Personal tools

FF:827-18D1

From FANTOM5_SSTAR

Jump to: navigation, search


Name:intestine, neonate N20
Species:Mouse (Mus musculus)
Library ID:CNhs11187
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 stage20 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  SAMD00005244
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11187 CAGE DRX009001 DRR009875
Accession ID Mm9

Library idBAMCTSS
CNhs11187 DRZ001300 DRZ002683
Accession ID Mm10

Library idBAMCTSS
CNhs11187 DRZ012650 DRZ014033
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11187

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0
1002 0.0569
1003 -0.102
1004 0
1005 0
1006 -0.0711
1007 -0.0345
1008 1.889
1009 0.0728
101 -0.0836
1010 0
1011 -0.111
1012 0
1013 0.229
1014 -0.0874
1015 -0.303
1016 -0.163
1017 0
1018 0.278
1019 0
102 0
1020 0
1021 0
1022 0
1023 0
1024 0
1025 0.505
1026 0
1027 -0.048
1028 0
1029 0.63
103 0.226
1030 0
1031 -0.105
1032 0.416
1033 -0.0752
1034 0
1035 0
1036 -0.223
1037 0
1038 0.108
1039 0.166
104 0
1040 -0.147
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: CNhs11187
Jaspar motif P-value
MA0002.2 0.015
MA0003.1 0.083
MA0004.1 0.676
MA0006.1 0.0735
MA0007.1 0.483
MA0009.1 0.663
MA0014.1 0.601
MA0017.1 3.71966e-18
MA0018.2 0.0109
MA0019.1 0.311
MA0024.1 0.0241
MA0025.1 0.0778
MA0027.1 0.653
MA0028.1 0.167
MA0029.1 0.591
MA0030.1 0.632
MA0031.1 0.663
MA0035.2 7.80492e-5
MA0038.1 0.379
MA0039.2 0.018
MA0040.1 0.186
MA0041.1 0.263
MA0042.1 0.852
MA0043.1 0.0396
MA0046.1 7.8573e-29
MA0047.2 0.0613
MA0048.1 0.493
MA0050.1 2.32909e-7
MA0051.1 2.8158e-5
MA0052.1 2.67406e-4
MA0055.1 0.364
MA0057.1 0.167
MA0058.1 0.461
MA0059.1 0.991
MA0060.1 5.27906e-4
MA0061.1 0.377
MA0062.2 0.108
MA0065.2 9.89822e-15
MA0066.1 0.216
MA0067.1 0.279
MA0068.1 0.295
MA0069.1 0.197
MA0070.1 0.217
MA0071.1 0.354
MA0072.1 0.306
MA0073.1 0.891
MA0074.1 0.0854
MA0076.1 0.0872
MA0077.1 0.676
MA0078.1 0.718
MA0079.2 0.264
MA0080.2 0.00559
MA0081.1 0.384
MA0083.1 0.586
MA0084.1 0.65
MA0087.1 0.894
MA0088.1 0.728
MA0090.1 0.779
MA0091.1 0.759
MA0092.1 0.308
MA0093.1 0.619
MA0099.2 0.0175
MA0100.1 0.18
MA0101.1 0.896
MA0102.2 0.124
MA0103.1 4.82241e-5
MA0104.2 0.149
MA0105.1 0.0933
MA0106.1 0.505
MA0107.1 0.868
MA0108.2 0.487
MA0111.1 0.962
MA0112.2 1.12886e-5
MA0113.1 0.743
MA0114.1 1.28767e-22
MA0115.1 1.25129e-11
MA0116.1 0.223
MA0117.1 0.768
MA0119.1 0.0461
MA0122.1 0.651
MA0124.1 0.383
MA0125.1 0.0724
MA0131.1 0.342
MA0135.1 0.984
MA0136.1 0.0828
MA0137.2 0.68
MA0138.2 0.405
MA0139.1 0.0467
MA0140.1 0.0461
MA0141.1 5.01623e-5
MA0142.1 0.39
MA0143.1 0.332
MA0144.1 0.0882
MA0145.1 0.00446
MA0146.1 0.264
MA0147.1 0.262
MA0148.1 0.00327
MA0149.1 0.0417
MA0150.1 0.698
MA0152.1 0.057
MA0153.1 4.93591e-28
MA0154.1 0.0103
MA0155.1 0.202
MA0156.1 0.448
MA0157.1 0.327
MA0159.1 0.00177
MA0160.1 0.00418
MA0162.1 0.214
MA0163.1 0.0125
MA0164.1 0.947
MA0258.1 0.00886
MA0259.1 0.265



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: CNhs11187
Novel motif P-value
1 0.15
10 0.148
100 0.913
101 0.907
102 0.658
103 0.116
104 0.976
105 0.386
106 0.00801
107 0.014
108 0.605
109 0.075
11 0.165
110 0.184
111 0.0902
112 0.0104
113 0.582
114 0.0572
115 0.685
116 0.275
117 0.296
118 0.648
119 0.0581
12 0.704
120 0.643
121 0.718
122 0.605
123 0.292
124 0.978
125 0.343
126 0.152
127 0.11
128 0.0623
129 0.487
13 0.00752
130 0.948
131 0.0409
132 0.729
133 0.984
134 0.99
135 0.86
136 0.299
137 0.524
138 0.913
139 0.0825
14 0.625
140 0.129
141 0.149
142 0.26
143 0.732
144 0.46
145 0.079
146 0.255
147 0.442
148 0.322
149 0.451
15 0.159
150 0.336
151 0.3
152 0.0621
153 0.962
154 0.66
155 0.314
156 0.302
157 0.986
158 0.689
159 0.611
160 0.192
161 0.336
162 0.917
163 0.346
164 0.0769
165 0.345
166 0.498
167 0.961
168 0.867
169 0.00933
17 0.0435
18 0.0394
19 0.0635
2 0.304
20 0.818
21 0.798
22 0.289
23 0.192
24 0.601
25 0.753
26 0.00307
27 0.456
28 0.64
29 0.291
3 0.225
30 0.497
31 0.565
32 0.0046
33 0.194
34 0.757
35 0.444
36 0.588
37 0.0299
38 0.32
39 0.249
4 0.383
40 0.308
41 0.299
42 0.465
43 0.208
44 0.103
45 0.418
46 0.225
47 0.296
48 0.278
49 0.156
5 0.479
50 0.495
51 0.538
52 0.0835
53 0.948
54 0.571
55 0.768
56 0.406
57 0.76
58 0.425
59 0.0427
6 0.873
60 0.0381
61 0.215
62 0.378
63 0.138
64 0.649
65 0.163
66 0.478
67 0.647
68 0.106
69 0.882
7 0.0749
70 0.0524
71 0.0735
72 0.438
73 0.125
74 0.855
75 0.144
76 0.745
77 0.097
78 0.0676
79 0.446
8 0.158
80 0.923
81 0.593
82 0.0987
83 0.34
84 0.483
85 0.0251
86 0.297
87 0.244
88 0.67
89 0.259
9 0.652
90 0.117
91 0.212
92 0.157
93 0.404
94 0.701
95 0.336
96 0.726
97 0.446
98 0.627
99 0.0656



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: CNhs11187


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000308 (mouse neonate N20 sample)
0011431 (mouse intestine- neonate N20 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)