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FF:10252-104B9

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Name:Ileum epithelium, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs13199
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
strainBalb/c
tissueileum
dev stageNA
sexfemale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationShinji Fukuda (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberCont_ileum_a
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005822
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13199 CAGE DRX008923 DRR009797
Accession ID Mm9

Library idBAMCTSS
CNhs13199 DRZ001222 DRZ002605
Accession ID Mm10

Library idBAMCTSS
CNhs13199 DRZ012572 DRZ013955
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

CNhs13199

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0749
1002 --0.107
1003 --0.123
1004 0
1005 0.328
1006 --0.183
1007 --0.201
1008 2.597
1009 --0.19
101 --0.203
1010 0
1011 --0.262
1012 0
1013 0.369
1014 --0.0874
1015 --0.327
1016 --0.589
1017 0
1018 0.401
1019 0
102 0
1020 0.0756
1021 0.221
1022 --0.124
1023 0
1024 --0.307
1025 0
1026 0
1027 --0.048
1028 0
1029 --0.1
103 --0.0887
1030 0
1031 --0.911
1032 0.768
1033 --0.0713
1034 0.0433
1035 0
1036 --0.184
1037 0
1038 0.0794
1039 0.0446
104 0.0756
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: CNhs13199

Jaspar motif P-value
MA0002.2 0.0159
MA0003.1 0.226
MA0004.1 0.765
MA0006.1 0.105
MA0007.1 0.212
MA0009.1 0.21
MA0014.1 0.0751
MA0017.1 4.25996e-24
MA0018.2 0.0429
MA0019.1 0.479
MA0024.1 0.0582
MA0025.1 0.1
MA0027.1 0.569
MA0028.1 0.0318
MA0029.1 0.428
MA0030.1 0.93
MA0031.1 0.624
MA0035.2 8.83498e-4
MA0038.1 0.406
MA0039.2 6.50169e-4
MA0040.1 0.0251
MA0041.1 0.346
MA0042.1 0.582
MA0043.1 0.00359
MA0046.1 7.98585e-48
MA0047.2 0.0148
MA0048.1 0.436
MA0050.1 1.05993e-4
MA0051.1 2.81571e-5
MA0052.1 3.66086e-4
MA0055.1 0.578
MA0057.1 0.0943
MA0058.1 0.775
MA0059.1 0.494
MA0060.1 0.0131
MA0061.1 0.335
MA0062.2 5.11138e-4
MA0065.2 6.81693e-13
MA0066.1 0.0947
MA0067.1 0.354
MA0068.1 0.0602
MA0069.1 0.417
MA0070.1 0.0421
MA0071.1 0.0927
MA0072.1 0.961
MA0073.1 0.638
MA0074.1 0.179
MA0076.1 0.0746
MA0077.1 0.503
MA0078.1 0.93
MA0079.2 0.288
MA0080.2 1.04047e-4
MA0081.1 0.839
MA0083.1 0.00502
MA0084.1 0.32
MA0087.1 0.598
MA0088.1 0.236
MA0090.1 0.791
MA0091.1 0.906
MA0092.1 0.688
MA0093.1 0.83
MA0099.2 7.30199e-5
MA0100.1 0.856
MA0101.1 0.509
MA0102.2 0.273
MA0103.1 3.9961e-7
MA0104.2 0.559
MA0105.1 0.141
MA0106.1 0.339
MA0107.1 0.679
MA0108.2 0.146
MA0111.1 0.971
MA0112.2 5.96042e-5
MA0113.1 0.453
MA0114.1 6.9978e-25
MA0115.1 5.71046e-13
MA0116.1 0.163
MA0117.1 0.609
MA0119.1 0.0587
MA0122.1 0.707
MA0124.1 0.167
MA0125.1 0.618
MA0131.1 0.957
MA0135.1 0.494
MA0136.1 1.74432e-8
MA0137.2 0.0712
MA0138.2 0.581
MA0139.1 0.0465
MA0140.1 0.0584
MA0141.1 3.22529e-7
MA0142.1 0.171
MA0143.1 0.0745
MA0144.1 0.0122
MA0145.1 0.0217
MA0146.1 0.205
MA0147.1 0.696
MA0148.1 0.00396
MA0149.1 0.00466
MA0150.1 0.0836
MA0152.1 0.0291
MA0153.1 3.0645e-42
MA0154.1 0.0836
MA0155.1 0.809
MA0156.1 7.23276e-5
MA0157.1 0.945
MA0159.1 1.89953e-4
MA0160.1 7.24291e-4
MA0162.1 0.403
MA0163.1 0.02
MA0164.1 0.67
MA0258.1 0.0143
MA0259.1 0.742



