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FF:12123-128C8

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Name:granulocyte macrophage progenitor GMP, biol_rep1
Species:Mouse (Mus musculus)
Library ID:CNhs12206
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 numberrep1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005912
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12206 CAGE DRX008782 DRR009654
Accession ID Mm9

Library idBAMCTSS
CNhs12206 DRZ001079 DRZ002464
Accession ID Mm10

Library idBAMCTSS
CNhs12206 DRZ012429 DRZ013814
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

CNhs12206

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 0.168
1006 --0.241
1007 --0.375
1008 0
1009 --0.19
101 0.301
1010 0
1011 --0.108
1012 0
1013 --0.161
1014 --0.0874
1015 --0.0718
1016 --0.594
1017 0
1018 0
1019 0
102 0
1020 0
1021 --0.0487
1022 --0.309
1023 0.904
1024 0.402
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.176
103 --0.0887
1030 0
1031 --0.917
1032 --0.391
1033 0
1034 0
1035 0
1036 0.393
1037 0
1038 --0.506
1039 --0.117
104 0
1040 --0.532
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: CNhs12206

Jaspar motif P-value
MA0002.2 2.34478e-7
MA0003.1 0.833
MA0004.1 0.0689
MA0006.1 0.955
MA0007.1 0.73
MA0009.1 0.957
MA0014.1 0.92
MA0017.1 0.0587
MA0018.2 0.00661
MA0019.1 0.496
MA0024.1 0.00271
MA0025.1 0.242
MA0027.1 0.387
MA0028.1 2.3887e-5
MA0029.1 0.237
MA0030.1 0.188
MA0031.1 0.992
MA0035.2 0.882
MA0038.1 0.0219
MA0039.2 0.85
MA0040.1 0.0485
MA0041.1 0.745
MA0042.1 0.63
MA0043.1 5.36064e-4
MA0046.1 7.22477e-9
MA0047.2 0.826
MA0048.1 0.0623
MA0050.1 0.00243
MA0051.1 0.0175
MA0052.1 0.349
MA0055.1 0.0257
MA0057.1 0.489
MA0058.1 0.0407
MA0059.1 0.00109
MA0060.1 0.0554
MA0061.1 8.79012e-4
MA0062.2 1.75276e-12
MA0065.2 0.0248
MA0066.1 0.052
MA0067.1 0.0847
MA0068.1 0.793
MA0069.1 0.427
MA0070.1 0.137
MA0071.1 0.0836
MA0072.1 0.499
MA0073.1 0.737
MA0074.1 0.183
MA0076.1 1.46395e-5
MA0077.1 0.636
MA0078.1 0.297
MA0079.2 0.0623
MA0080.2 7.65085e-12
MA0081.1 5.88254e-4
MA0083.1 0.0038
MA0084.1 0.708
MA0087.1 0.642
MA0088.1 0.14
MA0090.1 0.0333
MA0091.1 0.732
MA0092.1 0.911
MA0093.1 0.0697
MA0099.2 9.26632e-8
MA0100.1 2.62428e-4
MA0101.1 4.79263e-6
MA0102.2 3.13114e-4
MA0103.1 0.826
MA0104.2 0.0189
MA0105.1 8.86864e-7
MA0106.1 0.119
MA0107.1 3.24543e-5
MA0108.2 0.0938
MA0111.1 0.73
MA0112.2 0.00931
MA0113.1 0.397
MA0114.1 0.408
MA0115.1 0.423
MA0116.1 3.35907e-4
MA0117.1 0.394
MA0119.1 0.882
MA0122.1 0.09
MA0124.1 0.36
MA0125.1 0.0298
MA0131.1 0.405
MA0135.1 0.0834
MA0136.1 5.53065e-25
MA0137.2 0.00327
MA0138.2 0.0397
MA0139.1 0.351
MA0140.1 0.606
MA0141.1 0.0564
MA0142.1 0.588
MA0143.1 0.686
MA0144.1 0.0945
MA0145.1 0.913
MA0146.1 0.163
MA0147.1 0.00915
MA0148.1 0.963
MA0149.1 0.0358
MA0150.1 2.56621e-4
MA0152.1 0.971
MA0153.1 0.00173
MA0154.1 0.0701
MA0155.1 0.985
MA0156.1 6.91019e-15
MA0157.1 0.638
MA0159.1 0.00682
MA0160.1 0.0124
MA0162.1 0.256
MA0163.1 2.22617e-6
MA0164.1 0.863
MA0258.1 0.0294
MA0259.1 0.165



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: CNhs12206

Novel motif P-value
1 0.113
10 0.0314
100 0.808
101 0.662
102 0.572
103 0.025
104 0.575
105 0.868
106 0.243
107 0.891
108 0.906
109 0.0133
11 0.092
110 0.0932
111 0.0953
112 0.0457
113 0.933
114 0.7
115 0.452
116 0.492
117 0.00109
118 0.161
119 0.409
12 0.82
120 0.0927
121 0.295
122 0.627
123 0.833
124 0.729
125 0.259
126 0.47
127 0.261
128 0.357
129 0.237
13 0.0119
130 0.651
131 0.724
132 0.587
133 0.788
134 0.592
135 0.568
136 0.684
137 0.0237
138 0.149
139 0.0637
14 0.729
140 0.337
141 0.495
142 0.959
143 0.0521
144 0.704
145 0.0647
146 0.994
147 0.878
148 0.436
149 0.588
15 0.0205
150 0.828
151 0.481
152 0.865
153 0.48
154 0.756
155 0.57
156 0.397
157 0.629
158 0.0157
159 0.832
160 0.753
161 0.0384
162 0.581
163 0.316
164 0.0118
165 0.173
166 0.627
167 0.26
168 0.947
169 0.0126
17 0.352
18 0.227
19 0.995
2 0.34
20 0.071
21 0.275
22 0.601
23 0.735
24 0.0975
25 0.24
26 0.00264
27 0.78
28 0.687
29 0.00818
3 0.0901
30 0.333
31 0.951
32 0.935
33 0.0557
34 0.973
35 0.278
36 0.0169
37 0.0612
38 0.312
39 0.899
4 0.92
40 0.0986
41 0.025
42 0.269
43 0.237
44 0.472
45 0.957
46 0.134
47 0.355
48 0.174
49 0.177
5 0.204
50 0.682
51 0.741
52 0.621
53 0.709
54 0.819
55 0.326
56 0.535
57 0.225
58 0.12
59 0.316
6 0.815
60 0.356
61 0.155
62 0.0624
63 0.687
64 0.382
65 0.29
66 0.543
67 0.181
68 0.791
69 0.97
7 0.116
70 0.022
71 0.00796
72 0.154
73 0.104
74 0.45
75 0.0191
76 0.142
77 0.911
78 0.112
79 0.488
8 0.0108
80 0.375
81 0.669
82 0.465
83 0.0624
84 0.857
85 0.524
86 0.266
87 0.173
88 0.676
89 0.241
9 0.896
90 0.0126
91 0.93
92 0.346
93 0.0381
94 0.206
95 0.00699
96 0.453
97 0.961
98 0.134
99 0.652



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: CNhs12206


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)