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FF:11779-124A6

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Name:CD41+ megakaryocyte control, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs13201
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 typemegakaryocyte
cell lineNA
companyNA
collaborationHozumi Motohashi (Tohoku University Graduate School of Medicine)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberPBS-4
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005174
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13201 CAGE DRX008802 DRR009674
Accession ID Mm9

Library idBAMCTSS
CNhs13201 DRZ001099 DRZ002484
Accession ID Mm10

Library idBAMCTSS
CNhs13201 DRZ012449 DRZ013834
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

CNhs13201

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0631
1002 --0.116
1003 --0.175
1004 0
1005 0.0428
1006 --0.143
1007 --0.255
1008 0
1009 --0.19
101 0.0965
1010 0
1011 0.154
1012 0
1013 --0.278
1014 --0.0874
1015 --0.036
1016 --0.594
1017 0
1018 0
1019 0
102 0.154
1020 0.237
1021 0.267
1022 --0.187
1023 0
1024 --0.14
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.0989
103 --0.0887
1030 0.357
1031 --0.879
1032 --0.572
1033 0
1034 0.154
1035 0
1036 0.255
1037 0
1038 --0.283
1039 0.00654
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: CNhs13201

Jaspar motif P-value
MA0002.2 1.73444e-5
MA0003.1 0.47
MA0004.1 0.154
MA0006.1 0.774
MA0007.1 0.742
MA0009.1 0.918
MA0014.1 0.648
MA0017.1 0.235
MA0018.2 0.41
MA0019.1 0.307
MA0024.1 0.656
MA0025.1 0.417
MA0027.1 0.672
MA0028.1 6.58487e-5
MA0029.1 0.217
MA0030.1 0.224
MA0031.1 0.763
MA0035.2 0.719
MA0038.1 0.55
MA0039.2 0.997
MA0040.1 0.602
MA0041.1 0.165
MA0042.1 0.793
MA0043.1 0.645
MA0046.1 8.9154e-10
MA0047.2 0.982
MA0048.1 0.423
MA0050.1 1.54385e-11
MA0051.1 7.16199e-7
MA0052.1 0.0132
MA0055.1 0.302
MA0057.1 0.994
MA0058.1 0.163
MA0059.1 0.0454
MA0060.1 0.0912
MA0061.1 2.56501e-6
MA0062.2 1.91382e-14
MA0065.2 0.222
MA0066.1 0.0643
MA0067.1 0.328
MA0068.1 0.00972
MA0069.1 0.827
MA0070.1 0.487
MA0071.1 0.595
MA0072.1 0.684
MA0073.1 0.714
MA0074.1 0.582
MA0076.1 3.91176e-5
MA0077.1 0.177
MA0078.1 0.935
MA0079.2 0.0778
MA0080.2 7.36393e-14
MA0081.1 0.00109
MA0083.1 0.0297
MA0084.1 0.697
MA0087.1 0.711
MA0088.1 0.51
MA0090.1 0.018
MA0091.1 0.24
MA0092.1 0.883
MA0093.1 0.173
MA0099.2 0.372
MA0100.1 0.251
MA0101.1 3.92649e-6
MA0102.2 0.834
MA0103.1 0.208
MA0104.2 0.182
MA0105.1 2.6298e-8
MA0106.1 0.76
MA0107.1 4.50546e-6
MA0108.2 6.30819e-4
MA0111.1 0.537
MA0112.2 0.0122
MA0113.1 0.17
MA0114.1 1
MA0115.1 0.843
MA0116.1 0.00136
MA0117.1 0.74
MA0119.1 0.764
MA0122.1 0.862
MA0124.1 0.788
MA0125.1 0.0422
MA0131.1 0.428
MA0135.1 0.949
MA0136.1 1.31335e-17
MA0137.2 0.475
MA0138.2 0.0704
MA0139.1 0.137
MA0140.1 0.00736
MA0141.1 0.549
MA0142.1 1.74909e-4
MA0143.1 0.277
MA0144.1 0.632
MA0145.1 0.466
MA0146.1 0.378
MA0147.1 0.134
MA0148.1 0.841
MA0149.1 0.0691
MA0150.1 0.344
MA0152.1 0.263
MA0153.1 5.90707e-6
MA0154.1 0.0021
MA0155.1 0.645
MA0156.1 8.01576e-20
MA0157.1 0.526
MA0159.1 0.0121
MA0160.1 0.802
MA0162.1 0.549
MA0163.1 2.08077e-4
MA0164.1 0.466
MA0258.1 0.0334
MA0259.1 0.454



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: CNhs13201

Novel motif P-value
1 0.12
10 0.021
100 0.804
101 0.999
102 0.769
103 0.0867
104 0.777
105 0.72
106 0.304
107 0.981
108 0.527
109 0.115
11 0.142
110 0.0414
111 0.194
112 0.0431
113 0.312
114 0.378
115 0.802
116 0.881
117 5.73887e-4
118 0.0997
119 0.512
12 0.588
120 0.647
121 0.432
122 0.962
123 0.715
124 0.805
125 0.117
126 0.202
127 0.488
128 0.168
129 0.213
13 0.0473
130 0.83
131 0.568
132 0.531
133 0.887
134 0.664
135 0.847
136 0.9
137 0.163
138 0.636
139 0.196
14 0.996
140 0.833
141 0.285
142 0.407
143 0.0261
144 0.494
145 0.0945
146 0.893
147 0.938
148 0.0965
149 0.486
15 0.0781
150 0.323
151 0.187
152 0.692
153 0.288
154 0.405
155 0.234
156 2.95064e-31
157 0.796
158 0.075
159 0.459
160 0.92
161 0.0621
162 0.283
163 0.358
164 0.123
165 0.293
166 0.481
167 0.196
168 0.907
169 0.099
17 0.437
18 0.214
19 0.796
2 0.103
20 0.0298
21 0.278
22 0.844
23 0.375
24 0.451
25 0.118
26 0.0163
27 0.742
28 0.28
29 0.00977
3 0.0509
30 0.248
31 0.99
32 0.992
33 0.145
34 0.715
35 0.104
36 0.0362
37 0.112
38 0.928
39 0.461
4 0.648
40 0.147
41 0.421
42 0.114
43 0.143
44 0.345
45 0.601
46 0.171
47 0.274
48 0.195
49 0.1
5 0.0388
50 0.7
51 0.908
52 0.391
53 0.549
54 0.875
55 0.46
56 0.643
57 0.561
58 0.146
59 0.327
6 0.713
60 0.637
61 0.0934
62 0.0553
63 0.689
64 0.579
65 0.869
66 0.978
67 0.739
68 0.0417
69 0.845
7 0.154
70 0.0151
71 0.0347
72 0.287
73 0.0932
74 0.959
75 0.00609
76 0.0231
77 0.348
78 0.0739
79 0.833
8 0.0661
80 0.0167
81 0.479
82 0.227
83 0.104
84 0.62
85 0.45
86 0.156
87 0.563
88 0.501
89 0.877
9 0.942
90 0.0149
91 0.509
92 0.263
93 0.248
94 0.161
95 0.181
96 0.33
97 0.832
98 0.223
99 0.339



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: CNhs13201


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)
0000763 (myeloid cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000556 (megakaryocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002371 (bone marrow)
0001474 (bone element)
0000479 (tissue)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0004765 (skeletal element)
0010317 (germ layer / neural crest derived structure)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0002390 (hematopoietic system)
0002193 (hemolymphoid system)
0002405 (immune system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000343 (control treatment sample)
0011468 (mouse CD41-positive megakaryocyte control 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)