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FF:11820-124F2

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Name:CD4+CD25-CD44- naive conventional T cells, PMA and ionomycin stimulation, 02hr, pool2 (Balb_cAJcl)
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainBalb/cAJcl
tissueblood
dev stageNA
sexNA
ageNA
cell typeT cell
cell lineNA
companyNA
collaborationMorikawa (University of Kyoto)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberBLTsPI-2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  DRS008682
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{library_id}}} {{{accession_numbers}}}
Accession ID Mm9

Library idBAMCTSS
{{{library_id}}}
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

CNhs13226

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0668
1002 --0.116
1003 --0.14
1004 0
1005 --0.101
1006 --0.436
1007 --0.246
1008 0
1009 --0.19
101 0.657
1010 0
1011 0.0913
1012 0
1013 --0.183
1014 --0.0851
1015 0.176
1016 --0.448
1017 0
1018 0
1019 0
102 0.836
1020 0.037
1021 0
1022 --0.296
1023 0.167
1024 --0.14
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.0989
103 --0.0887
1030 0
1031 -1.056
1032 --0.717
1033 0.929
1034 0
1035 0
1036 0.583
1037 0
1038 --0.183
1039 --0.482
104 0
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: CNhs13226

Jaspar motif P-value
MA0002.2 0.0123
MA0003.1 0.132
MA0004.1 0.0237
MA0006.1 0.189
MA0007.1 0.939
MA0009.1 0.648
MA0014.1 0.91
MA0017.1 0.137
MA0018.2 2.07019e-9
MA0019.1 0.94
MA0024.1 0.92
MA0025.1 0.173
MA0027.1 0.744
MA0028.1 0.00249
MA0029.1 0.934
MA0030.1 0.961
MA0031.1 0.326
MA0035.2 0.892
MA0038.1 0.0248
MA0039.2 0.132
MA0040.1 0.96
MA0041.1 0.0585
MA0042.1 0.0987
MA0043.1 2.05521e-4
MA0046.1 5.92568e-11
MA0047.2 0.667
MA0048.1 0.265
MA0050.1 1.28568e-4
MA0051.1 0.00394
MA0052.1 0.532
MA0055.1 0.157
MA0057.1 0.829
MA0058.1 0.00664
MA0059.1 3.67959e-4
MA0060.1 0.00516
MA0061.1 5.00318e-11
MA0062.2 5.74142e-11
MA0065.2 0.385
MA0066.1 0.614
MA0067.1 9.17826e-4
MA0068.1 7.04658e-4
MA0069.1 0.679
MA0070.1 0.95
MA0071.1 0.631
MA0072.1 0.158
MA0073.1 0.522
MA0074.1 0.583
MA0076.1 0.00342
MA0077.1 0.798
MA0078.1 0.5
MA0079.2 0.326
MA0080.2 4.44885e-10
MA0081.1 8.28542e-4
MA0083.1 0.619
MA0084.1 0.341
MA0087.1 0.889
MA0088.1 0.0725
MA0090.1 0.0295
MA0091.1 0.877
MA0092.1 0.0846
MA0093.1 0.0243
MA0099.2 1.90857e-6
MA0100.1 0.263
MA0101.1 1.39184e-15
MA0102.2 0.401
MA0103.1 0.553
MA0104.2 1.26819e-4
MA0105.1 1.50427e-6
MA0106.1 0.582
MA0107.1 6.78646e-16
MA0108.2 0.475
MA0111.1 0.409
MA0112.2 0.389
MA0113.1 0.952
MA0114.1 0.00388
MA0115.1 0.268
MA0116.1 0.97
MA0117.1 0.0353
MA0119.1 0.0251
MA0122.1 0.632
MA0124.1 0.483
MA0125.1 0.114
MA0131.1 0.526
MA0135.1 0.88
MA0136.1 1.50298e-16
MA0137.2 0.00564
MA0138.2 2.57295e-4
MA0139.1 0.212
MA0140.1 0.721
MA0141.1 0.524
MA0142.1 0.585
MA0143.1 0.226
MA0144.1 0.183
MA0145.1 0.0226
MA0146.1 0.958
MA0147.1 7.41537e-6
MA0148.1 0.622
MA0149.1 0.246
MA0150.1 0.0778
MA0152.1 0.0654
MA0153.1 5.21671e-6
MA0154.1 0.739
MA0155.1 0.336
MA0156.1 1.56159e-14
MA0157.1 0.259
MA0159.1 0.679
MA0160.1 0.971
MA0162.1 0.0189
MA0163.1 0.748
MA0164.1 0.0466
MA0258.1 0.849
MA0259.1 0.0203



