Personal tools

FF:11718-123C8

From FANTOM5_SSTAR

Jump to: navigation, search


Name:Mouse Microglia, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs12629
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
strainNA
tissuebrain
dev stageNA
sexNA
ageNA
cell typemicroglial cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMG1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005195
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12629 CAGE DRX008828 DRR009700
Accession ID Mm9

Library idBAMCTSS
CNhs12629 DRZ001125 DRZ002510
Accession ID Mm10

Library idBAMCTSS
CNhs12629 DRZ012475 DRZ013860
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

CNhs12629

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.527
1001 --0.0749
1002 0.09
1003 0.314
1004 0
1005 0
1006 0.112
1007 --0.183
1008 0
1009 --0.0558
101 --0.611
1010 0
1011 0.00496
1012 0
1013 0.1
1014 --0.0874
1015 0.122
1016 0.381
1017 0
1018 0
1019 0
102 0
1020 0.491
1021 0.135
1022 --0.0704
1023 0
1024 --0.14
1025 0
1026 0
1027 0.114
1028 0
1029 --0.176
103 0.398
1030 0
1031 0.489
1032 0.523
1033 --0.0665
1034 0
1035 0
1036 --0.158
1037 0
1038 --0.0473
1039 0.0325
104 0
1040 0.275
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: CNhs12629

Jaspar motif P-value
MA0002.2 0.0571
MA0003.1 0.112
MA0004.1 0.727
MA0006.1 0.369
MA0007.1 0.513
MA0009.1 0.115
MA0014.1 0.724
MA0017.1 0.0502
MA0018.2 0.0496
MA0019.1 0.305
MA0024.1 4.70811e-4
MA0025.1 0.681
MA0027.1 0.824
MA0028.1 8.53097e-6
MA0029.1 0.82
MA0030.1 0.254
MA0031.1 0.235
MA0035.2 0.00289
MA0038.1 0.00331
MA0039.2 0.696
MA0040.1 0.515
MA0041.1 0.266
MA0042.1 0.677
MA0043.1 0.0868
MA0046.1 6.89682e-8
MA0047.2 0.0512
MA0048.1 0.691
MA0050.1 0.7
MA0051.1 0.936
MA0052.1 0.571
MA0055.1 0.347
MA0057.1 0.771
MA0058.1 0.878
MA0059.1 0.684
MA0060.1 7.77625e-4
MA0061.1 0.193
MA0062.2 1.32951e-7
MA0065.2 0.47
MA0066.1 0.196
MA0067.1 0.134
MA0068.1 0.809
MA0069.1 0.19
MA0070.1 0.427
MA0071.1 0.64
MA0072.1 0.334
MA0073.1 0.85
MA0074.1 0.107
MA0076.1 1.00789e-6
MA0077.1 0.444
MA0078.1 0.963
MA0079.2 0.0196
MA0080.2 0.423
MA0081.1 0.381
MA0083.1 0.315
MA0084.1 0.507
MA0087.1 0.91
MA0088.1 0.453
MA0090.1 0.436
MA0091.1 0.872
MA0092.1 0.491
MA0093.1 0.711
MA0099.2 0.00509
MA0100.1 0.306
MA0101.1 0.873
MA0102.2 0.242
MA0103.1 0.412
MA0104.2 0.598
MA0105.1 0.252
MA0106.1 0.152
MA0107.1 0.999
MA0108.2 0.271
MA0111.1 0.261
MA0112.2 0.0959
MA0113.1 0.657
MA0114.1 0.103
MA0115.1 0.0921
MA0116.1 0.0867
MA0117.1 0.448
MA0119.1 0.271
MA0122.1 0.724
MA0124.1 0.759
MA0125.1 0.943
MA0131.1 0.0287
MA0135.1 0.0858
MA0136.1 0.308
MA0137.2 0.17
MA0138.2 0.31
MA0139.1 0.373
MA0140.1 7.16934e-4
MA0141.1 0.385
MA0142.1 0.96
MA0143.1 0.8
MA0144.1 0.269
MA0145.1 0.0527
MA0146.1 0.0473
MA0147.1 0.621
MA0148.1 0.041
MA0149.1 0.398
MA0150.1 0.971
MA0152.1 0.166
MA0153.1 3.96012e-5
MA0154.1 0.0325
MA0155.1 0.0555
MA0156.1 1.4371e-4
MA0157.1 0.507
MA0159.1 0.523
MA0160.1 0.429
MA0162.1 0.303
MA0163.1 0.0154
MA0164.1 0.926
MA0258.1 0.234
MA0259.1 0.141



