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FF:11776-124A3

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Name:CD41+ megakaryocyte cancer, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs13213
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-2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005513
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13213 CAGE DRX008798 DRR009670
Accession ID Mm9

Library idBAMCTSS
CNhs13213 DRZ001095 DRZ002480
Accession ID Mm10

Library idBAMCTSS
CNhs13213 DRZ012445 DRZ013830
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

CNhs13213

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.00223
1001 --0.0749
1002 --0.116
1003 --0.105
1004 0
1005 0.0113
1006 --0.143
1007 --0.0726
1008 0
1009 --0.19
101 0.151
1010 0
1011 0.00595
1012 0
1013 --0.145
1014 --0.0874
1015 --0.167
1016 --0.421
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.393
1022 --0.237
1023 0
1024 --0.142
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.103
103 --0.0848
1030 0.148
1031 --0.831
1032 --0.397
1033 0
1034 0
1035 0
1036 0.491
1037 0
1038 --0.433
1039 --0.268
104 0
1040 --0.362
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: CNhs13213

Jaspar motif P-value
MA0002.2 0.00248
MA0003.1 0.37
MA0004.1 0.349
MA0006.1 0.661
MA0007.1 0.969
MA0009.1 0.501
MA0014.1 0.729
MA0017.1 0.24
MA0018.2 0.279
MA0019.1 0.559
MA0024.1 7.79132e-6
MA0025.1 0.339
MA0027.1 0.813
MA0028.1 0.00192
MA0029.1 0.579
MA0030.1 0.269
MA0031.1 0.825
MA0035.2 0.00119
MA0038.1 0.696
MA0039.2 0.659
MA0040.1 0.5
MA0041.1 0.54
MA0042.1 0.906
MA0043.1 0.117
MA0046.1 1.74447e-5
MA0047.2 0.879
MA0048.1 0.18
MA0050.1 4.11291e-4
MA0051.1 0.00337
MA0052.1 4.82069e-4
MA0055.1 0.066
MA0057.1 0.782
MA0058.1 0.361
MA0059.1 0.0654
MA0060.1 0.0699
MA0061.1 0.00451
MA0062.2 5.53273e-7
MA0065.2 0.21
MA0066.1 0.116
MA0067.1 0.615
MA0068.1 0.789
MA0069.1 0.558
MA0070.1 0.389
MA0071.1 0.762
MA0072.1 0.831
MA0073.1 0.921
MA0074.1 0.847
MA0076.1 0.0055
MA0077.1 0.382
MA0078.1 0.871
MA0079.2 0.0284
MA0080.2 1.39677e-9
MA0081.1 0.0426
MA0083.1 0.0169
MA0084.1 0.656
MA0087.1 0.287
MA0088.1 0.111
MA0090.1 0.0362
MA0091.1 0.304
MA0092.1 0.956
MA0093.1 0.396
MA0099.2 0.873
MA0100.1 0.0397
MA0101.1 0.00889
MA0102.2 0.91
MA0103.1 0.753
MA0104.2 0.203
MA0105.1 3.24651e-5
MA0106.1 0.392
MA0107.1 0.0247
MA0108.2 0.0208
MA0111.1 0.836
MA0112.2 0.0103
MA0113.1 0.344
MA0114.1 0.638
MA0115.1 0.794
MA0116.1 0.00428
MA0117.1 0.615
MA0119.1 0.38
MA0122.1 0.828
MA0124.1 0.85
MA0125.1 0.0722
MA0131.1 0.415
MA0135.1 0.535
MA0136.1 2.10337e-6
MA0137.2 0.453
MA0138.2 0.0264
MA0139.1 0.378
MA0140.1 6.42153e-24
MA0141.1 0.377
MA0142.1 0.0789
MA0143.1 0.174
MA0144.1 0.585
MA0145.1 0.638
MA0146.1 0.421
MA0147.1 0.145
MA0148.1 0.987
MA0149.1 0.055
MA0150.1 0.0168
MA0152.1 0.126
MA0153.1 9.39374e-4
MA0154.1 0.0238
MA0155.1 0.314
MA0156.1 2.47307e-7
MA0157.1 0.951
MA0159.1 0.068
MA0160.1 0.743
MA0162.1 0.367
MA0163.1 9.11967e-4
MA0164.1 0.413
MA0258.1 0.0676
MA0259.1 0.252



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: CNhs13213

Novel motif P-value
1 0.096
10 0.0223
100 0.454
101 0.794
102 0.79
103 0.0314
104 0.931
105 0.751
106 0.36
107 0.868
108 0.664
109 0.07
11 0.168
110 0.0505
111 0.0382
112 0.0374
113 0.728
114 0.717
115 0.874
116 0.868
117 6.14439e-4
118 0.121
119 0.575
12 0.685
120 0.953
121 0.211
122 0.997
123 0.244
124 0.625
125 0.214
126 0.291
127 0.303
128 0.463
129 0.189
13 0.00676
130 0.885
131 0.686
132 0.173
133 0.614
134 0.22
135 0.462
136 0.981
137 0.349
138 0.615
139 0.498
14 0.86
140 0.625
141 0.811
142 0.685
143 0.182
144 0.937
145 0.0259
146 0.866
147 0.981
148 0.104
149 0.417
15 0.053
150 0.362
151 0.322
152 0.404
153 0.602
154 0.664
155 0.247
156 1.12984e-116
157 0.755
158 0.0634
159 0.719
160 0.662
161 0.041
162 0.664
163 0.609
164 0.047
165 0.336
166 0.268
167 0.106
168 0.651
169 0.256
17 0.443
18 0.21
19 0.874
2 0.156
20 0.0186
21 0.385
22 0.894
23 0.119
24 0.626
25 0.194
26 0.00789
27 0.765
28 0.333
29 0.0159
3 0.0395
30 0.507
31 0.88
32 0.927
33 0.207
34 0.863
35 0.408
36 0.0305
37 0.172
38 0.521
39 0.734
4 0.875
40 0.156
41 0.534
42 0.0798
43 0.16
44 0.554
45 0.595
46 0.137
47 0.138
48 0.227
49 0.101
5 0.00292
50 0.856
51 0.767
52 0.856
53 0.528
54 0.816
55 0.187
56 0.665
57 0.296
58 0.38
59 0.543
6 0.766
60 0.431
61 0.387
62 0.155
63 0.599
64 0.613
65 0.544
66 0.205
67 0.447
68 0.284
69 0.944
7 0.0685
70 0.175
71 0.0144
72 0.259
73 0.287
74 0.795
75 0.0115
76 0.0846
77 0.568
78 0.0369
79 0.692
8 0.0264
80 0.0343
81 0.507
82 0.695
83 0.16
84 0.453
85 0.574
86 0.474
87 0.68
88 0.565
89 0.7
9 0.983
90 0.0741
91 0.332
92 0.453
93 0.615
94 0.159
95 0.101
96 0.284
97 0.869
98 0.265
99 0.533



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: CNhs13213


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)
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)