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FF:1384-42G1

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Name:intestine, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11131
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 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  SAMD00005553
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11131 CAGE DRX009003 DRR009877
Accession ID Mm9

Library idBAMCTSS
CNhs11131 DRZ001302 DRZ002685
Accession ID Mm10

Library idBAMCTSS
CNhs11131 DRZ012652 DRZ014035
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 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

CNhs11131

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0768
1001 0.0611
1002 0.0554
1003 --0.0124
1004 0
1005 0.244
1006 0
1007 --0.0139
1008 2.192
1009 --0.00526
101 --0.127
1010 0
1011 --0.0943
1012 0
1013 0.27
1014 --0.0874
1015 --0.381
1016 --0.183
1017 0
1018 0.578
1019 0
102 0
1020 0
1021 0
1022 0.189
1023 0
1024 --0.011
1025 0.661
1026 0
1027 --0.0105
1028 0
1029 0.521
103 0
1030 0
1031 --0.231
1032 0.694
1033 0.0398
1034 0.146
1035 0.146
1036 --0.129
1037 0
1038 0.058
1039 0.0603
104 0.321
1040 --0.0982
1041 0.146



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: CNhs11131

Jaspar motif P-value
MA0002.2 0.0259
MA0003.1 0.236
MA0004.1 0.558
MA0006.1 0.0385
MA0007.1 0.524
MA0009.1 0.234
MA0014.1 0.364
MA0017.1 3.7894e-24
MA0018.2 0.0162
MA0019.1 0.344
MA0024.1 0.0068
MA0025.1 0.574
MA0027.1 0.615
MA0028.1 0.577
MA0029.1 0.988
MA0030.1 0.248
MA0031.1 0.0774
MA0035.2 1.03811e-5
MA0038.1 0.645
MA0039.2 2.00468e-4
MA0040.1 0.0224
MA0041.1 0.35
MA0042.1 0.93
MA0043.1 0.079
MA0046.1 1.36682e-45
MA0047.2 6.6959e-5
MA0048.1 0.697
MA0050.1 3.23669e-6
MA0051.1 2.21811e-5
MA0052.1 9.82261e-5
MA0055.1 0.212
MA0057.1 0.131
MA0058.1 0.389
MA0059.1 0.653
MA0060.1 0.0105
MA0061.1 0.602
MA0062.2 0.729
MA0065.2 1.41528e-13
MA0066.1 0.396
MA0067.1 0.229
MA0068.1 0.274
MA0069.1 0.275
MA0070.1 0.15
MA0071.1 0.181
MA0072.1 0.907
MA0073.1 0.794
MA0074.1 0.175
MA0076.1 0.298
MA0077.1 0.442
MA0078.1 0.438
MA0079.2 0.679
MA0080.2 2.46621e-4
MA0081.1 0.373
MA0083.1 0.952
MA0084.1 0.408
MA0087.1 0.914
MA0088.1 0.666
MA0090.1 0.86
MA0091.1 0.834
MA0092.1 0.382
MA0093.1 0.533
MA0099.2 0.00145
MA0100.1 0.0858
MA0101.1 0.874
MA0102.2 0.367
MA0103.1 5.90173e-6
MA0104.2 0.0585
MA0105.1 0.459
MA0106.1 0.312
MA0107.1 0.758
MA0108.2 0.147
MA0111.1 0.956
MA0112.2 3.69009e-5
MA0113.1 0.543
MA0114.1 4.60054e-30
MA0115.1 3.86876e-11
MA0116.1 0.532
MA0117.1 0.979
MA0119.1 0.0135
MA0122.1 0.693
MA0124.1 0.363
MA0125.1 0.313
MA0131.1 0.384
MA0135.1 0.811
MA0136.1 6.46362e-4
MA0137.2 0.995
MA0138.2 0.33
MA0139.1 0.0284
MA0140.1 0.0412
MA0141.1 3.12728e-5
MA0142.1 0.148
MA0143.1 0.0856
MA0144.1 0.127
MA0145.1 0.00191
MA0146.1 0.272
MA0147.1 0.102
MA0148.1 9.83186e-7
MA0149.1 0.0194
MA0150.1 0.48
MA0152.1 0.181
MA0153.1 1.00364e-35
MA0154.1 0.0468
MA0155.1 0.525
MA0156.1 0.0147
MA0157.1 0.435
MA0159.1 0.00834
MA0160.1 0.00863
MA0162.1 0.367
MA0163.1 0.168
MA0164.1 0.914
MA0258.1 0.0163
MA0259.1 0.194



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: CNhs11131

Novel motif P-value
1 0.219
10 0.283
100 0.757
101 0.834
102 0.674
103 0.232
104 0.713
105 0.42
106 0.00877
107 0.0365
108 0.887
109 0.0586
11 0.193
110 0.331
111 0.201
112 0.0329
113 0.767
114 0.0701
115 0.681
116 0.444
117 0.481
118 0.529
119 0.109
12 0.789
120 0.743
121 0.994
122 0.599
123 0.224
124 0.844
125 0.679
126 0.0794
127 0.565
128 0.0477
129 0.309
13 0.00118
130 0.712
131 0.0264
132 0.602
133 0.526
134 0.654
135 0.454
136 0.118
137 0.476
138 0.471
139 0.0702
14 0.546
140 0.368
141 0.17
142 0.597
143 0.15
144 0.414
145 0.149
146 0.205
147 0.163
148 0.138
149 0.791
15 0.188
150 0.292
151 0.37
152 0.0353
153 0.911
154 0.5
155 0.413
156 0.126
157 0.755
158 0.757
159 0.625
160 0.262
161 0.482
162 0.867
163 0.247
164 0.1
165 0.282
166 0.987
167 0.949
168 0.806
169 0.00718
17 0.0739
18 0.183
19 0.0481
2 0.2
20 0.69
21 0.888
22 0.345
23 0.262
24 0.845
25 0.759
26 0.00875
27 0.544
28 0.488
29 0.345
3 0.251
30 0.32
31 0.649
32 0.0358
33 0.171
34 0.814
35 0.743
36 0.968
37 0.0245
38 0.321
39 0.206
4 0.463
40 0.306
41 0.678
42 0.603
43 0.273
44 0.449
45 0.275
46 0.27
47 0.469
48 0.356
49 0.175
5 0.589
50 0.572
51 0.603
52 0.0547
53 0.967
54 0.548
55 0.663
56 0.364
57 0.974
58 0.263
59 0.182
6 0.599
60 0.0311
61 0.235
62 0.304
63 0.17
64 0.769
65 0.154
66 0.485
67 0.0762
68 0.236
69 0.657
7 0.0842
70 0.0613
71 0.152
72 0.509
73 0.0859
74 0.914
75 0.142
76 0.715
77 0.104
78 0.0374
79 0.801
8 0.281
80 0.704
81 0.602
82 0.108
83 0.139
84 0.457
85 0.0336
86 0.145
87 0.294
88 0.832
89 0.265
9 0.709
90 0.21
91 0.244
92 0.485
93 0.651
94 0.5
95 0.105
96 0.985
97 0.321
98 0.705
99 0.0765



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: CNhs11131


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)
0000310 (mouse neonate N30 sample)
0011481 (mouse intestine- 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)