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FF:36-18H7

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Name:colon, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10468
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
tissuecolon
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  SAMD00005637
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10468 CAGE DRX008943 DRR009817
Accession ID Mm9

Library idBAMCTSS
CNhs10468 DRZ001242 DRZ002625
Accession ID Mm10

Library idBAMCTSS
CNhs10468 DRZ012592 DRZ013975
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

CNhs10468

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0494
1001 0.0455
1002 0.0772
1003 --0.074
1004 0
1005 0.202
1006 --0.00265
1007 --0.108
1008 2.569
1009 --0.0572
101 --0.111
1010 0.0988
1011 --0.129
1012 0
1013 0.392
1014 --0.0851
1015 --0.242
1016 --0.275
1017 0
1018 0.306
1019 0
102 0
1020 0
1021 0
1022 0.179
1023 0
1024 --0.0633
1025 0.296
1026 0
1027 --0.048
1028 0
1029 0.403
103 --0.0659
1030 0
1031 --0.393
1032 0.565
1033 --0.0648
1034 0.247
1035 0
1036 --0.219
1037 0
1038 0.00864
1039 0.097
104 0
1040 --0.297
1041 0.0988



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: CNhs10468

Jaspar motif P-value
MA0002.2 7.74532e-4
MA0003.1 0.13
MA0004.1 0.864
MA0006.1 0.0656
MA0007.1 0.615
MA0009.1 0.327
MA0014.1 0.454
MA0017.1 2.02301e-20
MA0018.2 0.0464
MA0019.1 0.0991
MA0024.1 0.026
MA0025.1 0.936
MA0027.1 0.22
MA0028.1 0.761
MA0029.1 0.899
MA0030.1 0.974
MA0031.1 0.775
MA0035.2 7.86193e-7
MA0038.1 0.522
MA0039.2 8.15231e-4
MA0040.1 0.0312
MA0041.1 0.407
MA0042.1 0.457
MA0043.1 0.0371
MA0046.1 3.25867e-34
MA0047.2 0.00264
MA0048.1 0.903
MA0050.1 1.02218e-7
MA0051.1 2.3939e-5
MA0052.1 2.62828e-4
MA0055.1 0.339
MA0057.1 0.0625
MA0058.1 0.657
MA0059.1 0.814
MA0060.1 0.00102
MA0061.1 0.222
MA0062.2 0.75
MA0065.2 7.04638e-12
MA0066.1 0.0965
MA0067.1 0.192
MA0068.1 0.0101
MA0069.1 0.238
MA0070.1 0.253
MA0071.1 0.399
MA0072.1 0.954
MA0073.1 0.862
MA0074.1 0.107
MA0076.1 0.429
MA0077.1 0.702
MA0078.1 0.98
MA0079.2 0.716
MA0080.2 7.20261e-7
MA0081.1 0.793
MA0083.1 0.63
MA0084.1 0.52
MA0087.1 0.727
MA0088.1 0.503
MA0090.1 0.986
MA0091.1 0.467
MA0092.1 0.612
MA0093.1 0.779
MA0099.2 0.0109
MA0100.1 0.2
MA0101.1 0.649
MA0102.2 0.168
MA0103.1 1.00916e-5
MA0104.2 0.22
MA0105.1 0.108
MA0106.1 0.387
MA0107.1 0.571
MA0108.2 0.617
MA0111.1 0.91
MA0112.2 7.13177e-5
MA0113.1 0.802
MA0114.1 2.18648e-21
MA0115.1 1.40062e-11
MA0116.1 0.201
MA0117.1 0.926
MA0119.1 0.0717
MA0122.1 0.566
MA0124.1 0.157
MA0125.1 0.281
MA0131.1 0.379
MA0135.1 0.274
MA0136.1 1.04844e-6
MA0137.2 0.314
MA0138.2 0.293
MA0139.1 0.0378
MA0140.1 0.00591
MA0141.1 1.81245e-4
MA0142.1 0.261
MA0143.1 0.105
MA0144.1 0.033
MA0145.1 0.0068
MA0146.1 0.241
MA0147.1 0.385
MA0148.1 4.12681e-4
MA0149.1 0.0283
MA0150.1 0.329
MA0152.1 0.119
MA0153.1 2.81052e-27
MA0154.1 0.0108
MA0155.1 0.514
MA0156.1 0.0033
MA0157.1 0.682
MA0159.1 0.00175
MA0160.1 0.0161
MA0162.1 0.249
MA0163.1 0.0564
MA0164.1 0.901
MA0258.1 0.00908
MA0259.1 0.289



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: CNhs10468

Novel motif P-value
1 0.161
10 0.178
100 0.996
101 0.993
102 0.922
103 0.209
104 0.732
105 0.392
106 0.0122
107 0.0358
108 0.712
109 0.0849
11 0.161
110 0.268
111 0.0746
112 0.0128
113 0.901
114 0.0523
115 0.336
116 0.24
117 0.22
118 0.496
119 0.045
12 0.77
120 0.434
121 0.778
122 0.628
123 0.293
124 0.913
125 0.327
126 0.0975
127 0.159
128 0.0385
129 0.269
13 0.00466
130 0.953
131 0.163
132 0.484
133 0.732
134 0.885
135 0.714
136 0.139
137 0.48
138 0.839
139 0.0396
14 0.614
140 0.301
141 0.126
142 0.314
143 0.67
144 0.223
145 0.147
146 0.241
147 0.428
148 0.258
149 0.521
15 0.158
150 0.312
151 0.336
152 0.0593
153 0.776
154 0.91
155 0.339
156 0.609
157 0.923
158 0.497
159 0.216
160 0.371
161 0.544
162 0.556
163 0.21
164 0.101
165 0.274
166 0.657
167 0.95
168 0.825
169 0.0114
17 0.0973
18 0.253
19 0.0898
2 0.222
20 0.775
21 0.921
22 0.326
23 0.244
24 0.683
25 0.649
26 0.00786
27 0.435
28 0.439
29 0.314
3 0.212
30 0.363
31 0.553
32 0.034
33 0.319
34 0.731
35 0.51
36 0.751
37 0.059
38 0.355
39 0.332
4 0.457
40 0.207
41 0.54
42 0.425
43 0.237
44 0.149
45 0.277
46 0.229
47 0.322
48 0.282
49 0.195
5 0.358
50 0.527
51 0.64
52 0.102
53 0.936
54 0.553
55 0.868
56 0.39
57 0.911
58 0.32
59 0.0561
6 0.684
60 0.0424
61 0.216
62 0.27
63 0.156
64 0.563
65 0.134
66 0.649
67 0.403
68 0.067
69 0.798
7 0.11
70 0.0179
71 0.101
72 0.468
73 0.132
74 0.78
75 0.0945
76 0.68
77 0.0823
78 0.0688
79 0.115
8 0.141
80 0.455
81 0.645
82 0.0428
83 0.16
84 0.147
85 0.0392
86 0.18
87 0.167
88 0.612
89 0.15
9 0.649
90 0.174
91 0.468
92 0.336
93 0.191
94 0.632
95 0.164
96 0.884
97 0.555
98 0.647
99 0.117



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: CNhs10468


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)
0001155 (colon)
0000160 (intestine)
0000479 (tissue)
0001007 (digestive system)
0000064 (organ part)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
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)
0000059 (large intestine)
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)
0011323 (mouse colon- 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)