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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00004975
 
|DRA_sample_Accession=CAGE@SAMD00004975
|accession_numbers=CAGE;DRX008790;DRR009662;DRZ001087;DRZ002472
+
|accession_numbers=CAGE;DRX008790;DRR009662;DRZ001087;DRZ002472;DRZ012437;DRZ013822
 
|ancestors_in_anatomy_facet=
 
|ancestors_in_anatomy_facet=
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0002371,CL:0000542,CL:0000219,CL:0000738,CL:0002087,CL:0002242,CL:0000255,CL:0000791,CL:0000084,CL:0000789,CL:0002419,CL:0000624,CL:0000815,CL:0000792
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0002371,CL:0000542,CL:0000219,CL:0000738,CL:0002087,CL:0002242,CL:0000255,CL:0000791,CL:0000084,CL:0000789,CL:0002419,CL:0000624,CL:0000815,CL:0000792
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|library_id=CNhs13221
 
|library_id=CNhs13221
 
|library_id_phase_based=2:CNhs13221
 
|library_id_phase_based=2:CNhs13221
 +
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11818
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11818
 +
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD4%252bCD25%252b%2520regulatory%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13221.11818-124E9.mm10.nobarcode.bam
 +
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/CD4%252bCD25%252b%2520regulatory%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13221.11818-124E9.mm10.nobarcode.ctss.bed.gz
 +
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/CD4%252bCD25%252b%2520regulatory%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13221.11818-124E9.mm9.nobarcode.bam
 +
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/CD4%252bCD25%252b%2520regulatory%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13221.11818-124E9.mm9.ctss.bed.gz
 +
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/CD4%252bCD25%252b%2520regulatory%2520T%2520cells%252c%2520pool2%2520%2528Balb_cAJcl%2529.CNhs13221.11818-124E9.mm9.nobarcode.rdna.fa.gz
 
|name=CD4+CD25+ regulatory T cells, pool2 (Balb_cAJcl)
 
|name=CD4+CD25+ regulatory T cells, pool2 (Balb_cAJcl)
 
|namespace=
 
|namespace=

Latest revision as of 12:16, 10 August 2017


Name:CD4+CD25+ regulatory T cells, pool2 (Balb_cAJcl)
Species:Mouse (Mus musculus)
Library ID:CNhs13221
Sample type:primary cells
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
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 numberBLTreg
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004975
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13221 CAGE DRX008790 DRR009662
Accession ID Mm9

Library idBAMCTSS
CNhs13221 DRZ001087 DRZ002472
Accession ID Mm10

Library idBAMCTSS
CNhs13221 DRZ012437 DRZ013822
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

CNhs13221

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 --0.148
1004 0
1005 0.0998
1006 --0.143
1007 --0.199
1008 0
1009 --0.19
101 0.151
1010 0
1011 0.0347
1012 0.083
1013 --0.0691
1014 --0.0874
1015 --0.109
1016 --0.594
1017 0
1018 0
1019 0
102 0.799
1020 0.0527
1021 0
1022 --0.315
1023 0.0527
1024 --0.14
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.0989
103 --0.0887
1030 0
1031 -1.093
1032 --0.655
1033 0.522
1034 0
1035 0
1036 0.373
1037 0
1038 --0.184
1039 --0.181
104 0
1040 --0.121
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: CNhs13221

