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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00004935
 
|DRA_sample_Accession=CAGE@SAMD00004935
|accession_numbers=CAGE;DRX008773;DRR009645;DRZ001070;DRZ002455
+
|accession_numbers=CAGE;DRX008773;DRR009645;DRZ001070;DRZ002455;DRZ012420;DRZ013805
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001134,UBERON:0000479,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002036,UBERON:0002385,UBERON:0010317,UBERON:0001015,UBERON:0002204,UBERON:0000383
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001134,UBERON:0000479,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002036,UBERON:0002385,UBERON:0010317,UBERON:0001015,UBERON:0002204,UBERON:0000383
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0000048,CL:0002371,CL:0000034,CL:0000355
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0000048,CL:0002371,CL:0000034,CL:0000355
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|microRNAs=
 
|microRNAs=
 
|microRNAs_nn=
 
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;12161
+
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;12161
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;12161
+
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12161
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/MC1%252bGr1%252b%2520myeloid-derived%2520suppressor%2520cells%2520cancer%252c%2520donor2%2520%25280127%25203LL%2529.CNhs12198.12161-128H1.mm10.nobarcode.bam
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/MC1%252bGr1%252b%2520myeloid-derived%2520suppressor%2520cells%2520cancer%252c%2520donor2%2520%25280127%25203LL%2529.CNhs12198.12161-128H1.mm10.nobarcode.bam
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/MC1%252bGr1%252b%2520myeloid-derived%2520suppressor%2520cells%2520cancer%252c%2520donor2%2520%25280127%25203LL%2529.CNhs12198.12161-128H1.mm10.nobarcode.ctss.bed.gz
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/MC1%252bGr1%252b%2520myeloid-derived%2520suppressor%2520cells%2520cancer%252c%2520donor2%2520%25280127%25203LL%2529.CNhs12198.12161-128H1.mm10.nobarcode.ctss.bed.gz

Latest revision as of 12:36, 10 August 2017


Name:MC1+Gr1+ myeloid-derived suppressor cells cancer, donor2 (0127 3LL)
Species:Mouse (Mus musculus)
Library ID:CNhs12198
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
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typestem cell
cell lineNA
companyNA
collaborationHozumi Motohashi (Tohoku University Graduate School of Medicine)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00004935
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12198 CAGE DRX008773 DRR009645
Accession ID Mm9

Library idBAMCTSS
CNhs12198 DRZ001070 DRZ002455
Accession ID Mm10

Library idBAMCTSS
CNhs12198 DRZ012420 DRZ013805
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

CNhs12198

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 1.157
1006 --0.143
1007 --0.277
1008 0
1009 --0.2
101 --0.243
1010 0
1011 --0.132
1012 0
1013 0.0704
1014 --0.0874
1015 --0.18
1016 --0.594
1017 0
1018 0
1019 0
102 0
1020 0
1021 --0.0487
1022 --0.315
1023 0.572
1024 --0.14
1025 --0.0611
1026 0
1027 0
1028 0
1029 --0.176
103 --0.0887
1030 0
1031 --0.911
1032 --0.655
1033 0.184
1034 0
1035 0
1036 0.12
1037 0
1038 --0.569
1039 --0.531
104 0
1040 --0.593
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: CNhs12198

Jaspar motif P-value
MA0002.2 3.04236e-11
MA0003.1 0.988
MA0004.1 0.951
MA0006.1 0.231
MA0007.1 0.346
MA0009.1 0.495
MA0014.1 0.137
MA0017.1 0.211
MA0018.2 0.216
MA0019.1 0.963
MA0024.1 0.733
MA0025.1 0.022
MA0027.1 0.392
MA0028.1 1.32689e-5
MA0029.1 0.655
MA0030.1 0.77
MA0031.1 0.172
MA0035.2 0.726
MA0038.1 0.34
MA0039.2 0.037
MA0040.1 0.0527
MA0041.1 0.497
MA0042.1 0.907
MA0043.1 9.81432e-4
MA0046.1 2.3079e-9
MA0047.2 0.137
MA0048.1 0.139
MA0050.1 1.59624e-4
MA0051.1 0.00151
MA0052.1 0.00788
MA0055.1 0.0802
MA0057.1 0.972
MA0058.1 0.798
MA0059.1 0.758
MA0060.1 0.668
MA0061.1 0.0167
MA0062.2 5.66825e-19
MA0065.2 0.114
MA0066.1 0.225
MA0067.1 0.0203
MA0068.1 0.496
MA0069.1 0.546
MA0070.1 0.274
MA0071.1 0.276
MA0072.1 0.148
MA0073.1 0.618
MA0074.1 0.345
MA0076.1 1.90445e-6
MA0077.1 0.152
MA0078.1 0.742
MA0079.2 0.274
MA0080.2 1.77081e-15
MA0081.1 1.81931e-4
MA0083.1 0.521
MA0084.1 0.72
MA0087.1 0.73
MA0088.1 0.621
MA0090.1 0.0313
MA0091.1 0.758
MA0092.1 0.546
MA0093.1 0.93
MA0099.2 0.00219
MA0100.1 0.0242
MA0101.1 0.0169
MA0102.2 1.90909e-8
MA0103.1 0.953
MA0104.2 0.307
MA0105.1 1.26111e-4
MA0106.1 0.559
MA0107.1 0.0242
MA0108.2 0.202
MA0111.1 0.69
MA0112.2 0.00171
MA0113.1 0.364
MA0114.1 0.611
MA0115.1 0.486
MA0116.1 0.00107
MA0117.1 0.199
MA0119.1 0.655
MA0122.1 0.7
MA0124.1 0.834
MA0125.1 0.0116
MA0131.1 0.555
MA0135.1 0.877
MA0136.1 1.21268e-30
MA0137.2 0.00335
MA0138.2 0.235
MA0139.1 0.486
MA0140.1 0.864
MA0141.1 0.202
MA0142.1 0.337
MA0143.1 0.149
MA0144.1 0.0303
MA0145.1 0.27
MA0146.1 0.0573
MA0147.1 0.285
MA0148.1 0.216
MA0149.1 0.316
MA0150.1 1.48743e-5
MA0152.1 0.341
MA0153.1 0.00787
MA0154.1 0.0396
MA0155.1 0.935
MA0156.1 1.47119e-27
MA0157.1 0.31
MA0159.1 0.00626
MA0160.1 0.146
MA0162.1 0.342
MA0163.1 0.00784
MA0164.1 0.485
MA0258.1 0.0121
MA0259.1 0.624



