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FF:178-9A3

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Name:intestine, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10496
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
strain
    1. Klotho
tissueintestine
dev stageadult
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  SAMD00004890
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10496 CAGE DRX008989 DRR009863
Accession ID Mm9

Library idBAMCTSS
CNhs10496 DRZ001288 DRZ002671
Accession ID Mm10

Library idBAMCTSS
CNhs10496 DRZ012638 DRZ014021
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
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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

CNhs10496

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0155
1001 -0.0353
1002 -0.0179
1003 -0.113
1004 0
1005 0.192
1006 -0.0408
1007 -0.0218
1008 2.207
1009 -0.19
101 -0.047
1010 0
1011 -0.298
1012 0
1013 0.282
1014 -0.0851
1015 -0.267
1016 -0.495
1017 0
1018 0.494
1019 0
102 0
1020 0
1021 0
1022 -0.0115
1023 0
1024 -0.288
1025 0.313
1026 0
1027 -0.048
1028 0
1029 0.386
103 -0.0659
1030 0
1031 -0.418
1032 0.577
1033 0.00318
1034 0
1035 0
1036 -0.176
1037 0
1038 -0.0125
1039 -0.139
104 0
1040 -0.325
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: CNhs10496
Jaspar motif P-value
MA0002.2 3.79891e-4
MA0003.1 0.176
MA0004.1 0.938
MA0006.1 0.0599
MA0007.1 0.402
MA0009.1 0.155
MA0014.1 0.466
MA0017.1 1.62093e-34
MA0018.2 0.138
MA0019.1 0.192
MA0024.1 0.0501
MA0025.1 0.648
MA0027.1 0.418
MA0028.1 0.37
MA0029.1 0.621
MA0030.1 0.704
MA0031.1 0.807
MA0035.2 3.75995e-6
MA0038.1 0.967
MA0039.2 0.00175
MA0040.1 0.152
MA0041.1 0.238
MA0042.1 0.326
MA0043.1 0.0166
MA0046.1 1.66693e-41
MA0047.2 0.0138
MA0048.1 0.56
MA0050.1 1.06481e-6
MA0051.1 2.43281e-6
MA0052.1 9.53432e-4
MA0055.1 0.997
MA0057.1 0.0541
MA0058.1 0.733
MA0059.1 0.982
MA0060.1 0.101
MA0061.1 0.512
MA0062.2 0.102
MA0065.2 4.49523e-18
MA0066.1 0.2
MA0067.1 0.35
MA0068.1 0.0296
MA0069.1 0.375
MA0070.1 0.0191
MA0071.1 0.146
MA0072.1 0.539
MA0073.1 0.922
MA0074.1 0.104
MA0076.1 0.758
MA0077.1 0.878
MA0078.1 0.932
MA0079.2 0.372
MA0080.2 6.00372e-5
MA0081.1 0.573
MA0083.1 0.593
MA0084.1 0.763
MA0087.1 0.867
MA0088.1 0.139
MA0090.1 0.721
MA0091.1 0.489
MA0092.1 0.601
MA0093.1 0.837
MA0099.2 4.11847e-5
MA0100.1 0.283
MA0101.1 0.899
MA0102.2 0.458
MA0103.1 6.53781e-6
MA0104.2 0.29
MA0105.1 0.374
MA0106.1 0.617
MA0107.1 0.96
MA0108.2 0.466
MA0111.1 0.887
MA0112.2 8.26733e-5
MA0113.1 0.524
MA0114.1 6.5817e-36
MA0115.1 1.24654e-19
MA0116.1 0.253
MA0117.1 0.761
MA0119.1 0.0318
MA0122.1 0.867
MA0124.1 0.413
MA0125.1 0.554
MA0131.1 0.56
MA0135.1 0.448
MA0136.1 2.51448e-6
MA0137.2 0.108
MA0138.2 0.468
MA0139.1 0.0605
MA0140.1 0.0102
MA0141.1 8.11301e-7
MA0142.1 0.326
MA0143.1 0.0879
MA0144.1 0.0295
MA0145.1 0.00481
MA0146.1 0.19
MA0147.1 0.354
MA0148.1 0.00282
MA0149.1 0.00783
MA0150.1 0.115
MA0152.1 0.0619
MA0153.1 1.28782e-41
MA0154.1 0.0422
MA0155.1 0.8
MA0156.1 4.04664e-4
MA0157.1 0.679
MA0159.1 6.31063e-4
MA0160.1 4.08454e-5
MA0162.1 0.283
MA0163.1 0.122
MA0164.1 0.887
MA0258.1 0.00781
MA0259.1 0.477



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: CNhs10496
Novel motif P-value
1 0.137
10 0.156
100 0.946
101 0.895
102 0.781
103 0.284
104 0.77
105 0.24
106 0.0424
107 0.0915
108 0.638
109 0.0432
11 0.193
110 0.19
111 0.0472
112 0.0218
113 0.581
114 0.0658
115 0.558
116 0.147
117 0.125
118 0.554
119 0.0675
12 0.832
120 0.597
121 0.518
122 0.667
123 0.353
124 0.267
125 0.362
126 0.0634
127 0.143
128 0.12
129 0.198
13 6.41804e-4
130 0.579
131 0.694
132 0.314
133 0.776
134 0.92
135 0.711
136 0.113
137 0.927
138 0.777
139 0.037
14 0.703
140 0.689
141 0.175
142 0.846
143 0.191
144 0.335
145 0.0897
146 0.211
147 0.892
148 0.54
149 0.681
15 0.109
150 0.36
151 0.487
152 0.0694
153 0.796
154 0.87
155 0.565
156 0.045
157 0.613
158 0.672
159 0.531
160 0.545
161 0.515
162 0.879
163 0.229
164 0.174
165 0.898
166 0.895
167 0.88
168 0.598
169 0.00965
17 0.0583
18 0.958
19 0.162
2 0.351
20 0.858
21 0.917
22 0.296
23 0.28
24 0.65
25 0.419
26 0.00389
27 0.722
28 0.489
29 0.193
3 0.169
30 0.364
31 0.744
32 0.12
33 0.151
34 0.747
35 0.522
36 0.606
37 0.0472
38 0.285
39 0.189
4 0.44
40 0.19
41 0.942
42 0.448
43 0.296
44 0.0664
45 0.303
46 0.25
47 0.276
48 0.198
49 0.229
5 0.418
50 0.504
51 0.618
52 0.121
53 0.973
54 0.529
55 0.776
56 0.511
57 0.886
58 0.316
59 0.107
6 0.512
60 0.044
61 0.306
62 0.233
63 0.116
64 0.619
65 0.187
66 0.89
67 0.276
68 0.151
69 0.956
7 0.0382
70 0.0211
71 0.0719
72 0.36
73 0.0827
74 0.991
75 0.0641
76 0.902
77 0.0887
78 0.0525
79 0.855
8 0.191
80 0.515
81 0.746
82 0.133
83 0.175
84 0.134
85 0.0446
86 0.158
87 0.138
88 0.436
89 0.4
9 0.693
90 0.0849
91 0.397
92 0.225
93 0.0878
94 0.879
95 0.162
96 0.867
97 0.782
98 0.541
99 0.0846



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: CNhs10496


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)
0000160 (intestine)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
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)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011285 (mouse intestine- 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)