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FF:3560-170A1

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Name:macrophage, bone marrow derived
Species:Mouse (Mus musculus)
Library ID:CNhs11457
Sample type:time courses
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainBALB/c
tissuebone marrow
dev stageUNDEFINED_DEV_STAGE
sexmale
ageNA
cell typemacrophage
cell lineNA
companyNA
collaborationFrank Brombacher (University of Cape Town, South Africa)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005517
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11457 CAGE DRX008914 DRR009788
Accession ID Mm9

Library idBAMCTSS
CNhs11457 DRZ001213 DRZ002596
Accession ID Mm10

Library idBAMCTSS
CNhs11457 DRZ012563 DRZ013946
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

CNhs11457

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0631
1002 --0.116
1003 --0.123
1004 0
1005 0
1006 --0.0364
1007 --0.142
1008 0
1009 --0.2
101 --0.0739
1010 0
1011 --0.177
1012 0
1013 --0.0294
1014 --0.0874
1015 --0.303
1016 --0.465
1017 0
1018 0
1019 0
102 0
1020 0.604
1021 0
1022 --0.141
1023 0.399
1024 --0.14
1025 --0.0611
1026 0
1027 0
1028 0
1029 --0.148
103 --0.0887
1030 0
1031 --0.832
1032 --0.288
1033 --0.0665
1034 0
1035 0
1036 0.0565
1037 0
1038 0.00805
1039 --0.107
104 0
1040 --0.536
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: CNhs11457

Jaspar motif P-value
MA0002.2 6.07125e-5
MA0003.1 0.498
MA0004.1 0.239
MA0006.1 0.517
MA0007.1 0.322
MA0009.1 0.191
MA0014.1 0.878
MA0017.1 0.142
MA0018.2 0.0377
MA0019.1 0.807
MA0024.1 0.0146
MA0025.1 0.721
MA0027.1 0.583
MA0028.1 0.14
MA0029.1 0.834
MA0030.1 0.285
MA0031.1 0.459
MA0035.2 0.276
MA0038.1 0.00315
MA0039.2 0.694
MA0040.1 0.701
MA0041.1 0.0732
MA0042.1 0.488
MA0043.1 0.0582
MA0046.1 1.48625e-8
MA0047.2 0.342
MA0048.1 0.728
MA0050.1 1.20175e-17
MA0051.1 1.31145e-12
MA0052.1 0.00135
MA0055.1 0.972
MA0057.1 0.841
MA0058.1 0.096
MA0059.1 0.101
MA0060.1 2.39358e-15
MA0061.1 0.00789
MA0062.2 3.3426e-4
MA0065.2 0.047
MA0066.1 0.0245
MA0067.1 0.466
MA0068.1 0.418
MA0069.1 0.807
MA0070.1 0.0958
MA0071.1 0.255
MA0072.1 0.343
MA0073.1 0.907
MA0074.1 0.131
MA0076.1 0.288
MA0077.1 0.137
MA0078.1 0.835
MA0079.2 0.157
MA0080.2 3.11114e-12
MA0081.1 0.00324
MA0083.1 0.00405
MA0084.1 0.256
MA0087.1 0.966
MA0088.1 0.127
MA0090.1 0.0701
MA0091.1 0.229
MA0092.1 0.66
MA0093.1 0.237
MA0099.2 0.0076
MA0100.1 0.475
MA0101.1 0.0152
MA0102.2 0.192
MA0103.1 0.83
MA0104.2 0.803
MA0105.1 1.23552e-4
MA0106.1 0.348
MA0107.1 0.0197
MA0108.2 1.34588e-9
MA0111.1 0.412
MA0112.2 8.82154e-5
MA0113.1 0.409
MA0114.1 0.354
MA0115.1 0.983
MA0116.1 0.00357
MA0117.1 0.758
MA0119.1 0.247
MA0122.1 0.374
MA0124.1 0.434
MA0125.1 0.121
MA0131.1 0.462
MA0135.1 0.0043
MA0136.1 4.61506e-14
MA0137.2 0.443
MA0138.2 0.979
MA0139.1 0.373
MA0140.1 0.6
MA0141.1 0.0559
MA0142.1 0.663
MA0143.1 0.179
MA0144.1 0.491
MA0145.1 0.183
MA0146.1 0.0215
MA0147.1 0.845
MA0148.1 0.565
MA0149.1 0.148
MA0150.1 0.0389
MA0152.1 0.986
MA0153.1 1.36817e-5
MA0154.1 0.00812
MA0155.1 0.959
MA0156.1 4.75709e-8
MA0157.1 0.623
MA0159.1 7.80757e-4
MA0160.1 0.255
MA0162.1 0.3
MA0163.1 1.07252e-5
MA0164.1 0.55
MA0258.1 0.00461
MA0259.1 0.941



