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FF:11777-124A4

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Name:CD41+ megakaryocyte control, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs13214
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-2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005393
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13214 CAGE DRX008801 DRR009673
Accession ID Mm9

Library idBAMCTSS
CNhs13214 DRZ001098 DRZ002483
Accession ID Mm10

Library idBAMCTSS
CNhs13214 DRZ012448 DRZ013833
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

CNhs13214

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.00757
1001 --0.0631
1002 --0.116
1003 --0.175
1004 0
1005 0.0558
1006 --0.143
1007 --0.164
1008 0
1009 --0.19
101 0.157
1010 0
1011 0.0697
1012 0.00527
1013 --0.161
1014 --0.0874
1015 --0.143
1016 --0.594
1017 0
1018 0
1019 0
102 0.15
1020 0.105
1021 0.192
1022 --0.136
1023 0.0558
1024 --0.14
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.121
103 --0.0887
1030 0.504
1031 --0.855
1032 --0.599
1033 0.0455
1034 0
1035 0
1036 0.256
1037 0
1038 --0.203
1039 --0.0349
104 0
1040 --0.121
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: CNhs13214

Jaspar motif P-value
MA0002.2 8.7005e-6
MA0003.1 0.359
MA0004.1 0.123
MA0006.1 0.762
MA0007.1 0.854
MA0009.1 0.704
MA0014.1 0.784
MA0017.1 0.402
MA0018.2 0.896
MA0019.1 0.351
MA0024.1 0.992
MA0025.1 0.197
MA0027.1 0.683
MA0028.1 8.50536e-6
MA0029.1 0.217
MA0030.1 0.213
MA0031.1 0.738
MA0035.2 0.792
MA0038.1 0.492
MA0039.2 0.764
MA0040.1 0.627
MA0041.1 0.105
MA0042.1 0.676
MA0043.1 0.337
MA0046.1 8.27038e-10
MA0047.2 0.808
MA0048.1 0.417
MA0050.1 5.91297e-13
MA0051.1 1.34668e-7
MA0052.1 0.0095
MA0055.1 0.579
MA0057.1 0.945
MA0058.1 0.15
MA0059.1 0.0437
MA0060.1 0.0139
MA0061.1 8.62155e-7
MA0062.2 2.60718e-17
MA0065.2 0.332
MA0066.1 0.0299
MA0067.1 0.267
MA0068.1 0.0176
MA0069.1 0.428
MA0070.1 0.469
MA0071.1 0.595
MA0072.1 0.433
MA0073.1 0.629
MA0074.1 0.545
MA0076.1 1.27376e-6
MA0077.1 0.174
MA0078.1 0.78
MA0079.2 0.0637
MA0080.2 4.83288e-14
MA0081.1 9.56359e-4
MA0083.1 0.0254
MA0084.1 0.817
MA0087.1 0.85
MA0088.1 0.71
MA0090.1 0.00802
MA0091.1 0.341
MA0092.1 0.913
MA0093.1 0.15
MA0099.2 0.2
MA0100.1 0.345
MA0101.1 8.96315e-7
MA0102.2 0.742
MA0103.1 0.136
MA0104.2 0.194
MA0105.1 2.40151e-8
MA0106.1 0.92
MA0107.1 8.54509e-7
MA0108.2 6.07766e-6
MA0111.1 0.507
MA0112.2 0.0102
MA0113.1 0.336
MA0114.1 0.572
MA0115.1 0.874
MA0116.1 6.64422e-4
MA0117.1 0.704
MA0119.1 0.468
MA0122.1 0.954
MA0124.1 0.681
MA0125.1 0.0428
MA0131.1 0.427
MA0135.1 0.781
MA0136.1 3.73966e-19
MA0137.2 0.373
MA0138.2 0.0631
MA0139.1 0.148
MA0140.1 0.419
MA0141.1 0.771
MA0142.1 1.84672e-4
MA0143.1 0.15
MA0144.1 0.551
MA0145.1 0.485
MA0146.1 0.334
MA0147.1 0.135
MA0148.1 0.703
MA0149.1 0.138
MA0150.1 0.688
MA0152.1 0.341
MA0153.1 2.49962e-7
MA0154.1 0.00164
MA0155.1 0.671
MA0156.1 7.44747e-23
MA0157.1 0.348
MA0159.1 0.0181
MA0160.1 0.825
MA0162.1 0.581
MA0163.1 3.8006e-4
MA0164.1 0.579
MA0258.1 0.0176
MA0259.1 0.45



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: CNhs13214

Novel motif P-value
1 0.146
10 0.0276
100 0.83
101 0.932
102 0.575
103 0.09
104 0.808
105 0.802
106 0.364
107 0.796
108 0.488
109 0.159
11 0.194
110 0.0695
111 0.119
112 0.0442
113 0.215
114 0.202
115 0.629
116 0.795
117 6.18812e-4
118 0.0876
119 0.561
12 0.483
120 0.523
121 0.412
122 0.866
123 0.726
124 0.981
125 0.111
126 0.247
127 0.385
128 0.19
129 0.101
13 0.0749
130 0.966
131 0.637
132 0.715
133 0.844
134 0.924
135 0.899
136 0.968
137 0.134
138 0.667
139 0.292
14 0.987
140 0.705
141 0.129
142 0.799
143 0.019
144 0.406
145 0.143
146 0.841
147 0.852
148 0.103
149 0.564
15 0.098
150 0.335
151 0.165
152 0.632
153 0.226
154 0.384
155 0.246
156 1.55351e-23
157 0.912
158 0.13
159 0.665
160 0.973
161 0.0349
162 0.357
163 0.255
164 0.0951
165 0.378
166 0.518
167 0.124
168 0.943
169 0.113
17 0.54
18 0.302
19 0.932
2 0.121
20 0.0276
21 0.332
22 0.866
23 0.326
24 0.457
25 0.151
26 0.0243
27 0.708
28 0.21
29 0.019
3 0.0557
30 0.196
31 0.974
32 0.649
33 0.196
34 0.638
35 0.1
36 0.0535
37 0.0827
38 0.781
39 0.463
4 0.751
40 0.222
41 0.431
42 0.131
43 0.142
44 0.306
45 0.684
46 0.178
47 0.266
48 0.208
49 0.113
5 0.034
50 0.565
51 0.895
52 0.299
53 0.404
54 0.791
55 0.506
56 0.779
57 0.73
58 0.0976
59 0.398
6 0.629
60 0.736
61 0.0915
62 0.0481
63 0.801
64 0.689
65 0.828
66 0.927
67 0.786
68 0.0816
69 0.885
7 0.19
70 0.0207
71 0.0388
72 0.35
73 0.103
74 0.974
75 0.00388
76 0.0124
77 0.334
78 0.0694
79 0.789
8 0.0688
80 0.0175
81 0.548
82 0.197
83 0.129
84 0.519
85 0.608
86 0.172
87 0.572
88 0.495
89 0.645
9 0.946
90 0.022
91 0.598
92 0.264
93 0.252
94 0.201
95 0.136
96 0.307
97 0.799
98 0.175
99 0.338



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: CNhs13214


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)


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