Jaspar motif P-value
MA0002.2 3.37776e-5
MA0003.1 0.419
MA0004.1 0.0505
MA0006.1 0.609
MA0007.1 0.446
MA0009.1 0.65
MA0014.1 0.815
MA0017.1 0.706
MA0018.2 2.00102e-5
MA0019.1 0.917
MA0024.1 0.721
MA0025.1 0.734
MA0027.1 0.75
MA0028.1 6.97893e-8
MA0029.1 0.427
MA0030.1 0.248
MA0031.1 0.00804
MA0035.2 0.627
MA0038.1 0.00785
MA0039.2 0.541
MA0040.1 0.239
MA0041.1 0.0862
MA0042.1 0.444
MA0043.1 0.0223
MA0046.1 9.58241e-10
MA0047.2 0.161
MA0048.1 0.3
MA0050.1 2.13614e-10
MA0051.1 5.99243e-7
MA0052.1 0.0903
MA0055.1 0.138
MA0057.1 0.88
MA0058.1 0.0407
MA0059.1 0.0439
MA0060.1 0.00526
MA0061.1 1.54223e-11
MA0062.2 2.5443e-24
MA0065.2 0.932
MA0066.1 0.111
MA0067.1 0.0178
MA0068.1 0.0102
MA0069.1 0.622
MA0070.1 0.784
MA0071.1 0.801
MA0072.1 0.0942
MA0073.1 0.732
MA0074.1 0.481
MA0076.1 1.5439e-10
MA0077.1 0.0717
MA0078.1 0.645
MA0079.2 0.0852
MA0080.2 1.28881e-13
MA0081.1 0.00164
MA0083.1 0.341
MA0084.1 0.677
MA0087.1 0.829
MA0088.1 0.998
MA0090.1 0.0632
MA0091.1 0.821
MA0092.1 0.597
MA0093.1 0.063
MA0099.2 0.92
MA0100.1 0.25
MA0101.1 5.72993e-12
MA0102.2 0.964
MA0103.1 0.183
MA0104.2 0.0711
MA0105.1 4.364e-11
MA0106.1 0.942
MA0107.1 6.07129e-12
MA0108.2 0.00199
MA0111.1 0.293
MA0112.2 0.292
MA0113.1 0.143
MA0114.1 0.111
MA0115.1 0.853
MA0116.1 0.0237
MA0117.1 0.244
MA0119.1 0.54
MA0122.1 0.404
MA0124.1 0.686
MA0125.1 0.165
MA0131.1 0.584
MA0135.1 0.945
MA0136.1 1.69552e-25
MA0137.2 1.53488e-6
MA0138.2 0.00179
MA0139.1 0.416
MA0140.1 0.18
MA0141.1 0.731
MA0142.1 0.26
MA0143.1 0.586
MA0144.1 0.00603
MA0145.1 0.299
MA0146.1 0.691
MA0147.1 0.0338
MA0148.1 0.143
MA0149.1 0.185
MA0150.1 0.933
MA0152.1 0.932
MA0153.1 6.53611e-5
MA0154.1 0.126
MA0155.1 0.588
MA0156.1 3.68403e-29
MA0157.1 0.00938
MA0159.1 0.133
MA0160.1 0.887
MA0162.1 0.825
MA0163.1 0.0197
MA0164.1 0.262
MA0258.1 0.148
MA0259.1 0.184



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: CNhs13221

Novel motif P-value
1 0.383
10 0.0343
100 0.54
101 0.895
102 0.507
103 0.644
104 0.845
105 0.659
106 0.684
107 0.472
108 0.577
109 0.291
11 0.336
110 0.0805
111 0.141
112 0.206
113 0.627
114 0.323
115 0.647
116 0.758
117 4.1361e-4
118 0.321
119 0.785
12 0.282
120 0.105
121 0.313
122 0.846
123 0.66
124 0.315
125 0.293
126 0.526
127 0.954
128 0.497
129 0.583
13 0.0889
130 0.808
131 0.765
132 0.993
133 0.821
134 0.514
135 0.848
136 0.273
137 0.327
138 0.558
139 0.401
14 0.725
140 0.668
141 0.251
142 0.328
143 2.66668e-4
144 0.382
145 0.224
146 0.987
147 0.365
148 0.165
149 0.135
15 0.12
150 0.796
151 0.249
152 0.499
153 0.372
154 0.306
155 0.104
156 0.114
157 0.939
158 0.0569
159 0.537
160 0.387
161 0.273
162 0.721
163 0.368
164 0.031
165 0.576
166 0.464
167 0.0936
168 0.63
169 0.889
17 0.671
18 0.391
19 0.0814
2 0.0386
20 0.0169
21 0.2
22 0.789
23 0.828
24 0.281
25 0.164
26 0.364
27 0.742
28 0.257
29 0.0417
3 0.293
30 0.0908
31 0.526
32 0.133
33 0.127
34 0.462
35 0.0582
36 0.0315
37 0.126
38 0.659
39 0.636
4 0.885
40 0.321
41 0.42
42 0.262
43 0.558
44 0.657
45 0.462
46 0.513
47 0.581
48 0.343
49 0.232
5 0.0428
50 0.49
51 0.794
52 0.106
53 0.685
54 0.59
55 0.543
56 0.854
57 0.905
58 0.331
59 0.809
6 0.729
60 0.961
61 0.217
62 0.0933
63 0.826
64 0.971
65 0.527
66 0.278
67 0.797
68 0.88
69 0.855
7 0.435
70 0.0124
71 0.0974
72 0.292
73 0.181
74 0.548
75 0.00563
76 0.0207
77 0.0516
78 0.19
79 0.795
8 0.583
80 0.233
81 0.728
82 0.311
83 0.0441
84 0.488
85 0.997
86 0.102
87 0.744
88 0.389
89 0.851
9 0.913
90 0.141
91 0.905
92 0.556
93 0.247
94 0.375
95 0.0712
96 0.278
97 0.498
98 0.534
99 0.0369



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: CNhs13221


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)
0000815 (regulatory T cell)
0000792 (CD4-positive, CD25-positive, alpha-beta regulatory T cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000343 (control treatment sample)
0011455 (CD4-positiveCD25-positive regulatory T cells (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)