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: CNhs13199

Novel motif P-value
1 0.0934
10 0.0734
100 0.616
101 0.831
102 0.74
103 0.15
104 0.866
105 0.474
106 0.0655
107 0.258
108 0.76
109 0.0412
11 0.112
110 0.145
111 0.123
112 0.0226
113 0.488
114 0.017
115 0.603
116 0.12
117 0.0296
118 0.393
119 0.105
12 0.569
120 0.308
121 0.665
122 0.927
123 0.0861
124 0.278
125 0.211
126 0.0508
127 0.276
128 0.184
129 0.161
13 1.50135e-4
130 0.646
131 0.603
132 0.537
133 0.962
134 0.876
135 0.107
136 0.0238
137 0.528
138 0.205
139 0.0489
14 0.726
140 0.0923
141 0.0692
142 0.842
143 0.457
144 0.25
145 0.0914
146 0.362
147 0.963
148 0.44
149 0.795
15 0.148
150 0.311
151 0.497
152 0.0885
153 0.655
154 0.967
155 0.172
156 0.0905
157 0.38
158 0.949
159 0.54
160 0.332
161 0.483
162 0.779
163 0.408
164 0.0888
165 0.166
166 0.646
167 0.445
168 0.532
169 0.029
17 0.0453
18 0.973
19 0.166
2 0.799
20 0.48
21 0.777
22 0.35
23 0.836
24 0.675
25 0.378
26 0.00774
27 0.731
28 0.407
29 0.0602
3 0.154
30 0.628
31 0.843
32 0.112
33 0.168
34 0.986
35 0.507
36 0.362
37 0.0454
38 0.585
39 0.235
4 0.381
40 0.168
41 0.358
42 0.599
43 0.29
44 0.103
45 0.599
46 0.232
47 0.288
48 0.186
49 0.269
5 0.41
50 0.594
51 0.715
52 0.167
53 0.459
54 0.643
55 0.777
56 0.5
57 0.819
58 0.373
59 0.275
6 0.456
60 0.0385
61 0.23
62 0.189
63 0.174
64 0.598
65 0.224
66 0.981
67 0.424
68 0.0106
69 0.881
7 0.0515
70 0.00535
71 0.0683
72 0.438
73 0.057
74 0.966
75 0.0211
76 0.668
77 0.143
78 0.0208
79 0.302
8 0.0905
80 0.925
81 0.873
82 0.0611
83 0.0562
84 0.128
85 0.0446
86 0.0777
87 0.0233
88 0.394
89 0.169
9 0.898
90 0.00794
91 0.514
92 0.293
93 0.377
94 0.712
95 0.0481
96 0.765
97 0.996
98 0.448
99 0.2



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: CNhs13199


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)
0002108 (small intestine)
0000160 (intestine)
0000331 (ileal mucosa)
0000483 (epithelium)
0002116 (ileum)
0001242 (intestinal mucosa)
0000479 (tissue)
0001007 (digestive system)
0000344 (mucosa)
0000064 (organ part)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0001204 (mucosa of small intestine)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0001262 (wall of intestine)
0004786 (gastrointestinal system mucosa)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)
0001168 (wall of small intestine)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011274 (mouse Ileum epithelium 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)