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FF:37-13H4

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Name:cecum, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10467
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
tissuececum
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  SAMD00005238
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10467 CAGE DRX008940 DRR009814
Accession ID Mm9

Library idBAMCTSS
CNhs10467 DRZ001239 DRZ002622
Accession ID Mm10

Library idBAMCTSS
CNhs10467 DRZ012589 DRZ013972
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

CNhs10467

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.157
1001 --0.0275
1002 --0.0941
1003 --0.123
1004 0
1005 0
1006 --0.0932
1007 --0.0402
1008 0.819
1009 --0.0572
101 --0.0955
1010 0
1011 --0.108
1012 0
1013 0.24
1014 --0.0874
1015 --0.329
1016 --0.594
1017 0
1018 0.457
1019 0
102 0
1020 0
1021 0
1022 0.457
1023 0
1024 0.0546
1025 0.856
1026 0
1027 --0.048
1028 0
1029 --0.115
103 --0.0754
1030 0
1031 --0.556
1032 0.595
1033 --0.0752
1034 0
1035 0
1036 --0.186
1037 0
1038 0.109
1039 0.109
104 1.014
1040 --0.216
1041 0



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: CNhs10467

Jaspar motif P-value
MA0002.2 0.00189
MA0003.1 0.0467
MA0004.1 0.732
MA0006.1 0.216
MA0007.1 0.346
MA0009.1 0.0141
MA0014.1 0.617
MA0017.1 2.10455e-6
MA0018.2 0.0806
MA0019.1 0.957
MA0024.1 0.0107
MA0025.1 0.698
MA0027.1 0.223
MA0028.1 0.157
MA0029.1 0.978
MA0030.1 0.118
MA0031.1 0.0388
MA0035.2 0.0118
MA0038.1 0.568
MA0039.2 0.00212
MA0040.1 0.00846
MA0041.1 0.131
MA0042.1 0.32
MA0043.1 0.0362
MA0046.1 7.66484e-29
MA0047.2 5.66148e-8
MA0048.1 0.474
MA0050.1 0.329
MA0051.1 0.376
MA0052.1 0.0292
MA0055.1 0.252
MA0057.1 0.0311
MA0058.1 0.582
MA0059.1 0.712
MA0060.1 0.00249
MA0061.1 0.251
MA0062.2 0.109
MA0065.2 1.18728e-6
MA0066.1 0.19
MA0067.1 0.416
MA0068.1 0.00374
MA0069.1 0.539
MA0070.1 0.389
MA0071.1 0.346
MA0072.1 0.342
MA0073.1 0.745
MA0074.1 0.245
MA0076.1 0.105
MA0077.1 0.921
MA0078.1 0.615
MA0079.2 0.254
MA0080.2 7.61443e-5
MA0081.1 0.297
MA0083.1 0.504
MA0084.1 0.247
MA0087.1 0.557
MA0088.1 0.694
MA0090.1 0.175
MA0091.1 0.707
MA0092.1 0.409
MA0093.1 0.693
MA0099.2 1.09565e-6
MA0100.1 0.562
MA0101.1 0.966
MA0102.2 0.451
MA0103.1 3.44406e-5
MA0104.2 0.487
MA0105.1 0.0138
MA0106.1 0.173
MA0107.1 0.913
MA0108.2 1.08918e-9
MA0111.1 0.538
MA0112.2 1.43007e-4
MA0113.1 0.37
MA0114.1 6.04186e-7
MA0115.1 0.00174
MA0116.1 0.0399
MA0117.1 0.794
MA0119.1 0.0395
MA0122.1 0.962
MA0124.1 0.0565
MA0125.1 0.473
MA0131.1 0.266
MA0135.1 0.62
MA0136.1 0.00127
MA0137.2 0.986
MA0138.2 0.0128
MA0139.1 0.183
MA0140.1 0.614
MA0141.1 0.0305
MA0142.1 0.75
MA0143.1 0.223
MA0144.1 0.228
MA0145.1 0.00719
MA0146.1 0.569
MA0147.1 0.521
MA0148.1 6.14666e-6
MA0149.1 0.0285
MA0150.1 0.112
MA0152.1 0.0676
MA0153.1 5.69894e-22
MA0154.1 0.0149
MA0155.1 0.627
MA0156.1 0.156
MA0157.1 0.0933
MA0159.1 0.00231
MA0160.1 0.121
MA0162.1 0.245
MA0163.1 0.0235
MA0164.1 0.658
MA0258.1 0.0241
MA0259.1 0.278



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: CNhs10467

Novel motif P-value
1 0.218
10 0.312
100 0.917
101 0.517
102 0.937
103 0.214
104 0.757
105 0.0699
106 0.0199
107 0.0361
108 0.736
109 0.0799
11 0.291
110 0.214
111 0.217
112 0.113
113 0.704
114 0.0604
115 0.679
116 0.428
117 0.793
118 0.602
119 0.0589
12 0.555
120 0.164
121 0.486
122 0.596
123 0.721
124 0.468
125 0.213
126 0.0607
127 0.083
128 0.0168
129 0.287
13 0.0392
130 0.898
131 0.00626
132 0.382
133 0.124
134 0.695
135 0.994
136 0.708
137 0.596
138 0.992
139 0.00992
14 0.575
140 0.567
141 0.264
142 0.394
143 0.266
144 0.269
145 0.172
146 0.141
147 0.541
148 0.626
149 0.211
15 0.0982
150 0.539
151 0.304
152 0.0754
153 0.859
154 0.963
155 0.176
156 0.597
157 0.972
158 0.349
159 0.634
160 0.265
161 0.221
162 0.996
163 0.279
164 0.478
165 0.347
166 0.657
167 0.721
168 0.68
169 0.00875
17 0.049
18 0.303
19 0.142
2 0.384
20 0.573
21 0.892
22 0.316
23 0.165
24 0.278
25 0.597
26 0.0963
27 0.427
28 0.57
29 0.303
3 0.323
30 0.462
31 0.555
32 0.0691
33 0.414
34 0.61
35 0.758
36 0.381
37 0.111
38 0.409
39 0.519
4 0.103
40 0.226
41 0.255
42 0.676
43 0.21
44 0.343
45 0.309
46 0.219
47 0.326
48 0.258
49 0.172
5 0.0923
50 0.683
51 0.661
52 0.0872
53 0.838
54 0.516
55 0.704
56 0.347
57 0.747
58 0.243
59 0.189
6 0.39
60 0.055
61 0.295
62 0.139
63 0.17
64 0.456
65 0.096
66 0.751
67 0.313
68 0.94
69 0.597
7 0.0995
70 0.0252
71 0.187
72 0.531
73 0.111
74 0.53
75 0.282
76 0.4
77 0.118
78 0.0961
79 0.641
8 0.162
80 0.482
81 0.448
82 0.0918
83 0.0915
84 0.0244
85 0.0466
86 0.457
87 0.372
88 0.803
89 0.0929
9 0.545
90 0.351
91 0.258
92 0.232
93 0.14
94 0.727
95 0.283
96 0.168
97 0.37
98 0.384
99 0.131



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: CNhs10467


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)
0001153 (caecum)
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)
0009854 (digestive tract diverticulum)
0010317 (germ layer / neural crest derived structure)
0009856 (sac)
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)
0011324 (mouse cecum - 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:0001045 (midgut)
UBERON:0010316 (germ layer / neural crest)