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FF:12129-128D5

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Name:granulocyte macrophage progenitor GMP, biol_rep3
Species:Mouse (Mus musculus)
Library ID:CNhs11928
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 typegranulocyte macrophage progenitor
cell lineNA
companyNA
collaborationKitamura/Nakahara
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberrep3
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005059
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11928 CAGE DRX008861 DRR009733
Accession ID Mm9

Library idBAMCTSS
CNhs11928 DRZ001158 DRZ002543
Accession ID Mm10

Library idBAMCTSS
CNhs11928 DRZ012508 DRZ013893
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
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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

CNhs11928

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0749
1002 --0.116
1003 --0.0999
1004 0
1005 0.345
1006 --0.271
1007 --0.403
1008 0
1009 --0.179
101 0.232
1010 0
1011 0
1012 0
1013 0.115
1014 --0.0874
1015 --0.038
1016 --0.465
1017 0
1018 0
1019 0
102 0
1020 0
1021 0.0599
1022 --0.0704
1023 0.515
1024 0.244
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.176
103 --0.0887
1030 0
1031 --0.911
1032 --0.561
1033 0.0671
1034 0
1035 0
1036 0.442
1037 0
1038 --0.582
1039 --0.00482
104 0
1040 --0.268
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: CNhs11928

Jaspar motif P-value
MA0002.2 6.0637e-5
MA0003.1 0.548
MA0004.1 0.0743
MA0006.1 0.916
MA0007.1 0.613
MA0009.1 0.728
MA0014.1 0.801
MA0017.1 0.0832
MA0018.2 0.0123
MA0019.1 0.551
MA0024.1 0.00102
MA0025.1 0.0821
MA0027.1 0.739
MA0028.1 6.04536e-7
MA0029.1 0.455
MA0030.1 0.0583
MA0031.1 0.846
MA0035.2 0.876
MA0038.1 0.00621
MA0039.2 0.96
MA0040.1 0.481
MA0041.1 0.0731
MA0042.1 0.334
MA0043.1 3.71601e-4
MA0046.1 8.11007e-16
MA0047.2 0.969
MA0048.1 0.0104
MA0050.1 2.81403e-6
MA0051.1 0.00181
MA0052.1 0.037
MA0055.1 0.00451
MA0057.1 0.67
MA0058.1 0.0342
MA0059.1 0.00122
MA0060.1 0.981
MA0061.1 0.00128
MA0062.2 5.83428e-14
MA0065.2 0.0999
MA0066.1 0.241
MA0067.1 0.0385
MA0068.1 0.0768
MA0069.1 0.225
MA0070.1 0.086
MA0071.1 0.109
MA0072.1 0.562
MA0073.1 0.857
MA0074.1 0.134
MA0076.1 3.11674e-7
MA0077.1 0.678
MA0078.1 0.384
MA0079.2 0.0673
MA0080.2 4.02874e-12
MA0081.1 4.55652e-4
MA0083.1 4.24347e-4
MA0084.1 0.468
MA0087.1 0.599
MA0088.1 0.256
MA0090.1 0.0121
MA0091.1 0.614
MA0092.1 0.765
MA0093.1 0.0714
MA0099.2 5.12809e-8
MA0100.1 3.14477e-4
MA0101.1 1.72041e-6
MA0102.2 5.18562e-5
MA0103.1 0.499
MA0104.2 0.0347
MA0105.1 1.50879e-5
MA0106.1 0.219
MA0107.1 2.61519e-5
MA0108.2 0.0321
MA0111.1 0.896
MA0112.2 0.0209
MA0113.1 0.59
MA0114.1 0.792
MA0115.1 0.473
MA0116.1 0.00186
MA0117.1 0.315
MA0119.1 0.697
MA0122.1 0.256
MA0124.1 0.568
MA0125.1 0.0243
MA0131.1 0.288
MA0135.1 0.0144
MA0136.1 1.42392e-26
MA0137.2 0.0139
MA0138.2 0.00687
MA0139.1 0.338
MA0140.1 0.41
MA0141.1 0.0994
MA0142.1 0.704
MA0143.1 0.516
MA0144.1 0.19
MA0145.1 0.904
MA0146.1 0.154
MA0147.1 0.0178
MA0148.1 0.537
MA0149.1 0.0499
MA0150.1 1.4761e-4
MA0152.1 0.794
MA0153.1 1.61018e-5
MA0154.1 0.228
MA0155.1 0.794
MA0156.1 5.87286e-18
MA0157.1 0.676
MA0159.1 0.0113
MA0160.1 0.0629
MA0162.1 0.352
MA0163.1 1.48558e-5
MA0164.1 0.41
MA0258.1 0.0509
MA0259.1 0.186



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: CNhs11928

Novel motif P-value
1 0.195
10 0.0347
100 0.648
101 0.994
102 0.56
103 0.0745
104 0.771
105 0.492
106 0.144
107 0.73
108 0.645
109 0.0416
11 0.129
110 0.0983
111 0.0868
112 0.147
113 0.62
114 0.784
115 0.467
116 0.424
117 3.34158e-4
118 0.244
119 0.523
12 0.68
120 0.308
121 0.289
122 0.482
123 0.349
124 0.669
125 0.177
126 0.275
127 0.546
128 0.132
129 0.253
13 0.00522
130 0.642
131 0.377
132 0.792
133 0.243
134 0.623
135 0.885
136 0.284
137 0.0263
138 0.672
139 0.246
14 0.475
140 0.156
141 0.74
142 0.574
143 0.065
144 0.651
145 0.0186
146 0.711
147 0.891
148 0.414
149 0.258
15 0.0197
150 0.432
151 0.78
152 0.75
153 0.392
154 0.596
155 0.759
156 0.504
157 0.959
158 0.0893
159 0.447
160 0.896
161 0.199
162 0.404
163 0.593
164 0.0123
165 0.299
166 0.476
167 0.266
168 0.336
169 0.0336
17 0.549
18 0.233
19 0.789
2 0.0911
20 0.0188
21 0.248
22 0.722
23 0.388
24 0.0789
25 0.285
26 0.00206
27 0.485
28 0.648
29 0.00758
3 0.109
30 0.242
31 0.897
32 0.591
33 0.08
34 0.702
35 0.301
36 0.031
37 0.0429
38 0.454
39 0.735
4 0.938
40 0.152
41 0.0536
42 0.292
43 0.327
44 0.412
45 0.773
46 0.189
47 0.456
48 0.253
49 0.218
5 0.343
50 0.689
51 0.952
52 0.601
53 0.458
54 0.82
55 0.59
56 0.672
57 0.229
58 0.23
59 0.776
6 0.737
60 0.402
61 0.19
62 0.117
63 0.86
64 0.594
65 0.569
66 0.445
67 0.119
68 0.851
69 0.895
7 0.188
70 0.0709
71 0.00877
72 0.249
73 0.0502
74 0.362
75 0.0087
76 0.0421
77 0.409
78 0.0906
79 0.665
8 0.0336
80 0.839
81 0.866
82 0.681
83 0.0718
84 0.507
85 0.996
86 0.227
87 0.0779
88 0.576
89 0.943
9 0.909
90 0.00861
91 0.951
92 0.68
93 0.0699
94 0.272
95 0.0141
96 0.778
97 0.939
98 0.374
99 0.575



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: CNhs11928


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)
0000763 (myeloid cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000557 (granulocyte monocyte progenitor cell)

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)
0000070 (granulocyte macrophage progenitor cell 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)