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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005084
 
|DRA_sample_Accession=CAGE@SAMD00005084
|accession_numbers=CAGE;DRX008780;DRR009652;DRZ001077;DRZ002462
+
|accession_numbers=CAGE;DRX008780;DRR009652;DRZ001077;DRZ002462;DRZ012427;DRZ013812
 
|ancestors_in_anatomy_facet=
 
|ancestors_in_anatomy_facet=
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0002032,CL:0002371,CL:0000255,CL:0000049
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0002032,CL:0002371,CL:0000255,CL:0000049

Latest revision as of 12:34, 10 August 2017


Name:common myeloid progenitor CMP, biol_rep2
Species:Mouse (Mus musculus)
Library ID:CNhs12203
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 numberrep2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005084
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12203 CAGE DRX008780 DRR009652
Accession ID Mm9

Library idBAMCTSS
CNhs12203 DRZ001077 DRZ002462
Accession ID Mm10

Library idBAMCTSS
CNhs12203 DRZ012427 DRZ013812
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

CNhs12203

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0749
1002 --0.116
1003 --0.175
1004 0
1005 0.163
1006 --0.18
1007 --0.472
1008 0
1009 --0.0572
101 0.234
1010 0
1011 --0.133
1012 0
1013 --0.0822
1014 --0.0874
1015 0.0104
1016 --0.46
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 --0.198
1023 0.914
1024 0.409
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.176
103 --0.0887
1030 0
1031 --0.889
1032 --0.315
1033 0.204
1034 0
1035 0
1036 0.583
1037 0
1038 --0.519
1039 0.0382
104 0
1040 --0.22
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: CNhs12203

Jaspar motif P-value
MA0002.2 2.6399e-7
MA0003.1 0.987
MA0004.1 0.079
MA0006.1 0.889
MA0007.1 0.566
MA0009.1 0.951
MA0014.1 0.884
MA0017.1 0.227
MA0018.2 3.5854e-7
MA0019.1 0.887
MA0024.1 2.35336e-4
MA0025.1 0.0221
MA0027.1 0.602
MA0028.1 8.39657e-9
MA0029.1 0.206
MA0030.1 0.692
MA0031.1 0.255
MA0035.2 0.913
MA0038.1 0.0678
MA0039.2 0.857
MA0040.1 0.0209
MA0041.1 0.654
MA0042.1 0.797
MA0043.1 1.14945e-6
MA0046.1 7.70224e-11
MA0047.2 0.579
MA0048.1 0.01
MA0050.1 1.72402e-4
MA0051.1 0.00183
MA0052.1 0.184
MA0055.1 5.59975e-4
MA0057.1 0.656
MA0058.1 0.0285
MA0059.1 0.00412
MA0060.1 0.404
MA0061.1 1.26877e-6
MA0062.2 2.77349e-19
MA0065.2 0.0473
MA0066.1 0.139
MA0067.1 0.00939
MA0068.1 0.927
MA0069.1 0.582
MA0070.1 0.134
MA0071.1 0.164
MA0072.1 0.833
MA0073.1 0.665
MA0074.1 0.259
MA0076.1 4.90704e-10
MA0077.1 0.954
MA0078.1 0.326
MA0079.2 0.092
MA0080.2 1.90147e-12
MA0081.1 3.26091e-5
MA0083.1 0.0356
MA0084.1 0.169
MA0087.1 0.457
MA0088.1 0.248
MA0090.1 0.0127
MA0091.1 0.531
MA0092.1 0.554
MA0093.1 0.0668
MA0099.2 3.67506e-15
MA0100.1 1.6226e-4
MA0101.1 2.30999e-11
MA0102.2 1.23121e-4
MA0103.1 0.338
MA0104.2 0.0281
MA0105.1 3.37495e-7
MA0106.1 0.214
MA0107.1 2.01382e-10
MA0108.2 0.55
MA0111.1 0.894
MA0112.2 0.0614
MA0113.1 0.34
MA0114.1 0.942
MA0115.1 0.706
MA0116.1 0.00194
MA0117.1 0.12
MA0119.1 0.475
MA0122.1 0.147
MA0124.1 0.489
MA0125.1 0.0696
MA0131.1 0.0986
MA0135.1 0.311
MA0136.1 2.51879e-29
MA0137.2 6.05948e-4
MA0138.2 0.00364
MA0139.1 0.591
MA0140.1 0.569
MA0141.1 0.28
MA0142.1 0.914
MA0143.1 0.501
MA0144.1 0.0645
MA0145.1 0.998
MA0146.1 0.161
MA0147.1 0.0185
MA0148.1 0.968
MA0149.1 0.0877
MA0150.1 9.31657e-6
MA0152.1 0.999
MA0153.1 0.00271
MA0154.1 0.251
MA0155.1 0.724
MA0156.1 2.11871e-21
MA0157.1 0.231
MA0159.1 0.0258
MA0160.1 0.0381
MA0162.1 0.348
MA0163.1 1.62159e-6
MA0164.1 0.798
MA0258.1 0.122
MA0259.1 0.254