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: CNhs11457

Novel motif P-value
1 0.0434
10 0.0174
100 0.955
101 0.866
102 0.854
103 0.0312
104 0.859
105 0.722
106 0.13
107 0.671
108 0.91
109 0.0443
11 0.0755
110 0.114
111 0.00336
112 0.0108
113 0.602
114 0.00568
115 0.687
116 0.476
117 4.88335e-4
118 0.0996
119 0.147
12 0.505
120 0.173
121 0.0758
122 0.561
123 0.824
124 0.699
125 0.415
126 0.296
127 0.252
128 0.207
129 0.119
13 0.0145
130 0.702
131 0.736
132 0.955
133 0.817
134 0.533
135 0.911
136 0.913
137 0.288
138 0.871
139 0.0871
14 0.594
140 0.0226
141 0.174
142 0.863
143 0.103
144 0.861
145 0.197
146 0.641
147 0.742
148 0.0456
149 0.038
15 0.0436
150 0.206
151 0.259
152 0.468
153 0.953
154 0.88
155 0.492
156 0.555
157 0.674
158 0.194
159 1
160 0.268
161 0.289
162 0.748
163 0.695
164 0.0492
165 0.0284
166 0.876
167 0.307
168 0.832
169 0.00485
17 0.22
18 0.132
19 0.148
2 0.715
20 0.118
21 0.393
22 0.219
23 0.625
24 0.192
25 0.456
26 0.00367
27 0.845
28 0.375
29 0.0726
3 0.00989
30 0.527
31 0.659
32 0.567
33 0.251
34 0.799
35 0.177
36 0.0192
37 0.0229
38 0.208
39 0.667
4 0.478
40 0.181
41 0.384
42 0.182
43 0.0363
44 0.196
45 0.742
46 0.0386
47 0.159
48 0.232
49 0.054
5 0.106
50 0.867
51 0.739
52 0.995
53 0.46
54 0.684
55 0.996
56 0.324
57 0.344
58 0.336
59 0.128
6 0.612
60 0.189
61 0.157
62 0.108
63 0.258
64 0.452
65 0.117
66 0.477
67 0.0867
68 0.0166
69 0.495
7 0.13
70 0.00369
71 0.0284
72 0.13
73 0.0355
74 0.862
75 0.00957
76 0.0604
77 0.383
78 0.122
79 0.496
8 0.0582
80 0.846
81 0.27
82 0.257
83 0.764
84 0.799
85 0.209
86 0.185
87 0.513
88 0.587
89 0.0862
9 0.507
90 0.0318
91 0.592
92 0.0823
93 0.119
94 0.345
95 0.11
96 0.734
97 0.789
98 0.159
99 0.97



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: CNhs11457


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)
0000766 (myeloid leukocyte)
0000219 (motile cell)
0000325 (stuff accumulating cell)
0000473 (defensive cell)
0000234 (phagocyte)
0000738 (leukocyte)
0000255 (eukaryotic cell)
0000235 (macrophage)
0000864 (tissue-resident macrophage)
0002476 (bone marrow macrophage)

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
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0200021 (macrophage, bone marrow-derived 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)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)