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FF:11778-124A5

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Name:CD41+ megakaryocyte cancer, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs13506
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 number3LL-4
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005119
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13506 CAGE DRX008799 DRR009671
Accession ID Mm9

Library idBAMCTSS
CNhs13506 DRZ001096 DRZ002481
Accession ID Mm10

Library idBAMCTSS
CNhs13506 DRZ012446 DRZ013831
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sample
Ranked 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 sample
Ranked 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

CNhs13506

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0436
1001 -0.0749
1002 -0.116
1003 -0.102
1004 0
1005 -0.0389
1006 -0.235
1007 -0.318
1008 0
1009 -0.19
101 0.0256
1010 0
1011 0
1012 0
1013 -0.108
1014 -0.0874
1015 -0.222
1016 -0.594
1017 0
1018 0
1019 0
102 0
1020 0.386
1021 0.38
1022 -0.16
1023 0
1024 -0.307
1025 -0.0611
1026 0
1027 -0.048
1028 0
1029 -0.115
103 -0.0887
1030 0
1031 -0.911
1032 -0.184
1033 -0.0752
1034 0
1035 0
1036 0.47
1037 0
1038 -0.475
1039 -0.348
104 0
1040 -0.718
1041 0



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs13506
Jaspar motif P-value
MA0002.2 0.0237
MA0003.1 0.344
MA0004.1 0.5
MA0006.1 0.757
MA0007.1 0.847
MA0009.1 0.538
MA0014.1 0.924
MA0017.1 0.176
MA0018.2 0.306
MA0019.1 0.521
MA0024.1 2.21887e-8
MA0025.1 0.246
MA0027.1 0.566
MA0028.1 0.0289
MA0029.1 0.485
MA0030.1 0.366
MA0031.1 0.837
MA0035.2 1.9254e-5
MA0038.1 0.986
MA0039.2 0.995
MA0040.1 0.212
MA0041.1 0.758
MA0042.1 0.63
MA0043.1 0.132
MA0046.1 4.04355e-5
MA0047.2 0.974
MA0048.1 0.0963
MA0050.1 0.189
MA0051.1 0.257
MA0052.1 9.70639e-5
MA0055.1 0.0287
MA0057.1 0.661
MA0058.1 0.5
MA0059.1 0.0616
MA0060.1 0.0132
MA0061.1 0.0585
MA0062.2 0.00168
MA0065.2 0.0788
MA0066.1 0.105
MA0067.1 0.64
MA0068.1 0.31
MA0069.1 0.356
MA0070.1 0.291
MA0071.1 0.437
MA0072.1 0.814
MA0073.1 0.954
MA0074.1 0.688
MA0076.1 0.0925
MA0077.1 0.465
MA0078.1 0.831
MA0079.2 0.0186
MA0080.2 4.42372e-4
MA0081.1 0.47
MA0083.1 0.0122
MA0084.1 0.531
MA0087.1 0.214
MA0088.1 0.0793
MA0090.1 0.0975
MA0091.1 0.113
MA0092.1 0.84
MA0093.1 0.591
MA0099.2 0.616
MA0100.1 0.00618
MA0101.1 0.144
MA0102.2 0.833
MA0103.1 0.611
MA0104.2 0.203
MA0105.1 1.1806e-4
MA0106.1 0.365
MA0107.1 0.337
MA0108.2 0.0224
MA0111.1 0.916
MA0112.2 0.0152
MA0113.1 0.37
MA0114.1 0.341
MA0115.1 0.305
MA0116.1 0.00578
MA0117.1 0.542
MA0119.1 0.259
MA0122.1 0.45
MA0124.1 0.973
MA0125.1 0.063
MA0131.1 0.494
MA0135.1 0.298
MA0136.1 0.00835
MA0137.2 0.746
MA0138.2 0.0546
MA0139.1 0.357
MA0140.1 1.29776e-25
MA0141.1 0.0409
MA0142.1 0.301
MA0143.1 0.295
MA0144.1 0.856
MA0145.1 0.714
MA0146.1 0.306
MA0147.1 0.123
MA0148.1 0.709
MA0149.1 0.0187
MA0150.1 0.00424
MA0152.1 0.181
MA0153.1 0.0101
MA0154.1 0.0441
MA0155.1 0.418
MA0156.1 0.0239
MA0157.1 0.931
MA0159.1 0.0234
MA0160.1 0.264
MA0162.1 0.389
MA0163.1 3.12106e-4
MA0164.1 0.274
MA0258.1 0.0651
MA0259.1 0.409



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs13506
Novel motif P-value
1 0.0728
10 0.022
100 0.344
101 0.799
102 0.71
103 0.00572
104 0.922
105 0.799
106 0.456
107 0.833
108 0.987
109 0.0555
11 0.154
110 0.0766
111 0.034
112 0.0277
113 0.743
114 0.307
115 0.95
116 0.635
117 7.41646e-4
118 0.112
119 0.372
12 0.867
120 0.981
121 0.311
122 0.662
123 0.273
124 0.239
125 0.091
126 0.199
127 0.334
128 0.499
129 0.407
13 0.00899
130 0.66
131 0.657
132 0.232
133 0.762
134 0.136
135 0.29
136 0.878
137 0.362
138 0.61
139 0.467
14 0.889
140 0.408
141 0.816
142 0.362
143 0.309
144 0.985
145 0.0313
146 0.962
147 0.839
148 0.488
149 0.675
15 0.0535
150 0.34
151 0.536
152 0.334
153 0.891
154 0.758
155 0.191
156 4.86729e-82
157 0.901
158 0.0337
159 0.572
160 0.623
161 0.0466
162 0.824
163 0.496
164 0.017
165 0.48
166 0.251
167 0.0283
168 0.875
169 0.36
17 0.436
18 0.0771
19 0.734
2 0.208
20 0.0191
21 0.284
22 0.862
23 0.22
24 0.638
25 0.213
26 0.00343
27 0.828
28 0.418
29 0.00632
3 0.0557
30 0.515
31 0.73
32 0.709
33 0.11
34 0.668
35 0.394
36 0.0171
37 0.151
38 0.589
39 0.952
4 0.881
40 0.124
41 0.314
42 0.117
43 0.198
44 0.471
45 0.5
46 0.139
47 0.173
48 0.313
49 0.0937
5 0.00553
50 0.834
51 0.719
52 0.839
53 0.525
54 0.728
55 0.0747
56 0.664
57 0.167
58 0.485
59 0.455
6 0.702
60 0.493
61 0.553
62 0.177
63 0.564
64 0.614
65 0.698
66 0.189
67 0.337
68 0.279
69 0.926
7 0.0756
70 0.128
71 0.0129
72 0.355
73 0.313
74 0.566
75 0.0194
76 0.123
77 0.993
78 0.0472
79 0.618
8 0.0193
80 0.0728
81 0.607
82 0.555
83 0.379
84 0.875
85 0.577
86 0.542
87 0.691
88 0.741
89 0.611
9 0.939
90 0.0466
91 0.181
92 0.478
93 0.572
94 0.188
95 0.135
96 0.163
97 0.975
98 0.548
99 0.488



de novo motifs identified by HOMER in promoters active in this sample
Summary:The result of HOMER in this sample is shown.
Analyst:NA

library id: CNhs13506


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)
0000003 (native cell)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000556 (megakaryocyte)
0002027 (CD9-positive, CD41-positive megakaryocyte cell)

DOID: Disease
4 (disease)
162 (cancer)
14566 (disease of cellular proliferation)

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)
0011131 (mouse CD41-positive megakaryocyte cancer 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)
CL:0002006 (Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell)