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FF:12159-128G8

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Name:MC1+Gr1+ myeloid-derived suppressor cells cancer, donor1 (10,11,12 3LL)
Species:Mouse (Mus musculus)
Library ID:CNhs12539
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  SAMD00005037
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12539 CAGE DRX008772 DRR009644
Accession ID Mm9

Library idBAMCTSS
CNhs12539 DRZ001069 DRZ002454
Accession ID Mm10

Library idBAMCTSS
CNhs12539 DRZ012419 DRZ013804
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

CNhs12539

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 1.213
1006 --0.143
1007 --0.137
1008 0
1009 --0.2
101 --0.304
1010 0
1011 --0.122
1012 0.101
1013 --0.0649
1014 --0.0851
1015 --0.151
1016 --0.594
1017 0
1018 0
1019 0
102 0
1020 0
1021 --0.0487
1022 --0.315
1023 0.678
1024 --0.14
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.0989
103 --0.0887
1030 0
1031 --0.911
1032 --0.687
1033 --0.0118
1034 0
1035 0
1036 0.137
1037 0
1038 --0.48
1039 --0.417
104 0
1040 --0.355
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: CNhs12539

Jaspar motif P-value
MA0002.2 7.61519e-12
MA0003.1 0.801
MA0004.1 0.569
MA0006.1 0.146
MA0007.1 0.579
MA0009.1 0.61
MA0014.1 0.217
MA0017.1 0.467
MA0018.2 0.146
MA0019.1 0.958
MA0024.1 0.48
MA0025.1 0.0167
MA0027.1 0.525
MA0028.1 4.43894e-6
MA0029.1 0.729
MA0030.1 0.901
MA0031.1 0.0438
MA0035.2 0.868
MA0038.1 0.164
MA0039.2 0.00971
MA0040.1 0.0752
MA0041.1 0.669
MA0042.1 0.939
MA0043.1 1.07844e-4
MA0046.1 2.65495e-10
MA0047.2 0.0479
MA0048.1 0.181
MA0050.1 7.60248e-6
MA0051.1 2.15609e-4
MA0052.1 0.00304
MA0055.1 0.167
MA0057.1 0.92
MA0058.1 0.772
MA0059.1 0.357
MA0060.1 0.461
MA0061.1 0.0161
MA0062.2 1.54276e-21
MA0065.2 0.267
MA0066.1 0.16
MA0067.1 0.0171
MA0068.1 0.383
MA0069.1 0.509
MA0070.1 0.397
MA0071.1 0.418
MA0072.1 0.214
MA0073.1 0.558
MA0074.1 0.517
MA0076.1 3.60152e-7
MA0077.1 0.136
MA0078.1 0.971
MA0079.2 0.652
MA0080.2 1.67736e-15
MA0081.1 2.07396e-4
MA0083.1 0.477
MA0084.1 0.894
MA0087.1 0.211
MA0088.1 0.902
MA0090.1 0.0225
MA0091.1 0.89
MA0092.1 0.716
MA0093.1 0.558
MA0099.2 0.00142
MA0100.1 0.0335
MA0101.1 0.0176
MA0102.2 2.93223e-9
MA0103.1 0.876
MA0104.2 0.071
MA0105.1 6.73137e-4
MA0106.1 0.883
MA0107.1 0.0152
MA0108.2 0.0274
MA0111.1 0.645
MA0112.2 0.00188
MA0113.1 0.487
MA0114.1 0.937
MA0115.1 0.473
MA0116.1 0.00198
MA0117.1 0.118
MA0119.1 0.562
MA0122.1 0.616
MA0124.1 0.613
MA0125.1 0.0252
MA0131.1 0.54
MA0135.1 0.763
MA0136.1 6.42253e-32
MA0137.2 0.0301
MA0138.2 0.184
MA0139.1 0.611
MA0140.1 0.579
MA0141.1 0.309
MA0142.1 0.351
MA0143.1 0.0498
MA0144.1 0.0503
MA0145.1 0.194
MA0146.1 0.0386
MA0147.1 0.0599
MA0148.1 0.165
MA0149.1 0.3
MA0150.1 6.60405e-6
MA0152.1 0.318
MA0153.1 0.0135
MA0154.1 0.0594
MA0155.1 0.754
MA0156.1 1.40605e-29
MA0157.1 0.17
MA0159.1 0.0148
MA0160.1 0.262
MA0162.1 0.619
MA0163.1 0.055
MA0164.1 0.565
MA0258.1 0.0115
MA0259.1 0.411



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: CNhs12539

Novel motif P-value
1 0.171
10 0.0553
100 0.705
101 0.729
102 0.263
103 0.193
104 0.746
105 0.496
106 0.0565
107 0.779
108 0.846
109 0.0485
11 0.0896
110 0.271
111 0.43
112 0.0564
113 0.926
114 0.0977
115 0.996
116 0.894
117 4.04043e-4
118 0.42
119 0.587
12 0.427
120 0.0376
121 0.67
122 0.496
123 0.314
124 0.835
125 0.26
126 0.487
127 0.21
128 0.152
129 0.45
13 0.09
130 0.367
131 0.601
132 0.913
133 0.0526
134 0.766
135 0.436
136 0.286
137 0.0549
138 0.388
139 0.0728
14 0.379
140 0.63
141 0.735
142 0.0161
143 0.00103
144 0.928
145 0.109
146 0.976
147 0.656
148 0.163
149 0.993
15 0.051
150 0.42
151 0.194
152 0.167
153 0.361
154 0.697
155 0.557
156 0.812
157 0.902
158 0.0545
159 0.631
160 0.681
161 0.097
162 0.529
163 0.381
164 0.0332
165 0.256
166 0.696
167 0.988
168 0.194
169 0.0162
17 0.234
18 0.108
19 0.635
2 0.298
20 0.036
21 0.426
22 0.394
23 0.276
24 0.144
25 0.216
26 0.13
27 0.676
28 0.0977
29 0.0172
3 0.0577
30 0.441
31 0.68
32 0.873
33 0.194
34 0.807
35 0.684
36 0.155
37 0.0675
38 0.348
39 0.827
4 0.63
40 0.214
41 0.0114
42 0.268
43 0.145
44 0.767
45 0.809
46 0.361
47 0.294
48 0.207
49 0.13
5 0.135
50 0.757
51 0.736
52 0.895
53 0.549
54 0.676
55 0.458
56 0.293
57 0.967
58 0.174
59 0.484
6 0.563
60 0.201
61 0.278
62 0.0898
63 0.693
64 0.676
65 0.323
66 0.544
67 0.212
68 0.954
69 0.495
7 0.155
70 0.08
71 0.0692
72 0.148
73 0.0267
74 0.19
75 0.00498
76 0.189
77 0.976
78 0.11
79 0.511
8 0.447
80 0.0399
81 0.523
82 0.498
83 0.492
84 0.958
85 0.209
86 0.0888
87 0.0951
88 0.476
89 0.996
9 0.526
90 0.17
91 0.558
92 0.681
93 0.406
94 0.142
95 0.00589
96 0.9
97 0.874
98 0.344
99 0.159



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: CNhs12539


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)