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FF:10253-104C1

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Name:Ileum epithelium, pool2
Species:Mouse (Mus musculus)
Library ID:CNhs13232
Sample type:tissues
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_b
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004676
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13232 CAGE DRX008768 DRR009640
Accession ID Mm9

Library idBAMCTSS
CNhs13232 DRZ001065 DRZ002450
Accession ID Mm10

Library idBAMCTSS
CNhs13232 DRZ012415 DRZ013800
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

CNhs13232

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 -0.0355
1001 -0.0749
1002 -0.116
1003 -0.175
1004 0
1005 0.177
1006 -0.351
1007 -0.117
1008 1.964
1009 -0.19
101 -0.172
1010 0
1011 -0.298
1012 0
1013 0.266
1014 -0.0874
1015 -0.424
1016 -0.594
1017 0
1018 0.245
1019 0
102 0
1020 0
1021 0
1022 -0.0264
1023 0
1024 -0.307
1025 0
1026 0
1027 -0.048
1028 0
1029 -0.176
103 -0.0887
1030 0
1031 -0.911
1032 0.751
1033 -0.00394
1034 0.156
1035 0
1036 -0.111
1037 0
1038 0.0793
1039 0.198
104 0
1040 -0.546
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: CNhs13232
Jaspar motif P-value
MA0002.2 0.00226
MA0003.1 0.294
MA0004.1 0.532
MA0006.1 0.0824
MA0007.1 0.188
MA0009.1 0.371
MA0014.1 0.0526
MA0017.1 3.8895e-28
MA0018.2 0.279
MA0019.1 0.176
MA0024.1 0.175
MA0025.1 0.355
MA0027.1 0.348
MA0028.1 0.00404
MA0029.1 0.467
MA0030.1 0.739
MA0031.1 0.468
MA0035.2 4.63856e-5
MA0038.1 0.881
MA0039.2 8.36757e-5
MA0040.1 0.006
MA0041.1 0.333
MA0042.1 0.436
MA0043.1 0.108
MA0046.1 8.96583e-53
MA0047.2 0.0066
MA0048.1 0.3
MA0050.1 7.09907e-7
MA0051.1 3.73292e-7
MA0052.1 9.54187e-4
MA0055.1 0.299
MA0057.1 0.136
MA0058.1 0.61
MA0059.1 0.651
MA0060.1 0.484
MA0061.1 0.457
MA0062.2 1.38613e-6
MA0065.2 5.02225e-14
MA0066.1 0.112
MA0067.1 0.451
MA0068.1 0.214
MA0069.1 0.635
MA0070.1 0.0893
MA0071.1 0.114
MA0072.1 0.892
MA0073.1 0.805
MA0074.1 0.224
MA0076.1 0.0122
MA0077.1 0.869
MA0078.1 0.755
MA0079.2 0.74
MA0080.2 1.51114e-6
MA0081.1 0.822
MA0083.1 0.00288
MA0084.1 0.26
MA0087.1 0.408
MA0088.1 0.181
MA0090.1 0.87
MA0091.1 0.744
MA0092.1 0.891
MA0093.1 0.613
MA0099.2 1.37367e-5
MA0100.1 0.717
MA0101.1 0.395
MA0102.2 0.468
MA0103.1 4.3532e-7
MA0104.2 0.549
MA0105.1 0.543
MA0106.1 0.485
MA0107.1 0.471
MA0108.2 0.373
MA0111.1 0.892
MA0112.2 6.73084e-4
MA0113.1 0.208
MA0114.1 2.75598e-31
MA0115.1 5.45715e-13
MA0116.1 0.289
MA0117.1 0.654
MA0119.1 0.0909
MA0122.1 0.757
MA0124.1 0.181
MA0125.1 0.74
MA0131.1 0.693
MA0135.1 0.405
MA0136.1 9.74748e-12
MA0137.2 0.0373
MA0138.2 0.996
MA0139.1 0.0804
MA0140.1 0.0131
MA0141.1 4.6358e-7
MA0142.1 0.232
MA0143.1 0.0975
MA0144.1 0.0112
MA0145.1 0.0161
MA0146.1 0.131
MA0147.1 0.67
MA0148.1 0.00685
MA0149.1 0.00656
MA0150.1 0.0557
MA0152.1 0.0799
MA0153.1 1.2829e-41
MA0154.1 0.119
MA0155.1 0.517
MA0156.1 1.25198e-7
MA0157.1 0.95
MA0159.1 2.2059e-4
MA0160.1 1.10584e-4
MA0162.1 0.65
MA0163.1 0.141
MA0164.1 0.792
MA0258.1 0.0376
MA0259.1 0.828



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: CNhs13232
Novel motif P-value
1 0.126
10 0.105
100 0.733
101 0.76
102 0.568
103 0.227
104 0.894
105 0.216
106 0.0465
107 0.246
108 0.943
109 0.0357
11 0.109
110 0.224
111 0.294
112 0.0218
113 0.456
114 0.0593
115 0.832
116 0.223
117 0.0247
118 0.381
119 0.259
12 0.674
120 0.531
121 0.584
122 0.824
123 0.0431
124 0.1
125 0.169
126 0.0412
127 0.212
128 0.355
129 0.254
13 9.35114e-5
130 0.642
131 0.627
132 0.524
133 0.81
134 0.999
135 0.154
136 0.0219
137 0.756
138 0.0852
139 0.0866
14 0.727
140 0.208
141 0.222
142 1
143 0.236
144 0.318
145 0.0907
146 0.292
147 0.96
148 0.624
149 0.989
15 0.0901
150 0.372
151 0.637
152 0.0737
153 0.848
154 0.833
155 0.291
156 0.0586
157 0.461
158 0.624
159 0.655
160 0.716
161 0.657
162 0.911
163 0.299
164 0.0792
165 0.295
166 0.748
167 0.618
168 0.883
169 0.0428
17 0.0413
18 0.909
19 0.247
2 0.725
20 0.437
21 0.878
22 0.33
23 0.957
24 0.546
25 0.344
26 0.00915
27 0.736
28 0.334
29 0.0839
3 0.174
30 0.454
31 0.958
32 0.2
33 0.164
34 0.933
35 0.635
36 0.406
37 0.0389
38 0.52
39 0.289
4 0.476
40 0.137
41 0.249
42 0.645
43 0.359
44 0.138
45 0.488
46 0.272
47 0.335
48 0.184
49 0.278
5 0.444
50 0.62
51 0.744
52 0.184
53 0.445
54 0.598
55 0.619
56 0.606
57 0.958
58 0.279
59 0.265
6 0.544
60 0.0474
61 0.22
62 0.229
63 0.189
64 0.557
65 0.326
66 0.829
67 0.291
68 0.195
69 0.851
7 0.0525
70 0.0173
71 0.0995
72 0.245
73 0.0371
74 0.682
75 0.0296
76 0.648
77 0.192
78 0.0144
79 0.69
8 0.148
80 0.603
81 0.884
82 0.132
83 0.0467
84 0.125
85 0.131
86 0.0649
87 0.00766
88 0.28
89 0.181
9 0.914
90 0.111
91 0.613
92 0.469
93 0.516
94 0.451
95 0.00528
96 0.877
97 0.932
98 0.517
99 0.264



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: CNhs13232


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

CL: Cell type
0000000 (cell)
0000003 (native cell)

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)
0000002 (in vivo cell sample)
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)