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FF:12163-128H3

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Name:MC1+Gr1+ myeloid-derived suppressor cells cancer, donor3 (0128 3LL)
Species:Mouse (Mus musculus)
Library ID:CNhs12542
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  SAMD00005808
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12542 CAGE DRX008774 DRR009646
Accession ID Mm9

Library idBAMCTSS
CNhs12542 DRZ001071 DRZ002456
Accession ID Mm10

Library idBAMCTSS
CNhs12542 DRZ012421 DRZ013806
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

CNhs12542

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 --0.123
1004 0
1005 1.244
1006 --0.3
1007 --0.186
1008 0
1009 --0.2
101 --0.235
1010 0
1011 --0.115
1012 0
1013 --0.0868
1014 --0.0874
1015 --0.12
1016 --0.594
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 --0.315
1023 0.617
1024 --0.14
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 0.00687
103 --0.0887
1030 0
1031 --0.911
1032 --0.768
1033 0.148
1034 0
1035 0
1036 0.214
1037 0
1038 --0.585
1039 --0.638
104 0
1040 --0.315
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: CNhs12542

Jaspar motif P-value
MA0002.2 4.57167e-12
MA0003.1 0.905
MA0004.1 0.582
MA0006.1 0.218
MA0007.1 0.47
MA0009.1 0.925
MA0014.1 0.177
MA0017.1 0.258
MA0018.2 0.545
MA0019.1 0.855
MA0024.1 0.875
MA0025.1 0.143
MA0027.1 0.518
MA0028.1 2.21434e-6
MA0029.1 0.576
MA0030.1 0.671
MA0031.1 0.135
MA0035.2 0.724
MA0038.1 0.237
MA0039.2 0.0478
MA0040.1 0.135
MA0041.1 0.562
MA0042.1 0.852
MA0043.1 0.00122
MA0046.1 1.37792e-10
MA0047.2 0.154
MA0048.1 0.115
MA0050.1 2.23317e-6
MA0051.1 8.33824e-5
MA0052.1 4.88255e-4
MA0055.1 0.0816
MA0057.1 0.884
MA0058.1 0.828
MA0059.1 0.587
MA0060.1 0.753
MA0061.1 0.0272
MA0062.2 5.33287e-20
MA0065.2 0.175
MA0066.1 0.2
MA0067.1 0.0237
MA0068.1 0.83
MA0069.1 0.535
MA0070.1 0.488
MA0071.1 0.4
MA0072.1 0.145
MA0073.1 0.697
MA0074.1 0.451
MA0076.1 1.95043e-7
MA0077.1 0.111
MA0078.1 0.844
MA0079.2 0.377
MA0080.2 2.72352e-15
MA0081.1 2.40404e-4
MA0083.1 0.146
MA0084.1 0.799
MA0087.1 0.566
MA0088.1 0.579
MA0090.1 0.0252
MA0091.1 0.996
MA0092.1 0.601
MA0093.1 0.57
MA0099.2 0.0306
MA0100.1 0.0125
MA0101.1 0.0211
MA0102.2 2.13315e-8
MA0103.1 0.824
MA0104.2 0.172
MA0105.1 1.4307e-4
MA0106.1 0.531
MA0107.1 0.0361
MA0108.2 0.00838
MA0111.1 0.647
MA0112.2 0.00109
MA0113.1 0.467
MA0114.1 0.607
MA0115.1 0.563
MA0116.1 6.86261e-4
MA0117.1 0.284
MA0119.1 0.498
MA0122.1 0.502
MA0124.1 0.599
MA0125.1 0.0447
MA0131.1 0.438
MA0135.1 0.78
MA0136.1 4.0494e-32
MA0137.2 0.00669
MA0138.2 0.0876
MA0139.1 0.361
MA0140.1 0.893
MA0141.1 0.282
MA0142.1 0.185
MA0143.1 0.116
MA0144.1 0.0243
MA0145.1 0.304
MA0146.1 0.0746
MA0147.1 0.157
MA0148.1 0.322
MA0149.1 0.297
MA0150.1 1.2134e-4
MA0152.1 0.421
MA0153.1 0.00616
MA0154.1 0.0363
MA0155.1 0.804
MA0156.1 1.73228e-29
MA0157.1 0.254
MA0159.1 0.0188
MA0160.1 0.301
MA0162.1 0.349
MA0163.1 0.00517
MA0164.1 0.495
MA0258.1 0.00848
MA0259.1 0.645



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: CNhs12542

Novel motif P-value
1 0.148
10 0.0491
100 0.727
101 0.698
102 0.383
103 0.102
104 0.918
105 0.514
106 0.112
107 0.8
108 0.82
109 0.0426
11 0.0842
110 0.181
111 0.52
112 0.0378
113 0.91
114 0.146
115 0.706
116 0.843
117 4.89974e-4
118 0.485
119 0.485
12 0.69
120 0.0727
121 0.667
122 0.502
123 0.319
124 0.909
125 0.2
126 0.406
127 0.209
128 0.266
129 0.337
13 0.049
130 0.468
131 0.681
132 0.92
133 0.195
134 0.836
135 0.258
136 0.338
137 0.0481
138 0.358
139 0.0699
14 0.385
140 0.834
141 0.594
142 0.0472
143 0.00159
144 0.965
145 0.102
146 0.896
147 0.691
148 0.298
149 0.946
15 0.0427
150 0.35
151 0.243
152 0.329
153 0.39
154 0.897
155 0.591
156 0.247
157 0.87
158 0.0906
159 0.674
160 0.946
161 0.0996
162 0.513
163 0.435
164 0.0132
165 0.17
166 0.547
167 0.726
168 0.327
169 0.00864
17 0.237
18 0.0888
19 0.576
2 0.325
20 0.0352
21 0.374
22 0.421
23 0.413
24 0.0913
25 0.174
26 0.135
27 0.767
28 0.128
29 0.012
3 0.0525
30 0.436
31 0.747
32 0.665
33 0.186
34 0.776
35 0.538
36 0.148
37 0.0653
38 0.281
39 0.786
4 0.702
40 0.234
41 0.0181
42 0.251
43 0.159
44 0.791
45 0.955
46 0.335
47 0.203
48 0.162
49 0.123
5 0.142
50 0.698
51 0.658
52 0.668
53 0.485
54 0.648
55 0.455
56 0.277
57 0.633
58 0.189
59 0.409
6 0.606
60 0.302
61 0.253
62 0.117
63 0.632
64 0.625
65 0.306
66 0.569
67 0.141
68 0.842
69 0.591
7 0.126
70 0.0928
71 0.0415
72 0.176
73 0.0507
74 0.121
75 0.00638
76 0.151
77 0.865
78 0.101
79 0.51
8 0.287
80 0.0315
81 0.578
82 0.579
83 0.679
84 0.872
85 0.328
86 0.122
87 0.165
88 0.47
89 0.739
9 0.43
90 0.088
91 0.592
92 0.55
93 0.679
94 0.0512
95 0.00657
96 0.822
97 0.86
98 0.419
99 0.264



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: CNhs12542


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)