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: CNhs12198

Novel motif P-value
1 0.155
10 0.0505
100 0.717
101 0.654
102 0.401
103 0.0924
104 0.854
105 0.476
106 0.0794
107 0.912
108 0.838
109 0.028
11 0.0602
110 0.163
111 0.416
112 0.0208
113 0.892
114 0.209
115 0.738
116 0.843
117 5.10109e-4
118 0.369
119 0.46
12 0.576
120 0.08
121 0.614
122 0.634
123 0.544
124 0.989
125 0.23
126 0.435
127 0.214
128 0.219
129 0.401
13 0.0525
130 0.669
131 0.625
132 0.99
133 0.0306
134 0.751
135 0.537
136 0.41
137 0.0455
138 0.307
139 0.109
14 0.433
140 0.521
141 0.636
142 0.0501
143 0.00173
144 0.821
145 0.102
146 0.975
147 0.439
148 0.16
149 0.98
15 0.0433
150 0.315
151 0.279
152 0.231
153 0.552
154 0.869
155 0.492
156 0.746
157 0.855
158 0.0434
159 0.593
160 0.843
161 0.0727
162 0.73
163 0.335
164 0.0247
165 0.144
166 0.853
167 0.712
168 0.281
169 0.00458
17 0.113
18 0.127
19 0.65
2 0.34
20 0.0531
21 0.491
22 0.379
23 0.485
24 0.0881
25 0.159
26 0.0912
27 0.661
28 0.181
29 0.00852
3 0.0561
30 0.475
31 0.718
32 0.809
33 0.118
34 0.831
35 0.512
36 0.0797
37 0.0655
38 0.253
39 0.908
4 0.584
40 0.147
41 0.0115
42 0.259
43 0.171
44 0.797
45 0.891
46 0.309
47 0.226
48 0.152
49 0.124
5 0.17
50 0.816
51 0.716
52 0.733
53 0.654
54 0.713
55 0.278
56 0.296
57 0.769
58 0.188
59 0.347
6 0.609
60 0.21
61 0.174
62 0.0944
63 0.592
64 0.474
65 0.218
66 0.567
67 0.19
68 0.785
69 0.619
7 0.0892
70 0.0822
71 0.0375
72 0.131
73 0.0395
74 0.107
75 0.00489
76 0.191
77 0.863
78 0.0898
79 0.471
8 0.205
80 0.0627
81 0.571
82 0.537
83 0.386
84 0.946
85 0.291
86 0.16
87 0.0975
88 0.455
89 0.662
9 0.455
90 0.125
91 0.533
92 0.397
93 0.352
94 0.0969
95 0.00888
96 0.817
97 0.841
98 0.362
99 0.351



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: CNhs12198


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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0002371 (somatic cell)
0000034 (stem cell)
0000355 (multi-potent skeletal muscle stem cell)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
0060100 (musculoskeletal system cancer)
4045 (muscle cancer)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001134 (skeletal muscle tissue)
0000479 (tissue)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002036 (striated muscle tissue)
0002385 (muscle tissue)
0010317 (germ layer / neural crest derived structure)
0001015 (musculature)
0002204 (musculoskeletal system)
0000383 (musculature of body)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000267 (mouse muscle derived stem cell sample)
0000268 (cancer related muscle derived stem cell (Mouse) 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:0000355 (multi-potent skeletal muscle stem cell)