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FF:12126-128D2

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Name:granulocyte macrophage progenitor GMP, biol_rep2
Species:Mouse (Mus musculus)
Library ID:CNhs12202
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 numberrep2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00004987
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12202 CAGE DRX008783 DRR009655
Accession ID Mm9

Library idBAMCTSS
CNhs12202 DRZ001080 DRZ002465
Accession ID Mm10

Library idBAMCTSS
CNhs12202 DRZ012430 DRZ013815
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

CNhs12202

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 --0.123
1004 0
1005 0.18
1006 --0.162
1007 --0.307
1008 0
1009 --0.19
101 0.282
1010 0
1011 --0.108
1012 0
1013 0.0479
1014 --0.0874
1015 --0.0147
1016 --0.484
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 --0.124
1023 0.824
1024 0.358
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.176
103 --0.0887
1030 0
1031 --0.956
1032 --0.556
1033 0.0886
1034 0
1035 0
1036 0.343
1037 0
1038 --0.354
1039 0.00502
104 0
1040 --0.343
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: CNhs12202

Jaspar motif P-value
MA0002.2 7.5987e-6
MA0003.1 0.993
MA0004.1 0.0424
MA0006.1 0.939
MA0007.1 0.719
MA0009.1 0.746
MA0014.1 0.978
MA0017.1 0.109
MA0018.2 4.37527e-4
MA0019.1 0.705
MA0024.1 0.00149
MA0025.1 0.0478
MA0027.1 0.488
MA0028.1 3.83408e-8
MA0029.1 0.267
MA0030.1 0.405
MA0031.1 0.626
MA0035.2 0.887
MA0038.1 0.0336
MA0039.2 0.788
MA0040.1 0.115
MA0041.1 0.566
MA0042.1 0.91
MA0043.1 7.30284e-7
MA0046.1 1.55133e-10
MA0047.2 0.822
MA0048.1 0.0178
MA0050.1 2.49745e-4
MA0051.1 0.00404
MA0052.1 0.197
MA0055.1 0.0016
MA0057.1 0.678
MA0058.1 0.0152
MA0059.1 0.00206
MA0060.1 0.552
MA0061.1 2.16211e-4
MA0062.2 2.47989e-17
MA0065.2 0.063
MA0066.1 0.223
MA0067.1 0.0257
MA0068.1 0.936
MA0069.1 0.526
MA0070.1 0.0987
MA0071.1 0.156
MA0072.1 0.726
MA0073.1 0.632
MA0074.1 0.16
MA0076.1 1.75614e-9
MA0077.1 0.706
MA0078.1 0.533
MA0079.2 0.0898
MA0080.2 2.42269e-12
MA0081.1 9.0918e-5
MA0083.1 0.00555
MA0084.1 0.727
MA0087.1 0.933
MA0088.1 0.119
MA0090.1 0.0249
MA0091.1 0.851
MA0092.1 0.694
MA0093.1 0.0352
MA0099.2 4.58458e-11
MA0100.1 8.63912e-5
MA0101.1 8.77923e-8
MA0102.2 5.30246e-6
MA0103.1 0.483
MA0104.2 0.0213
MA0105.1 6.86915e-6
MA0106.1 0.188
MA0107.1 9.5441e-7
MA0108.2 0.31
MA0111.1 0.896
MA0112.2 0.0422
MA0113.1 0.447
MA0114.1 0.722
MA0115.1 0.486
MA0116.1 0.00123
MA0117.1 0.338
MA0119.1 0.638
MA0122.1 0.233
MA0124.1 0.429
MA0125.1 0.103
MA0131.1 0.163
MA0135.1 0.384
MA0136.1 5.46861e-28
MA0137.2 5.93632e-4
MA0138.2 0.00677
MA0139.1 0.295
MA0140.1 0.374
MA0141.1 0.151
MA0142.1 0.766
MA0143.1 0.392
MA0144.1 0.0766
MA0145.1 0.926
MA0146.1 0.193
MA0147.1 0.0124
MA0148.1 0.922
MA0149.1 0.0715
MA0150.1 2.90256e-5
MA0152.1 0.973
MA0153.1 0.00294
MA0154.1 0.175
MA0155.1 0.757
MA0156.1 7.60856e-20
MA0157.1 0.432
MA0159.1 0.00988
MA0160.1 0.0457
MA0162.1 0.286
MA0163.1 2.88525e-6
MA0164.1 0.827
MA0258.1 0.109
MA0259.1 0.147



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: CNhs12202

Novel motif P-value
1 0.247
10 0.0409
100 0.806
101 0.816
102 0.623
103 0.0674
104 0.791
105 0.624
106 0.286
107 0.8
108 0.761
109 0.0238
11 0.151
110 0.0814
111 0.296
112 0.109
113 0.536
114 0.723
115 0.672
116 0.413
117 3.18966e-4
118 0.266
119 0.751
12 0.85
120 0.129
121 0.434
122 0.614
123 0.366
124 0.243
125 0.386
126 0.392
127 0.357
128 0.42
129 0.428
13 0.00256
130 0.84
131 0.284
132 0.57
133 0.543
134 0.753
135 0.506
136 0.265
137 0.0239
138 0.35
139 0.17
14 0.555
140 0.719
141 0.945
142 0.968
143 0.111
144 0.66
145 0.086
146 0.905
147 0.826
148 0.431
149 0.265
15 0.0305
150 0.678
151 0.8
152 0.717
153 0.694
154 0.929
155 0.763
156 0.272
157 0.735
158 0.0448
159 0.679
160 0.691
161 0.207
162 0.328
163 0.408
164 0.00425
165 0.138
166 0.493
167 0.344
168 0.6
169 0.0202
17 0.417
18 0.306
19 0.798
2 0.169
20 0.0202
21 0.297
22 0.781
23 0.359
24 0.0458
25 0.216
26 0.00393
27 0.551
28 0.797
29 0.00536
3 0.12
30 0.25
31 0.82
32 0.626
33 0.0696
34 0.85
35 0.506
36 0.0292
37 0.0432
38 0.379
39 0.73
4 0.955
40 0.0794
41 0.0141
42 0.381
43 0.456
44 0.434
45 0.842
46 0.252
47 0.562
48 0.213
49 0.379
5 0.416
50 0.702
51 0.948
52 0.419
53 0.582
54 0.889
55 0.509
56 0.764
57 0.447
58 0.2
59 0.452
6 0.81
60 0.47
61 0.154
62 0.128
63 0.911
64 0.575
65 0.556
66 0.236
67 0.222
68 0.64
69 0.676
7 0.121
70 0.0284
71 0.00731
72 0.103
73 0.0499
74 0.332
75 0.00731
76 0.0904
77 0.487
78 0.0685
79 0.451
8 0.0368
80 0.611
81 0.844
82 0.827
83 0.0132
84 0.963
85 0.827
86 0.286
87 0.035
88 0.556
89 0.463
9 0.936
90 0.0139
91 0.927
92 0.7
93 0.0302
94 0.303
95 0.00175
96 0.964
97 0.924
98 0.295
99 0.371



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: CNhs12202


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)