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FF:12122-128C7

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Name:common myeloid progenitor CMP, biol_rep1
Species:Mouse (Mus musculus)
Library ID:CNhs12550
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
strainC57BL/8J
tissuebone marrow
dev stageNA
sexmale
age9-10weeks
cell typecommon myeloid progenitor
cell lineNA
companyNA
collaborationKitamura/Nakahara
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberrep1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005978
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12550 CAGE DRX008779 DRR009651
Accession ID Mm9

Library idBAMCTSS
CNhs12550 DRZ001076 DRZ002461
Accession ID Mm10

Library idBAMCTSS
CNhs12550 DRZ012426 DRZ013811
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
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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

CNhs12550

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0109
1001 --0.0749
1002 --0.116
1003 --0.102
1004 0
1005 0.0491
1006 --0.159
1007 --0.384
1008 0
1009 --0.126
101 0.274
1010 0
1011 0
1012 0
1013 --0.122
1014 --0.0874
1015 --0.0109
1016 --0.424
1017 0
1018 0
1019 0
102 0.0933
1020 0
1021 0
1022 --0.124
1023 0.552
1024 0.623
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.128
103 --0.0887
1030 0
1031 --0.911
1032 --0.427
1033 0.0491
1034 0
1035 0
1036 0.527
1037 0
1038 --0.351
1039 --0.0122
104 0
1040 --0.216
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: CNhs12550

Jaspar motif P-value
MA0002.2 4.13101e-6
MA0003.1 0.519
MA0004.1 0.102
MA0006.1 0.892
MA0007.1 0.622
MA0009.1 0.303
MA0014.1 0.64
MA0017.1 0.856
MA0018.2 2.20543e-7
MA0019.1 0.859
MA0024.1 2.15406e-5
MA0025.1 0.152
MA0027.1 0.275
MA0028.1 1.2842e-7
MA0029.1 0.205
MA0030.1 0.462
MA0031.1 0.384
MA0035.2 0.855
MA0038.1 0.0101
MA0039.2 0.858
MA0040.1 0.0441
MA0041.1 0.0925
MA0042.1 0.328
MA0043.1 1.04618e-5
MA0046.1 4.79814e-15
MA0047.2 0.923
MA0048.1 0.00546
MA0050.1 2.35473e-8
MA0051.1 4.88554e-5
MA0052.1 0.734
MA0055.1 0.00547
MA0057.1 0.747
MA0058.1 0.0346
MA0059.1 0.00179
MA0060.1 0.694
MA0061.1 6.62776e-8
MA0062.2 3.5711e-17
MA0065.2 0.38
MA0066.1 0.253
MA0067.1 0.00253
MA0068.1 0.00638
MA0069.1 0.537
MA0070.1 0.266
MA0071.1 0.346
MA0072.1 0.848
MA0073.1 0.682
MA0074.1 0.254
MA0076.1 3.89232e-8
MA0077.1 0.396
MA0078.1 0.595
MA0079.2 0.0606
MA0080.2 1.07993e-12
MA0081.1 4.06049e-5
MA0083.1 0.0562
MA0084.1 0.162
MA0087.1 0.659
MA0088.1 0.481
MA0090.1 0.0106
MA0091.1 0.99
MA0092.1 0.516
MA0093.1 0.0872
MA0099.2 3.56343e-16
MA0100.1 6.01054e-4
MA0101.1 2.56929e-12
MA0102.2 0.00116
MA0103.1 0.193
MA0104.2 0.0269
MA0105.1 5.21834e-7
MA0106.1 0.401
MA0107.1 1.03351e-11
MA0108.2 0.259
MA0111.1 0.975
MA0112.2 0.117
MA0113.1 0.624
MA0114.1 0.277
MA0115.1 0.923
MA0116.1 0.00257
MA0117.1 0.117
MA0119.1 0.312
MA0122.1 0.146
MA0124.1 0.813
MA0125.1 0.0494
MA0131.1 0.0744
MA0135.1 0.0312
MA0136.1 1.92411e-28
MA0137.2 0.0114
MA0138.2 5.66019e-5
MA0139.1 0.582
MA0140.1 0.476
MA0141.1 0.955
MA0142.1 0.824
MA0143.1 0.197
MA0144.1 0.168
MA0145.1 0.43
MA0146.1 0.192
MA0147.1 0.0158
MA0148.1 0.88
MA0149.1 0.169
MA0150.1 4.63556e-5
MA0152.1 0.972
MA0153.1 1.23413e-4
MA0154.1 0.39
MA0155.1 0.659
MA0156.1 2.53741e-22
MA0157.1 0.345
MA0159.1 0.0982
MA0160.1 0.606
MA0162.1 0.483
MA0163.1 8.35981e-5
MA0164.1 0.541
MA0258.1 0.0979
MA0259.1 0.214



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: CNhs12550

Novel motif P-value
1 0.497
10 0.0484
100 0.714
101 0.676
102 0.666
103 0.616
104 0.735
105 0.409
106 0.107
107 0.996
108 0.623
109 0.14
11 0.316
110 0.199
111 0.427
112 0.188
113 0.569
114 0.331
115 0.654
116 0.759
117 2.04396e-4
118 0.219
119 0.731
12 0.84
120 0.361
121 0.285
122 0.347
123 0.166
124 0.348
125 0.549
126 0.445
127 0.741
128 0.177
129 0.582
13 8.3281e-4
130 0.537
131 0.361
132 0.403
133 0.577
134 0.868
135 0.528
136 0.202
137 0.00546
138 0.791
139 0.719
14 0.504
140 0.895
141 0.515
142 0.915
143 0.132
144 0.913
145 0.103
146 0.514
147 0.578
148 0.17
149 0.124
15 0.0423
150 0.516
151 0.852
152 0.661
153 0.351
154 0.409
155 0.755
156 0.0983
157 0.875
158 0.0661
159 0.535
160 0.478
161 0.217
162 0.285
163 0.215
164 0.0201
165 0.106
166 0.198
167 0.258
168 0.512
169 0.0938
17 0.803
18 0.462
19 0.478
2 0.0591
20 0.0127
21 0.494
22 0.901
23 0.203
24 0.0334
25 0.344
26 0.00346
27 0.348
28 0.736
29 0.0263
3 0.199
30 0.124
31 0.568
32 0.236
33 0.107
34 0.553
35 0.566
36 0.0629
37 0.0469
38 0.587
39 0.605
4 0.487
40 0.19
41 0.066
42 0.46
43 0.639
44 0.575
45 0.647
46 0.389
47 0.875
48 0.396
49 0.545
5 0.568
50 0.653
51 0.877
52 0.534
53 0.625
54 0.649
55 0.593
56 0.855
57 0.65
58 0.265
59 0.994
6 0.83
60 0.505
61 0.271
62 0.224
63 0.913
64 0.889
65 0.886
66 0.314
67 0.347
68 0.558
69 0.808
7 0.361
70 0.178
71 0.0197
72 0.18
73 0.0491
74 0.926
75 0.00611
76 0.0347
77 0.0728
78 0.127
79 0.712
8 0.181
80 0.872
81 0.892
82 0.251
83 0.0526
84 0.33
85 0.433
86 0.257
87 0.0372
88 0.519
89 0.521
9 0.829
90 0.0395
91 0.789
92 0.943
93 0.132
94 0.779
95 0.00223
96 0.938
97 0.883
98 0.716
99 0.194



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: CNhs12550


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)
0002032 (hematopoietic oligopotent progenitor cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000049 (common myeloid progenitor)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000041 (common myeloid progenitor 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:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)