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|repeat_enrich_byfamily=0.069119766685487,0,0,0,0,0,-0.109111830177157,0,0,0,0,-0.0843392403965415,0,0,0,0,0.353571802418294,0,-0.191893350882575,0,0,0,0.281033021353425,0,0,0,0,0,0,0,0,0,-0.558422792324031,0,0.515210800008536,0,0,0,0.015801594387893,-0.143307567793531,0.368974497170017,-0.984211366477826,-0.107005871718675,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0.13932832075821,0,-0.130696565450787,0,0,-0.00336631083942764,-0.243225778194271,-0.310650657339386,-0.158091042771083,-0.140687683267293,0,-0.0148250452003048,-0.0760168881589905,-0.279559504296028,0,0,0,0.189558961749357,-0.314881859387145,-0.0788315948399074,0,0,0,0,0,0,-0.0843878890072914,-0.530973139023784,-0.129286491554687,0,0,0,0,0
 
|rna_box=124
 
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|rna_catalog_number=

Revision as of 01:13, 24 September 2012


Name:CD326+ enterocyte isolated from mice, treated with RANKL, day03, pool2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainBalb/c
tissueileum
dev stageadult
sexmale
ageNA
cell typeenterocyte
cell lineNA
companyNA
collaborationShinji Fukuda (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRANKL_Ep+_b
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs13233

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0631
1002 --0.116
1003 --0.175
1004 0
1005 1.037
1006 --0.269
1007 0.134
1008 0.893
1009 --0.19
101 --0.478
1010 0
1011 --0.298
1012 0
1013 0.406
1014 --0.0874
1015 --0.479
1016 --0.465
1017 0
1018 0.744
1019 0
102 0
1020 0
1021 0
1022 --0.0704
1023 0
1024 --0.307
1025 0
1026 0
1027 --0.048
1028 0
1029 --0.176
103 --0.0887
1030 0
1031 --0.819
1032 1.16
1033 0
1034 0
1035 0
1036 --0.254
1037 0
1038 0.19
1039 --0.1
104 0
1040 --0.687
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: CNhs13233

Jaspar motif P-value
MA0002.2 0.0209
MA0003.1 0.462
MA0004.1 0.994
MA0006.1 0.0305
MA0007.1 0.25
MA0009.1 0.082
MA0014.1 0.045
MA0017.1 3.35925e-31
MA0018.2 0.126
MA0019.1 0.0332
MA0024.1 4.64553e-6
MA0025.1 0.371
MA0027.1 0.827
MA0028.1 0.19
MA0029.1 0.946
MA0030.1 0.344
MA0031.1 0.155
MA0035.2 7.34492e-6
MA0038.1 0.324
MA0039.2 1.36521e-5
MA0040.1 0.0695
MA0041.1 0.217
MA0042.1 0.255
MA0043.1 0.247
MA0046.1 4.217e-52
MA0047.2 0.0184
MA0048.1 0.29
MA0050.1 1.54369e-4
MA0051.1 2.14905e-6
MA0052.1 0.925
MA0055.1 0.268
MA0057.1 0.083
MA0058.1 0.834
MA0059.1 0.227
MA0060.1 0.12
MA0061.1 0.00428
MA0062.2 8.47813e-4
MA0065.2 6.45114e-16
MA0066.1 0.16
MA0067.1 0.373
MA0068.1 0.114
MA0069.1 0.647
MA0070.1 0.459
MA0071.1 0.0206
MA0072.1 0.71
MA0073.1 0.98
MA0074.1 0.318
MA0076.1 0.285
MA0077.1 0.481
MA0078.1 0.745
MA0079.2 0.0715
MA0080.2 1.02959e-4
MA0081.1 0.792
MA0083.1 0.82
MA0084.1 0.216
MA0087.1 0.362
MA0088.1 0.94
MA0090.1 0.384
MA0091.1 0.0418
MA0092.1 0.524
MA0093.1 0.951
MA0099.2 1.00415e-13
MA0100.1 0.589
MA0101.1 6.29262e-6
MA0102.2 0.78
MA0103.1 1.36819e-6
MA0104.2 0.0238
MA0105.1 0.723
MA0106.1 0.592
MA0107.1 3.08643e-6
MA0108.2 2.58478e-4
MA0111.1 0.289
MA0112.2 0.0193
MA0113.1 0.952
MA0114.1 3.87727e-40
MA0115.1 4.89658e-18
MA0116.1 0.757
MA0117.1 0.178
MA0119.1 0.114
MA0122.1 0.857
MA0124.1 0.451
MA0125.1 0.86
MA0131.1 0.466
MA0135.1 0.173
MA0136.1 2.06075e-7
MA0137.2 0.0393
MA0138.2 0.932
MA0139.1 0.495
MA0140.1 0.116
MA0141.1 1.14424e-7
MA0142.1 0.0246
MA0143.1 0.0603
MA0144.1 0.00392
MA0145.1 0.00589
MA0146.1 0.0577
MA0147.1 0.0206
MA0148.1 0.0282
MA0149.1 0.0438
MA0150.1 0.00436
MA0152.1 0.202
MA0153.1 3.47036e-40
MA0154.1 0.0887
MA0155.1 0.739
MA0156.1 2.17193e-4
MA0157.1 0.992
MA0159.1 0.00187
MA0160.1 5.94681e-6
MA0162.1 0.866
MA0163.1 0.7
MA0164.1 0.815
MA0258.1 0.149
MA0259.1 0.343



