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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008718
|DRA_sample_Accession=CAGE@SAMD00005195
|accession_numbers=CAGE;DRX008828;DRR009700;DRZ001125;DRZ002510
|accession_numbers=CAGE;DRX008828;DRR009700;DRZ001125;DRZ002510
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000479,UBERON:0004121,UBERON:0011216,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001017,UBERON:0001016
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000479,UBERON:0004121,UBERON:0011216,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0001017,UBERON:0001016

Revision as of 20:20, 31 July 2014


Name:Mouse Microglia, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs12629
Sample type:primary cells
Genomic View: UCSC
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

CAGE 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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs12629

00
10
100
1000
10000.527
1001-0.0749
10020.09
10030.314
10040
10050
10060.112
1007-0.183
10080
1009-0.0558
101-0.611
10100
10110.00496
10120
10130.1
1014-0.0874
10150.122
10160.381
10170
10180
10190
1020
10200.491
10210.135
1022-0.0704
10230
1024-0.14
10250
10260
10270.114
10280
1029-0.176
1030.398
10300
10310.489
10320.523
1033-0.0665
10340
10350
1036-0.158
10370
1038-0.0473
10390.0325
1040
10400.275
10410



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12629

Jaspar motifP-value
MA0002.20.0571
MA0003.10.112
MA0004.10.727
MA0006.10.369
MA0007.10.513
MA0009.10.115
MA0014.10.724
MA0017.10.0502
MA0018.20.0496
MA0019.10.305
MA0024.14.70811e-4
MA0025.10.681
MA0027.10.824
MA0028.18.53097e-6
MA0029.10.82
MA0030.10.254
MA0031.10.235
MA0035.20.00289
MA0038.10.00331
MA0039.20.696
MA0040.10.515
MA0041.10.266
MA0042.10.677
MA0043.10.0868
MA0046.16.89682e-8
MA0047.20.0512
MA0048.10.691
MA0050.10.7
MA0051.10.936
MA0052.10.571
MA0055.10.347
MA0057.10.771
MA0058.10.878
MA0059.10.684
MA0060.17.77625e-4
MA0061.10.193
MA0062.21.32951e-7
MA0065.20.47
MA0066.10.196
MA0067.10.134
MA0068.10.809
MA0069.10.19
MA0070.10.427
MA0071.10.64
MA0072.10.334
MA0073.10.85
MA0074.10.107
MA0076.11.00789e-6
MA0077.10.444
MA0078.10.963
MA0079.20.0196
MA0080.20.423
MA0081.10.381
MA0083.10.315
MA0084.10.507
MA0087.10.91
MA0088.10.453
MA0090.10.436
MA0091.10.872
MA0092.10.491
MA0093.10.711
MA0099.20.00509
MA0100.10.306
MA0101.10.873
MA0102.20.242
MA0103.10.412
MA0104.20.598
MA0105.10.252
MA0106.10.152
MA0107.10.999
MA0108.20.271
MA0111.10.261
MA0112.20.0959
MA0113.10.657
MA0114.10.103
MA0115.10.0921
MA0116.10.0867
MA0117.10.448
MA0119.10.271
MA0122.10.724
MA0124.10.759
MA0125.10.943
MA0131.10.0287
MA0135.10.0858
MA0136.10.308
MA0137.20.17
MA0138.20.31
MA0139.10.373
MA0140.17.16934e-4
MA0141.10.385
MA0142.10.96
MA0143.10.8
MA0144.10.269
MA0145.10.0527
MA0146.10.0473
MA0147.10.621
MA0148.10.041
MA0149.10.398
MA0150.10.971
MA0152.10.166
MA0153.13.96012e-5
MA0154.10.0325
MA0155.10.0555
MA0156.11.4371e-4
MA0157.10.507
MA0159.10.523
MA0160.10.429
MA0162.10.303
MA0163.10.0154
MA0164.10.926
MA0258.10.234
MA0259.10.141



FANTOM5 phase1 novel unique motifs<b>Summary:</b>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 in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12629

Novel motifP-value
10.905
100.927
1000.671
1010.583
1020.778
1030.623
1040.765
1050.779
1060.0109
1070.124
1080.128
1090.137
110.24
1100.719
1110.983
1120.668
1130.759
1140.446
1150.558
1160.00814
1170.338
1180.78
1190.777
120.784
1200.314
1210.183
1220.698
1230.837
1240.704
1250.549
1260.427
1270.726
1280.04
1290.704
130.414
1300.887
1310.692
1320.111
1330.64
1340.714
1350.0673
1360.375
1370.511
1380.944
1390.705
140.324
1400.395
1410.775
1420.026
1430.17
1440.911
1450.89
1460.315
1470.874
1480.283
1490.0281
150.789
1500.242
1510.21
1520.0414
1530.51
1540.164
1550.576
1560.0537
1570.321
1580.0364
1590.206
1600.656
1610.497
1620.455
1630.288
1640.0354
1650.669
1660.856
1670.0182
1680.907
1690.0881
170.279
180.259
190.188
20.0538
200.562
210.265
220.0895
230.0111
240.515
250.402
260.43
270.329
280.592
290.791
30.43
300.109
310.259
320.00286
330.881
340.0461
350.792
360.831
370.348
380.347
390.425
40.355
400.497
410.967
420.608
430.128
440.142
450.222
460.698
470.515
480.563
490.458
50.403
500.158
510.942
520.0995
530.542
540.948
550.184
560.162
570.988
580.629
590.00331
60.825
600.158
610.757
620.902
630.0968
640.336
650.0274
660.912
670.257
680.258
690.0243
70.321
700.198
710.44
720.72
730.0966
740.549
750.844
760.241
770.00658
780.283
790.949
80.362
800.64
810.0563
820.743
830.529
840.519
850.133
860.921
870.0276
880.113
890.387
90.437
900.193
910.224
920.345
930.182
940.106
950.187
960.201
970.679
980.0917
990.27



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs12629


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>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)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
CL:0000133 (neurectodermal cell)
CL:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)
CL:0000339 (glioblast (sensu Vertebrata))
CL:0000221 (ectodermal cell)

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