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FF:3632-171A1

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Name:macrophage, bone marrow derived
Species:Mouse (Mus musculus)
Library ID:CNhs11532
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  SAMD00005999
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11532 CAGE DRX008915 DRR009789
Accession ID Mm9

Library idBAMCTSS
CNhs11532 DRZ001214 DRZ002597
Accession ID Mm10

Library idBAMCTSS
CNhs11532 DRZ012564 DRZ013947
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


Relative expression to median (log10)


Transcription factors with enriched expression in this sample
Ranked 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 sample
Ranked 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

CNhs11532

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 0.055
1002 -0.116
1003 -0.123
1004 0
1005 0
1006 -0.143
1007 -0.277
1008 0
1009 -0.19
101 -0.0725
1010 0
1011 -0.0175
1012 0
1013 -0.0281
1014 -0.0874
1015 -0.267
1016 -0.465
1017 0
1018 0
1019 0
102 0
1020 0.42
1021 0.0839
1022 -0.315
1023 0
1024 -0.241
1025 -0.0611
1026 0
1027 0
1028 0
1029 -0.0989
103 -0.0887
1030 0
1031 -0.873
1032 -0.184
1033 0
1034 0
1035 0
1036 -0.158
1037 0
1038 0.0361
1039 -0.0849
104 0
1040 -0.809
1041 0



Repeat families with enriched expression in this sample
Summary: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 motifs
Summary: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: CNhs11532
Jaspar motif P-value
MA0002.2 2.18394e-5
MA0003.1 0.392
MA0004.1 0.243
MA0006.1 0.509
MA0007.1 0.594
MA0009.1 0.192
MA0014.1 0.493
MA0017.1 0.0566
MA0018.2 0.0181
MA0019.1 0.629
MA0024.1 0.0511
MA0025.1 0.99
MA0027.1 0.665
MA0028.1 0.0345
MA0029.1 0.804
MA0030.1 0.139
MA0031.1 0.457
MA0035.2 0.134
MA0038.1 0.00399
MA0039.2 0.707
MA0040.1 0.437
MA0041.1 0.0918
MA0042.1 0.66
MA0043.1 0.178
MA0046.1 6.38582e-11
MA0047.2 0.377
MA0048.1 0.482
MA0050.1 2.17068e-24
MA0051.1 1.62823e-17
MA0052.1 1.95666e-4
MA0055.1 0.583
MA0057.1 0.698
MA0058.1 0.0881
MA0059.1 0.0553
MA0060.1 6.76966e-12
MA0061.1 0.00167
MA0062.2 6.96372e-6
MA0065.2 0.0242
MA0066.1 0.00903
MA0067.1 0.436
MA0068.1 0.626
MA0069.1 0.936
MA0070.1 0.0595
MA0071.1 0.299
MA0072.1 0.374
MA0073.1 0.893
MA0074.1 0.138
MA0076.1 0.0977
MA0077.1 0.2
MA0078.1 0.895
MA0079.2 0.173
MA0080.2 9.78586e-13
MA0081.1 0.00255
MA0083.1 0.00374
MA0084.1 0.345
MA0087.1 0.849
MA0088.1 0.197
MA0090.1 0.0438
MA0091.1 0.341
MA0092.1 0.618
MA0093.1 0.217
MA0099.2 0.00299
MA0100.1 0.409
MA0101.1 0.00152
MA0102.2 0.0147
MA0103.1 0.829
MA0104.2 0.728
MA0105.1 2.79239e-4
MA0106.1 0.151
MA0107.1 0.00106
MA0108.2 3.45002e-9
MA0111.1 0.378
MA0112.2 7.75125e-5
MA0113.1 0.477
MA0114.1 0.194
MA0115.1 0.441
MA0116.1 0.0016
MA0117.1 0.877
MA0119.1 0.321
MA0122.1 0.212
MA0124.1 0.869
MA0125.1 0.0792
MA0131.1 0.777
MA0135.1 0.00157
MA0136.1 3.10862e-15
MA0137.2 0.162
MA0138.2 0.769
MA0139.1 0.24
MA0140.1 0.135
MA0141.1 0.0603
MA0142.1 0.685
MA0143.1 0.0861
MA0144.1 0.368
MA0145.1 0.165
MA0146.1 0.00856
MA0147.1 0.716
MA0148.1 0.626
MA0149.1 0.107
MA0150.1 0.00916
MA0152.1 0.75
MA0153.1 1.94603e-6
MA0154.1 0.0151
MA0155.1 0.853
MA0156.1 1.04402e-9
MA0157.1 0.644
MA0159.1 0.00106
MA0160.1 0.209
MA0162.1 0.273
MA0163.1 3.34615e-5
MA0164.1 0.9
MA0258.1 0.00475
MA0259.1 0.775



FANTOM5 phase1 novel unique motifs
Summary: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: CNhs11532
Novel motif P-value
1 0.039
10 0.0233
100 0.947
101 0.824
102 0.571
103 0.0251
104 0.892
105 0.843
106 0.101
107 0.487
108 0.826
109 0.0345
11 0.0604
110 0.0493
111 0.00274
112 0.00894
113 0.63
114 0.0126
115 0.675
116 0.522
117 6.5589e-4
118 0.263
119 0.175
12 0.823
120 0.174
121 0.183
122 0.673
123 0.675
124 0.764
125 0.179
126 0.292
127 0.45
128 0.0546
129 0.0758
13 0.0118
130 0.865
131 0.423
132 0.662
133 0.823
134 0.526
135 0.908
136 0.995
137 0.103
138 0.998
139 0.0546
14 0.843
140 0.047
141 0.088
142 0.606
143 0.0309
144 0.881
145 0.0737
146 0.708
147 0.678
148 0.0546
149 0.0927
15 0.0615
150 0.206
151 0.282
152 0.267
153 0.536
154 0.729
155 0.6
156 0.308
157 0.866
158 0.222
159 0.895
160 0.377
161 0.17
162 0.775
163 0.783
164 0.0689
165 0.0589
166 0.783
167 0.391
168 0.955
169 0.00335
17 0.126
18 0.175
19 0.159
2 0.575
20 0.116
21 0.51
22 0.224
23 0.667
24 0.281
25 0.311
26 0.00461
27 0.975
28 0.417
29 0.0549
3 0.0179
30 0.537
31 0.649
32 0.836
33 0.123
34 0.955
35 0.46
36 0.0247
37 0.0243
38 0.292
39 0.731
4 0.428
40 0.124
41 0.373
42 0.234
43 0.041
44 0.309
45 0.9
46 0.0593
47 0.112
48 0.204
49 0.0546
5 0.178
50 0.987
51 0.864
52 0.888
53 0.571
54 0.75
55 0.95
56 0.476
57 0.43
58 0.311
59 0.161
6 0.885
60 0.203
61 0.151
62 0.0996
63 0.313
64 0.574
65 0.263
66 0.519
67 0.104
68 0.00381
69 0.651
7 0.119
70 0.0054
71 0.0284
72 0.178
73 0.0279
74 0.831
75 0.012
76 0.0674
77 0.553
78 0.0843
79 0.549
8 0.0329
80 0.692
81 0.243
82 0.276
83 0.879
84 0.687
85 0.355
86 0.226
87 0.62
88 0.699
89 0.154
9 0.518
90 0.0348
91 0.553
92 0.093
93 0.118
94 0.279
95 0.0476
96 0.5
97 0.819
98 0.283
99 1



de novo motifs identified by HOMER in promoters active in this sample
Summary:The result of HOMER in this sample is shown.
Analyst:NA

library id: CNhs11532


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)
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)