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: CNhs13233

Novel motif P-value
1 0.274
10 0.596
100 0.994
101 0.893
102 0.894
103 0.98
104 0.713
105 0.0999
106 0.0104
107 0.162
108 0.566
109 0.112
11 0.23
110 0.64
111 0.132
112 0.0421
113 0.26
114 0.12
115 0.634
116 0.103
117 0.109
118 0.544
119 0.119
12 0.663
120 0.667
121 0.339
122 0.689
123 0.112
124 0.196
125 0.585
126 0.0971
127 0.212
128 0.0367
129 0.199
13 5.08485e-5
130 0.755
131 0.969
132 0.453
133 0.484
134 0.735
135 0.151
136 0.00725
137 0.615
138 0.139
139 0.468
14 0.577
140 0.806
141 0.136
142 0.579
143 0.126
144 0.255
145 0.165
146 0.241
147 0.58
148 0.922
149 0.945
15 0.208
150 0.269
151 0.986
152 0.0188
153 0.643
154 0.546
155 0.512
156 0.136
157 0.399
158 0.379
159 0.685
160 0.498
161 0.83
162 0.913
163 0.0308
164 0.268
165 0.243
166 0.823
167 0.908
168 0.927
169 0.0848
17 0.0363
18 0.848
19 0.358
2 0.607
20 0.295
21 0.938
22 0.215
23 0.168
24 0.894
25 0.534
26 0.0436
27 0.629
28 0.204
29 0.367
3 0.296
30 0.222
31 0.821
32 0.258
33 0.282
34 0.856
35 0.881
36 0.732
37 0.0211
38 0.401
39 0.462
4 0.362
40 0.377
41 0.16
42 0.871
43 0.338
44 0.28
45 0.209
46 0.613
47 0.8
48 0.442
49 0.445
5 0.907
50 0.359
51 0.643
52 0.096
53 0.514
54 0.317
55 0.374
56 0.569
57 0.542
58 0.309
59 0.305
6 0.707
60 0.0237
61 0.632
62 0.326
63 0.119
64 0.912
65 0.324
66 0.858
67 0.364
68 0.0364
69 0.973
7 0.0707
70 0.018
71 0.476
72 0.368
73 0.0103
74 0.635
75 0.0572
76 0.876
77 0.0488
78 0.0276
79 0.804
8 0.77
80 0.989
81 0.768
82 0.0982
83 0.712
84 0.059
85 0.119
86 0.144
87 0.0104
88 0.203
89 0.522
9 0.983
90 0.774
91 0.854
92 0.623
93 0.248
94 0.648
95 0.00832
96 0.823
97 0.807
98 0.671
99 0.601



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: CNhs13233


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), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000075 (columnar/cuboidal epithelial cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002563 (intestinal epithelial cell)
0000255 (eukaryotic cell)
0000239 (brush border epithelial cell)
0000677 (gut absorptive cell)
0000212 (absorptive cell)
0002076 (endo-epithelial cell)
0002251 (epithelial cell of alimentary canal)
0000584 (enterocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000160 (intestine)
0000483 (epithelium)
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)
0005911 (endo-epithelium)
0004923 (organ component layer)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0000060 (anatomical wall)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0000490 (unilaminar epithelium)
0001262 (wall of intestine)
0004786 (gastrointestinal system mucosa)
0000485 (simple columnar epithelium)
0003350 (epithelium of mucosa)
0003929 (gut epithelium)
0004808 (gastrointestinal system epithelium)
0001277 (intestinal epithelium)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000383 (3 days sample)
0000627 (RANK ligand treatment sample)
0011113 (mouse CD326-positive enterocyte isolated from mice- treated with RANKL- day03 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

CL:0000223 (endodermal cell)