Personal tools

FF:483-18I2

From FANTOM5_SSTAR

Revision as of 15:55, 4 July 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:kidney, embryo E17
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuekidney
dev stage17 days embryo
sexmixture
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
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

CNhs11028

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.0395
1002 0.504
1003 0.00599
1004 0
1005 --0.0382
1006 0.0366
1007 0.111
1008 0
1009 0.0171
101 0.0824
1010 0
1011 0
1012 0
1013 --0.0296
1014 0.305
1015 0.143
1016 0.206
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.0216
1023 0
1024 0.0805
1025 0.12
1026 0
1027 0
1028 0
1029 0.321
103 0.0907
1030 0
1031 0.353
1032 0.0135
1033 0.014
1034 0
1035 0.0805
1036 0.164
1037 0
1038 0.053
1039 0.0305
104 0
1040 0.195
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
no result for this sample


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: CNhs11028

Jaspar motif P-value
MA0002.2 0.00344
MA0003.1 0.848
MA0004.1 0.481
MA0006.1 0.464
MA0007.1 0.492
MA0009.1 0.563
MA0014.1 0.788
MA0017.1 0.182
MA0018.2 5.0839e-6
MA0019.1 0.812
MA0024.1 9.40417e-6
MA0025.1 1.31749e-4
MA0027.1 0.548
MA0028.1 0.674
MA0029.1 0.199
MA0030.1 0.722
MA0031.1 0.31
MA0035.2 2.59498e-5
MA0038.1 0.484
MA0039.2 0.172
MA0040.1 0.409
MA0041.1 0.177
MA0042.1 0.437
MA0043.1 0.00157
MA0046.1 2.35814e-69
MA0047.2 0.942
MA0048.1 1.68431e-4
MA0050.1 2.98739e-4
MA0051.1 3.30283e-5
MA0052.1 0.0028
MA0055.1 0.00282
MA0057.1 0.531
MA0058.1 0.35
MA0059.1 0.864
MA0060.1 0.0067
MA0061.1 0.088
MA0062.2 2.00038e-4
MA0065.2 0.639
MA0066.1 0.968
MA0067.1 0.0594
MA0068.1 0.737
MA0069.1 0.0947
MA0070.1 0.64
MA0071.1 0.237
MA0072.1 0.00466
MA0073.1 0.789
MA0074.1 0.737
MA0076.1 0.187
MA0077.1 0.436
MA0078.1 0.0878
MA0079.2 0.165
MA0080.2 2.23609e-8
MA0081.1 0.0789
MA0083.1 0.215
MA0084.1 0.883
MA0087.1 0.847
MA0088.1 0.987
MA0090.1 0.0753
MA0091.1 0.651
MA0092.1 0.654
MA0093.1 0.507
MA0099.2 7.54449e-5
MA0100.1 0.158
MA0101.1 0.251
MA0102.2 0.0138
MA0103.1 0.359
MA0104.2 0.273
MA0105.1 0.771
MA0106.1 0.89
MA0107.1 0.124
MA0108.2 0.36
MA0111.1 0.369
MA0112.2 0.394
MA0113.1 0.744
MA0114.1 0.0642
MA0115.1 0.893
MA0116.1 0.215
MA0117.1 0.0089
MA0119.1 0.404
MA0122.1 0.317
MA0124.1 0.825
MA0125.1 0.662
MA0131.1 0.555
MA0135.1 0.633
MA0136.1 1.53564e-11
MA0137.2 0.0313
MA0138.2 0.06
MA0139.1 0.984
MA0140.1 0.0238
MA0141.1 0.902
MA0142.1 0.131
MA0143.1 0.834
MA0144.1 0.181
MA0145.1 0.864
MA0146.1 0.453
MA0147.1 0.276
MA0148.1 0.479
MA0149.1 0.0924
MA0150.1 0.00667
MA0152.1 0.0373
MA0153.1 6.47626e-31
MA0154.1 0.291
MA0155.1 0.0756
MA0156.1 5.4675e-8
MA0157.1 0.337
MA0159.1 0.43
MA0160.1 0.272
MA0162.1 0.261
MA0163.1 0.433
MA0164.1 0.895
MA0258.1 0.048
MA0259.1 0.601



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: CNhs11028

Novel motif P-value
1 0.0808
10 0.765
100 0.656
101 0.827
102 0.612
103 0.89
104 0.643
105 0.944
106 0.523
107 0.254
108 0.503
109 0.691
11 0.175
110 0.999
111 0.0553
112 0.865
113 0.541
114 0.00503
115 0.787
116 0.583
117 0.0949
118 0.141
119 0.319
12 0.644
120 0.265
121 0.379
122 0.976
123 0.0546
124 0.984
125 0.204
126 0.768
127 0.0541
128 0.467
129 0.281
13 0.051
130 0.228
131 0.113
132 0.183
133 0.388
134 0.624
135 0.621
136 0.503
137 0.287
138 0.0159
139 0.105
14 0.377
140 0.54
141 0.836
142 0.317
143 0.481
144 0.335
145 0.251
146 0.376
147 0.189
148 0.55
149 0.273
15 0.103
150 0.31
151 0.0262
152 0.819
153 0.337
154 0.154
155 0.794
156 0.39
157 0.899
158 0.783
159 0.173
160 0.186
161 0.579
162 0.388
163 0.099
164 0.396
165 0.659
166 0.205
167 0.739
168 0.897
169 0.44
17 0.458
18 0.0445
19 0.211
2 0.539
20 0.805
21 0.985
22 0.629
23 0.334
24 0.779
25 0.307
26 0.593
27 0.759
28 0.164
29 0.594
3 0.921
30 0.97
31 0.41
32 0.138
33 0.966
34 0.988
35 0.0768
36 0.0543
37 0.717
38 0.557
39 0.455
4 0.969
40 0.0925
41 0.0544
42 0.67
43 0.257
44 0.399
45 0.565
46 0.576
47 0.291
48 0.408
49 0.193
5 0.253
50 0.443
51 0.647
52 0.62
53 0.641
54 0.303
55 0.192
56 0.238
57 0.934
58 0.597
59 0.304
6 0.93
60 0.996
61 0.534
62 0.0998
63 0.258
64 0.6
65 0.276
66 0.713
67 0.0807
68 0.0618
69 0.759
7 0.997
70 0.00536
71 0.749
72 0.159
73 0.202
74 0.913
75 0.135
76 0.935
77 0.935
78 0.374
79 0.464
8 0.349
80 0.038
81 0.277
82 0.164
83 0.449
84 0.86
85 0.165
86 0.49
87 8.82079e-5
88 0.848
89 0.397
9 0.843
90 0.505
91 0.872
92 0.28
93 0.761
94 0.555
95 0.0937
96 0.637
97 0.918
98 0.2
99 0.748



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: CNhs11028


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)
0000922 (embryo)
0002113 (kidney)
0002100 (trunk)
0000479 (tissue)
0000062 (organ)
0000475 (organism subdivision)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0009569 (subdivision of trunk)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0005172 (abdomen element)
0005173 (abdominal segment element)
0011143 (upper urinary tract)
0001008 (renal system)
0002417 (abdominal segment of trunk)
0000916 (abdomen)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000300 (mouse embryonic day 17 sample)
0011371 (mouse kidney- embryo E17 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

NA