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: CNhs13226

Novel motif P-value
1 0.972
10 0.228
100 0.474
101 0.463
102 0.434
103 0.16
104 0.493
105 0.425
106 0.215
107 0.971
108 0.77
109 0.722
11 0.702
110 0.407
111 0.129
112 0.296
113 0.91
114 0.975
115 0.462
116 0.543
117 2.80937e-4
118 0.66
119 0.899
12 0.295
120 0.162
121 0.373
122 0.981
123 0.648
124 0.221
125 0.579
126 0.452
127 0.502
128 0.191
129 0.513
13 0.259
130 0.461
131 0.305
132 0.612
133 0.196
134 0.454
135 0.253
136 0.954
137 0.872
138 0.976
139 0.143
14 0.0871
140 0.992
141 0.847
142 0.562
143 0.0167
144 0.36
145 0.192
146 0.854
147 0.662
148 0.244
149 0.115
15 0.486
150 1
151 0.973
152 0.673
153 0.467
154 0.165
155 0.22
156 0.00111
157 0.983
158 0.0143
159 0.714
160 0.119
161 0.322
162 0.203
163 0.767
164 0.0701
165 0.807
166 0.0774
167 0.133
168 0.709
169 0.212
17 0.921
18 0.29
19 0.0105
2 0.00773
20 0.00328
21 0.167
22 0.356
23 0.683
24 0.533
25 0.357
26 0.55
27 0.122
28 0.421
29 0.251
3 0.984
30 0.12
31 0.444
32 0.0509
33 0.223
34 0.298
35 0.278
36 0.157
37 0.371
38 0.446
39 0.589
4 0.788
40 0.914
41 0.151
42 0.787
43 0.686
44 0.728
45 0.32
46 0.883
47 0.646
48 0.794
49 0.696
5 0.205
50 0.635
51 0.658
52 0.497
53 0.641
54 0.564
55 0.992
56 0.757
57 0.63
58 0.74
59 0.428
6 0.654
60 0.458
61 0.243
62 0.264
63 0.699
64 0.592
65 0.791
66 0.668
67 0.621
68 0.157
69 0.523
7 0.689
70 0.0204
71 0.235
72 0.818
73 0.369
74 0.668
75 0.042
76 0.0327
77 0.02
78 0.0608
79 0.857
8 0.989
80 0.415
81 0.877
82 0.803
83 0.243
84 0.284
85 0.582
86 0.129
87 0.423
88 0.544
89 0.322
9 0.819
90 0.524
91 0.554
92 0.622
93 0.258
94 0.486
95 0.482
96 0.567
97 0.502
98 0.852
99 0.0483



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: CNhs13226


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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002371 (somatic cell)
0000542 (lymphocyte)
0000219 (motile cell)
0000738 (leukocyte)
0002087 (nongranular leukocyte)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0000791 (mature alpha-beta T cell)
0000084 (T cell)
0000789 (alpha-beta T cell)
0002419 (mature T cell)
0000624 (CD4-positive, alpha-beta T cell)
0000898 (naive T cell)
0000895 (naive thymus-derived CD4-positive, alpha-beta T cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000359 (2 hr sample)
0000409 (T cell expansion sample)
0011449 (CD4-positiveCD25-CD44- naive conventional T cells stimulated with PMA an ionomycin- 02hr- (Balb_cAJcl) 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:0000134 (mesenchymal cell)
CL:0000051 (common lymphoid progenitor)
CL:0000790 (immature alpha-beta T cell)
CL:0002425 (early T lineage precursor)
CL:0002427 (resting double-positive thymocyte)

{{{1}}} Accession numbers
MethodSample accession id
{{{2}}} 
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{4}}} {{{3}}}
Accession ID

Library idBAMCTSS
{{{4}}}