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FF:12160-128G9

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Name:MC1+Gr1+ myeloid-derived suppressor cells control, donor1 (4,5,6PBS)
Species:Mouse (Mus musculus)
Library ID:CNhs12540
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  SAMD00006004
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12540 CAGE DRX008775 DRR009647
Accession ID Mm9

Library idBAMCTSS
CNhs12540 DRZ001072 DRZ002457
Accession ID Mm10

Library idBAMCTSS
CNhs12540 DRZ012422 DRZ013807
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

CNhs12540

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 1.111
1006 0
1007 --0.182
1008 0
1009 --0.2
101 --0.349
1010 0
1011 --0.211
1012 0.103
1013 --0.199
1014 --0.0874
1015 --0.319
1016 --0.594
1017 0
1018 0
1019 0
102 0
1020 0
1021 --0.0487
1022 --0.315
1023 0.525
1024 --0.22
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.0989
103 --0.0887
1030 0
1031 --0.911
1032 --0.802
1033 0.392
1034 0
1035 0
1036 0.183
1037 0
1038 --0.58
1039 --0.53
104 0
1040 --0.342
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: CNhs12540

Jaspar motif P-value
MA0002.2 9.02178e-12
MA0003.1 0.885
MA0004.1 0.704
MA0006.1 0.193
MA0007.1 0.459
MA0009.1 0.71
MA0014.1 0.18
MA0017.1 0.435
MA0018.2 0.002
MA0019.1 0.979
MA0024.1 0.125
MA0025.1 7.31685e-4
MA0027.1 0.536
MA0028.1 6.01563e-5
MA0029.1 0.675
MA0030.1 0.861
MA0031.1 0.0133
MA0035.2 0.647
MA0038.1 0.0598
MA0039.2 0.0303
MA0040.1 0.0602
MA0041.1 0.975
MA0042.1 0.907
MA0043.1 1.51686e-7
MA0046.1 1.39389e-9
MA0047.2 0.0371
MA0048.1 0.236
MA0050.1 1.07405e-4
MA0051.1 0.00159
MA0052.1 0.883
MA0055.1 0.184
MA0057.1 0.857
MA0058.1 0.978
MA0059.1 0.404
MA0060.1 0.176
MA0061.1 0.00111
MA0062.2 4.31936e-20
MA0065.2 0.169
MA0066.1 0.218
MA0067.1 0.00127
MA0068.1 0.187
MA0069.1 0.554
MA0070.1 0.154
MA0071.1 0.244
MA0072.1 0.123
MA0073.1 0.539
MA0074.1 0.415
MA0076.1 1.70861e-5
MA0077.1 0.165
MA0078.1 0.91
MA0079.2 0.49
MA0080.2 1.21408e-15
MA0081.1 1.26927e-4
MA0083.1 0.313
MA0084.1 0.681
MA0087.1 0.348
MA0088.1 0.626
MA0090.1 0.0423
MA0091.1 0.956
MA0092.1 0.649
MA0093.1 0.729
MA0099.2 2.93304e-4
MA0100.1 0.0468
MA0101.1 0.0027
MA0102.2 9.30247e-10
MA0103.1 0.843
MA0104.2 0.0787
MA0105.1 8.64534e-6
MA0106.1 0.97
MA0107.1 8.55053e-4
MA0108.2 0.324
MA0111.1 0.675
MA0112.2 8.86788e-4
MA0113.1 0.865
MA0114.1 0.902
MA0115.1 0.524
MA0116.1 9.48156e-4
MA0117.1 0.0282
MA0119.1 0.696
MA0122.1 0.716
MA0124.1 0.764
MA0125.1 0.0231
MA0131.1 0.726
MA0135.1 0.729
MA0136.1 3.99908e-31
MA0137.2 0.184
MA0138.2 0.113
MA0139.1 0.705
MA0140.1 0.987
MA0141.1 0.361
MA0142.1 0.184
MA0143.1 0.144
MA0144.1 0.106
MA0145.1 0.206
MA0146.1 0.0827
MA0147.1 0.0504
MA0148.1 0.174
MA0149.1 0.514
MA0150.1 1.03704e-7
MA0152.1 0.421
MA0153.1 0.0223
MA0154.1 0.0488
MA0155.1 0.754
MA0156.1 1.62448e-28
MA0157.1 0.0996
MA0159.1 0.00871
MA0160.1 0.216
MA0162.1 0.582
MA0163.1 0.0379
MA0164.1 0.699
MA0258.1 0.0126
MA0259.1 0.409



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: CNhs12540

Novel motif P-value
1 0.211
10 0.054
100 0.71
101 0.676
102 0.688
103 0.293
104 0.611
105 0.386
106 0.0272
107 0.753
108 0.984
109 0.0969
11 0.116
110 0.22
111 0.599
112 0.0554
113 0.91
114 0.114
115 0.995
116 0.666
117 8.93524e-4
118 0.474
119 0.558
12 0.425
120 0.0785
121 0.444
122 0.446
123 0.218
124 0.422
125 0.184
126 0.456
127 0.323
128 0.0578
129 0.446
13 0.0692
130 0.415
131 0.84
132 0.96
133 0.0227
134 0.863
135 0.471
136 0.365
137 0.0315
138 0.401
139 0.0507
14 0.425
140 0.316
141 0.696
142 0.00104
143 0.00186
144 0.651
145 0.146
146 0.967
147 0.736
148 0.14
149 0.964
15 0.0576
150 0.347
151 0.143
152 0.226
153 0.252
154 0.93
155 0.717
156 0.465
157 0.734
158 0.013
159 0.526
160 0.555
161 0.194
162 0.506
163 0.164
164 0.0627
165 0.198
166 0.636
167 0.994
168 0.156
169 0.0049
17 0.271
18 0.184
19 0.492
2 0.287
20 0.0481
21 0.639
22 0.358
23 0.0997
24 0.204
25 0.29
26 0.13
27 0.534
28 0.0861
29 0.0487
3 0.099
30 0.392
31 0.755
32 0.917
33 0.226
34 0.782
35 0.621
36 0.127
37 0.0609
38 0.377
39 0.78
4 0.523
40 0.21
41 0.00824
42 0.282
43 0.136
44 0.914
45 0.867
46 0.387
47 0.401
48 0.283
49 0.117
5 0.139
50 0.702
51 0.836
52 0.949
53 0.663
54 0.655
55 0.598
56 0.253
57 0.93
58 0.196
59 0.62
6 0.819
60 0.226
61 0.443
62 0.106
63 0.735
64 0.669
65 0.29
66 0.539
67 0.3
68 0.935
69 0.49
7 0.186
70 0.0682
71 0.0394
72 0.307
73 0.0378
74 0.0571
75 0.00665
76 0.21
77 0.925
78 0.185
79 0.744
8 0.554
80 0.0834
81 0.47
82 0.362
83 0.187
84 0.976
85 0.219
86 0.08
87 0.207
88 0.525
89 0.954
9 0.514
90 0.0873
91 0.515
92 0.48
93 0.0874
94 0.136
95 0.0213
96 0.821
97 0.867
98 0.26
99 0.0871



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: CNhs12540


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)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (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

NA