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FF:1251-16I5

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Name:intestine, embryo E12
Species:Mouse (Mus musculus)
Library ID:CNhs11019
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
tissueintestine
dev stage12 days embryo
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  SAMD00004885
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11019 CAGE DRX008990 DRR009864
Accession ID Mm9

Library idBAMCTSS
CNhs11019 DRZ001289 DRZ002672
Accession ID Mm10

Library idBAMCTSS
CNhs11019 DRZ012639 DRZ014022
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

CNhs11019

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0.0477
1000 0
1001 -0.0275
1002 0.75
1003 -0.156
1004 0
1005 -0.0389
1006 -0.11
1007 0.15
1008 0
1009 0.00821
101 0.159
1010 0.084
1011 0.0175
1012 0
1013 -0.217
1014 0.551
1015 0.32
1016 0.324
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0
1023 0
1024 0.0081
1025 0.843
1026 0
1027 0.0933
1028 0
1029 0.175
103 0.0672
1030 0
1031 0.342
1032 -0.0536
1033 0.0867
1034 0
1035 0.084
1036 0.212
1037 0
1038 -0.0714
1039 -0.145
104 0
1040 0.125
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: CNhs11019
Jaspar motif P-value
MA0002.2 2.26863e-4
MA0003.1 0.134
MA0004.1 0.777
MA0006.1 0.277
MA0007.1 0.384
MA0009.1 0.384
MA0014.1 0.351
MA0017.1 2.65087e-4
MA0018.2 0.73
MA0019.1 0.719
MA0024.1 1.51362e-6
MA0025.1 5.80579e-5
MA0027.1 0.0516
MA0028.1 0.0534
MA0029.1 0.368
MA0030.1 0.241
MA0031.1 0.051
MA0035.2 0.106
MA0038.1 0.0711
MA0039.2 0.00767
MA0040.1 0.374
MA0041.1 0.114
MA0042.1 0.346
MA0043.1 0.489
MA0046.1 0.107
MA0047.2 0.12
MA0048.1 0.00931
MA0050.1 1.26772e-5
MA0051.1 5.44563e-6
MA0052.1 1.28283e-9
MA0055.1 0.0149
MA0057.1 0.0616
MA0058.1 0.563
MA0059.1 0.329
MA0060.1 7.41325e-11
MA0061.1 0.119
MA0062.2 0.326
MA0065.2 1.09072e-4
MA0066.1 0.054
MA0067.1 0.376
MA0068.1 0.771
MA0069.1 0.726
MA0070.1 0.881
MA0071.1 0.0571
MA0072.1 0.0164
MA0073.1 0.325
MA0074.1 0.81
MA0076.1 0.0492
MA0077.1 0.284
MA0078.1 0.592
MA0079.2 0.0564
MA0080.2 9.63726e-9
MA0081.1 0.219
MA0083.1 0.0359
MA0084.1 0.554
MA0087.1 0.538
MA0088.1 0.911
MA0090.1 0.895
MA0091.1 0.922
MA0092.1 0.702
MA0093.1 0.762
MA0099.2 5.96972e-7
MA0100.1 0.591
MA0101.1 0.569
MA0102.2 0.621
MA0103.1 0.00184
MA0104.2 0.259
MA0105.1 0.387
MA0106.1 0.253
MA0107.1 0.209
MA0108.2 0.0379
MA0111.1 0.658
MA0112.2 4.79069e-4
MA0113.1 0.79
MA0114.1 0.00155
MA0115.1 0.0846
MA0116.1 0.247
MA0117.1 0.0409
MA0119.1 0.0296
MA0122.1 0.446
MA0124.1 0.217
MA0125.1 0.564
MA0131.1 0.122
MA0135.1 0.297
MA0136.1 3.10422e-4
MA0137.2 0.264
MA0138.2 8.01999e-4
MA0139.1 0.343
MA0140.1 0.555
MA0141.1 0.00637
MA0142.1 0.45
MA0143.1 0.0161
MA0144.1 0.258
MA0145.1 0.0177
MA0146.1 0.389
MA0147.1 0.294
MA0148.1 0.0234
MA0149.1 0.0771
MA0150.1 6.25113e-4
MA0152.1 0.255
MA0153.1 0.167
MA0154.1 0.0272
MA0155.1 0.97
MA0156.1 0.0999
MA0157.1 0.0394
MA0159.1 0.0408
MA0160.1 0.0136
MA0162.1 0.95
MA0163.1 0.888
MA0164.1 0.685
MA0258.1 6.84469e-4
MA0259.1 0.502



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: CNhs11019
Novel motif P-value
1 0.149
10 0.853
100 0.762
101 0.639
102 0.617
103 0.177
104 0.882
105 0.161
106 0.0101
107 0.0724
108 0.871
109 0.14
11 0.191
110 0.575
111 0.265
112 0.0841
113 0.375
114 0.0106
115 0.404
116 0.461
117 0.969
118 0.845
119 0.031
12 0.695
120 0.83
121 0.449
122 0.668
123 0.0827
124 0.291
125 0.939
126 0.753
127 0.0937
128 0.0335
129 0.0782
13 0.738
130 0.379
131 0.144
132 0.615
133 0.823
134 0.447
135 0.965
136 0.659
137 0.946
138 0.423
139 0.0142
14 0.321
140 0.00305
141 0.399
142 0.842
143 0.846
144 0.934
145 0.92
146 0.216
147 0.584
148 0.467
149 0.186
15 0.068
150 0.616
151 0.0793
152 0.0349
153 0.202
154 0.839
155 0.935
156 0.0134
157 0.932
158 0.623
159 0.322
160 0.856
161 0.617
162 0.767
163 0.0887
164 0.818
165 0.341
166 0.0899
167 0.321
168 0.501
169 0.0429
17 0.12
18 0.397
19 0.578
2 0.444
20 0.431
21 0.912
22 0.295
23 0.0492
24 0.393
25 0.312
26 0.632
27 0.259
28 0.251
29 0.967
3 0.477
30 0.6
31 0.328
32 0.327
33 0.734
34 0.692
35 0.458
36 0.658
37 0.163
38 0.317
39 0.724
4 0.45
40 0.383
41 0.0869
42 0.824
43 0.248
44 0.0619
45 0.286
46 0.386
47 0.197
48 0.195
49 0.18
5 0.126
50 0.898
51 0.596
52 0.321
53 0.556
54 0.389
55 0.774
56 0.366
57 0.846
58 0.304
59 0.0615
6 0.754
60 0.126
61 0.511
62 0.0905
63 0.172
64 0.498
65 0.143
66 0.789
67 0.703
68 0.114
69 0.545
7 0.31
70 4.19463e-4
71 0.672
72 0.511
73 0.083
74 0.888
75 0.248
76 0.295
77 0.162
78 0.182
79 0.479
8 0.282
80 0.0654
81 0.338
82 0.0629
83 0.537
84 0.27
85 0.0062
86 0.516
87 0.0507
88 0.843
89 0.128
9 0.424
90 0.446
91 0.191
92 0.188
93 0.999
94 0.815
95 0.0954
96 0.604
97 0.769
98 0.0688
99 0.984



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: CNhs11019


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

CL: Cell type
0000000 (cell)
0000003 (native cell)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0002679 (natural helper lymphocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
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)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000350 (experimentally modified sample)
0000391 (15 days sample)
0000636 (IL-2 treatment sample)
0000295 (mouse embryonic day 12 sample)
0011524 (mouse natural helper cells- IL2 treated, day15 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


CL:0000134 (mesenchymal cell)
CL:0000051 (common lymphoid progenitor)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)