
MA0079.2 0.378
MA0080.2 0.697
MA0081.1 0.0465
MA0083.1 0.0324
MA0084.1 0.548
MA0087.1 0.628
MA0088.1 0.246
MA0090.1 0.288
MA0091.1 0.347
MA0092.1 0.207
MA0093.1 0.88
MA0099.2 5.95523e-5
MA0100.1 0.301
MA0101.1 0.547
MA0102.2 0.188
MA0103.1 1.14931e-4
MA0104.2 0.825
MA0105.1 0.0246
MA0106.1 0.074
MA0107.1 0.588
MA0108.2 0.0167
MA0111.1 0.255
MA0112.2 5.02786e-6
MA0113.1 0.662
MA0114.1 0.014
MA0115.1 0.201
MA0116.1 0.0138
MA0117.1 0.831
MA0119.1 0.0667
MA0122.1 0.681
MA0124.1 0.214
MA0125.1 0.0546
MA0131.1 0.172
MA0135.1 0.139
MA0136.1 0.0406
MA0137.2 0.652
MA0138.2 0.076
MA0139.1 0.0412
MA0140.1 0.884
MA0141.1 0.0762
MA0142.1 0.873
MA0143.1 0.479
MA0144.1 0.516
MA0145.1 0.00529
MA0146.1 0.237
MA0147.1 0.977
MA0148.1 1.92768e-6
MA0149.1 0.0145
MA0150.1 0.262
MA0152.1 0.249
MA0153.1 4.29083e-6
MA0154.1 0.00675
MA0155.1 0.384
MA0156.1 0.144
MA0157.1 0.495
MA0159.1 0.0147
MA0160.1 0.492
MA0162.1 0.21
MA0163.1 0.00809
MA0164.1 0.783
MA0258.1 0.00122
MA0259.1 0.668



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: CNhs10503

Novel motif P-value
1 0.12
10 0.215
100 0.63
101 0.632
102 0.373
103 0.0369
104 0.703
105 0.425
106 0.0158
107 0.119
108 0.678
109 0.0796
11 0.191
110 0.214
111 0.0202
112 0.0726
113 0.966
114 0.112
115 0.499
116 0.497
117 0.31
118 0.898
119 0.0322
12 0.753
120 0.441
121 0.678
122 0.957
123 0.888
124 0.884
125 0.844
126 0.266
127 0.951
128 0.0333
129 0.382
13 0.0532
130 0.651
131 0.862
132 0.698
133 0.754
134 0.667
135 0.521
136 0.646
137 0.357
138 0.531
139 0.00513
14 0.653
140 0.00623
141 0.108
142 0.586
143 0.395
144 0.144
145 0.131
146 0.2
147 0.987
148 0.229
149 0.0952
15 0.139
150 0.398
151 0.339
152 0.0674
153 0.983
154 0.947
155 0.443
156 2.18241e-39
157 0.812
158 0.626
159 0.723
160 0.264
161 0.424
162 0.736
163 0.896
164 0.362
165 0.0796
166 0.882
167 0.761
168 0.301
169 0.00137
17 0.0263
18 0.812
19 0.105
2 0.477
20 0.669
21 0.902
22 0.227
23 0.437
24 0.416
25 0.87
26 0.103
27 0.38
28 0.583
29 0.409
3 0.207
30 0.408
31 0.28
32 0.0188
33 0.655
34 0.777
35 0.321
36 0.123
37 0.0415
38 0.745
39 0.278
4 0.0553
40 0.218
41 0.832
42 0.494
43 0.178
44 0.275
45 0.384
46 0.153
47 0.191
48 0.318
49 0.169
5 0.0596
50 0.767
51 0.58
52 0.103
53 0.684
54 0.481
55 0.424
56 0.299
57 0.509
58 0.278
59 0.12
6 0.786
60 0.0399
61 0.244
62 0.188
63 0.132
64 0.45
65 0.311
66 0.813
67 0.445
68 0.797
69 0.587
7 0.167
70 0.0103
71 0.0934
72 0.601
73 0.0931
74 0.588
75 0.141
76 0.609
77 0.0209
78 0.127
79 0.0987
8 0.0626
80 0.824
81 0.481
82 0.0144
83 0.306
84 0.465
85 0.0152
86 0.356
87 0.736
88 0.378
89 0.0271
9 0.465
90 0.532
91 0.149
92 0.133
93 0.366
94 0.969
95 0.383
96 0.0607
97 0.00327
98 0.26
99 0.162



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: CNhs10503


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)
0007023 (adult 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)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011312 (mouse stomach- adult 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)