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: CNhs12629

Novel motif P-value
1 0.905
10 0.927
100 0.671
101 0.583
102 0.778
103 0.623
104 0.765
105 0.779
106 0.0109
107 0.124
108 0.128
109 0.137
11 0.24
110 0.719
111 0.983
112 0.668
113 0.759
114 0.446
115 0.558
116 0.00814
117 0.338
118 0.78
119 0.777
12 0.784
120 0.314
121 0.183
122 0.698
123 0.837
124 0.704
125 0.549
126 0.427
127 0.726
128 0.04
129 0.704
13 0.414
130 0.887
131 0.692
132 0.111
133 0.64
134 0.714
135 0.0673
136 0.375
137 0.511
138 0.944
139 0.705
14 0.324
140 0.395
141 0.775
142 0.026
143 0.17
144 0.911
145 0.89
146 0.315
147 0.874
148 0.283
149 0.0281
15 0.789
150 0.242
151 0.21
152 0.0414
153 0.51
154 0.164
155 0.576
156 0.0537
157 0.321
158 0.0364
159 0.206
160 0.656
161 0.497
162 0.455
163 0.288
164 0.0354
165 0.669
166 0.856
167 0.0182
168 0.907
169 0.0881
17 0.279
18 0.259
19 0.188
2 0.0538
20 0.562
21 0.265
22 0.0895
23 0.0111
24 0.515
25 0.402
26 0.43
27 0.329
28 0.592
29 0.791
3 0.43
30 0.109
31 0.259
32 0.00286
33 0.881
34 0.0461
35 0.792
36 0.831
37 0.348
38 0.347
39 0.425
4 0.355
40 0.497
41 0.967
42 0.608
43 0.128
44 0.142
45 0.222
46 0.698
47 0.515
48 0.563
49 0.458
5 0.403
50 0.158
51 0.942
52 0.0995
53 0.542
54 0.948
55 0.184
56 0.162
57 0.988
58 0.629
59 0.00331
6 0.825
60 0.158
61 0.757
62 0.902
63 0.0968
64 0.336
65 0.0274
66 0.912
67 0.257
68 0.258
69 0.0243
7 0.321
70 0.198
71 0.44
72 0.72
73 0.0966
74 0.549
75 0.844
76 0.241
77 0.00658
78 0.283
79 0.949
8 0.362
80 0.64
81 0.0563
82 0.743
83 0.529
84 0.519
85 0.133
86 0.921
87 0.0276
88 0.113
89 0.387
9 0.437
90 0.193
91 0.224
92 0.345
93 0.182
94 0.106
95 0.187
96 0.201
97 0.679
98 0.0917
99 0.27



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: CNhs12629


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)
0002319 (neural cell)
0000095 (neuron associated cell)
0000243 (glial cell (sensu Vertebrata))
0000878 (central nervous system macrophage)
0000219 (motile cell)
0000325 (stuff accumulating cell)
0000473 (defensive cell)
0000234 (phagocyte)
0000125 (glial cell)
0000738 (leukocyte)
0000255 (eukaryotic cell)
0000235 (macrophage)
0000864 (tissue-resident macrophage)
0000129 (microglial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000113 (mouse microglial 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:0000133 (neurectodermal cell)
CL:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)
CL:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)