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: CNhs12203

Novel motif P-value
1 0.276
10 0.0611
100 0.886
101 0.958
102 0.811
103 0.136
104 0.569
105 0.6
106 0.15
107 0.634
108 0.702
109 0.0519
11 0.161
110 0.105
111 0.278
112 0.104
113 0.623
114 0.479
115 0.479
116 0.597
117 3.4265e-4
118 0.273
119 0.981
12 0.656
120 0.213
121 0.63
122 0.501
123 0.528
124 0.453
125 0.447
126 0.435
127 0.647
128 0.481
129 0.42
13 0.00416
130 0.965
131 0.624
132 0.326
133 0.159
134 0.518
135 0.778
136 0.231
137 0.0115
138 0.305
139 0.4
14 0.585
140 0.91
141 0.978
142 0.982
143 0.0435
144 0.872
145 0.132
146 0.906
147 0.768
148 0.404
149 0.29
15 0.0289
150 0.651
151 0.858
152 0.516
153 0.619
154 0.927
155 0.802
156 0.223
157 0.642
158 0.0224
159 0.624
160 0.751
161 0.0617
162 0.623
163 0.0929
164 0.0119
165 0.129
166 0.166
167 0.274
168 0.724
169 0.0149
17 0.458
18 0.394
19 0.614
2 0.153
20 0.0181
21 0.377
22 0.68
23 0.367
24 0.0355
25 0.268
26 0.00775
27 0.429
28 0.723
29 0.0149
3 0.114
30 0.258
31 0.722
32 0.595
33 0.0784
34 0.929
35 0.35
36 0.0309
37 0.0642
38 0.378
39 0.655
4 0.727
40 0.0683
41 0.0152
42 0.378
43 0.567
44 0.387
45 0.795
46 0.337
47 0.756
48 0.265
49 0.469
5 0.563
50 0.679
51 0.874
52 0.427
53 0.689
54 0.824
55 0.57
56 0.692
57 0.436
58 0.178
59 0.447
6 0.637
60 0.389
61 0.148
62 0.175
63 0.9
64 0.51
65 0.716
66 0.263
67 0.376
68 0.592
69 0.562
7 0.221
70 0.0857
71 0.0111
72 0.0932
73 0.0342
74 0.331
75 0.0103
76 0.13
77 0.284
78 0.193
79 0.734
8 0.0593
80 0.443
81 0.939
82 0.425
83 0.00824
84 0.995
85 0.757
86 0.22
87 0.0276
88 0.529
89 0.63
9 0.913
90 0.0321
91 0.931
92 0.696
93 0.0537
94 0.449
95 0.00154
96 0.931
97 0.898
98 0.268
99 0.334



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: CNhs12203


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)