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|library_id=CNhs12634
|library_id=CNhs12634
|library_id_phase_based=2:CNhs12634
|library_id_phase_based=2:CNhs12634
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Microglia%252c%2520donor2.CNhs12634.11736-123E8.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Microglia%252c%2520donor2.CNhs12634.11736-123E8.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Microglia%252c%2520donor2.CNhs12634.11736-123E8.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Microglia%252c%2520donor2.CNhs12634.11736-123E8.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Microglia%252c%2520donor2.CNhs12634.11736-123E8.mm9.nobarcode.rdna.fa.gz
|name=Mouse Microglia, donor2
|name=Mouse Microglia, donor2
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 16:32, 17 May 2017


Name:Mouse Microglia, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12634
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 numberRNAMG2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005410
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12634 CAGE DRX008829 DRR009701
Accession ID Mm9

Library idBAMCTSS
CNhs12634 DRZ001126 DRZ002511
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. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs12634

00
10
100
1000
10000.664
1001-0.0749
10020.0639
10030.583
10040
10050
10060.256
1007-0.229
10080
10090.0576
101-0.552
10100
10110.0337
10120
10130.117
10140
10150.256
10160.213
10170
10180
10190
1020
10200.61
10210.141
10220.012
10230
1024-0.156
1025-0.0196
10260
10270.405
10280.141
1029-0.176
1030.164
10300
10310.403
10320.756
1033-0.0665
10340
10350
1036-0.183
10370
1038-0.217
10390.127
1040
10400.283
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: CNhs12634

Jaspar motifP-value
MA0002.20.621
MA0003.10.153
MA0004.10.383
MA0006.10.405
MA0007.10.61
MA0009.10.159
MA0014.10.787
MA0017.19.73702e-4
MA0018.20.586
MA0019.10.23
MA0024.10.00289
MA0025.10.837
MA0027.10.245
MA0028.15.23907e-4
MA0029.10.656
MA0030.10.677
MA0031.10.601
MA0035.20.00184
MA0038.10.0678
MA0039.20.928
MA0040.10.47
MA0041.10.258
MA0042.10.726
MA0043.10.936
MA0046.12.79439e-6
MA0047.20.106
MA0048.10.443
MA0050.10.34
MA0051.10.81
MA0052.10.34
MA0055.10.652
MA0057.10.682
MA0058.10.589
MA0059.10.946
MA0060.10.985
MA0061.10.601
MA0062.23.25868e-6
MA0065.20.833
MA0066.10.616
MA0067.10.185
MA0068.10.598
MA0069.10.211
MA0070.10.368
MA0071.10.301
MA0072.10.321
MA0073.10.921
MA0074.10.227
MA0076.10.00129
MA0077.10.372
MA0078.10.548
MA0079.20.0146
MA0080.20.0695
MA0081.10.754
MA0083.10.975
MA0084.10.374
MA0087.10.955
MA0088.10.552
MA0090.10.914
MA0091.10.307
MA0092.10.805
MA0093.10.438
MA0099.20.675
MA0100.10.627
MA0101.10.332
MA0102.20.214
MA0103.10.123
MA0104.20.429
MA0105.10.815
MA0106.10.424
MA0107.10.413
MA0108.20.367
MA0111.10.529
MA0112.20.751
MA0113.10.864
MA0114.10.00386
MA0115.10.0212
MA0116.10.709
MA0117.10.539
MA0119.10.616
MA0122.10.872
MA0124.10.778
MA0125.10.637
MA0131.10.0957
MA0135.10.0752
MA0136.10.0266
MA0137.20.428
MA0138.20.58
MA0139.10.642
MA0140.13.80558e-5
MA0141.10.814
MA0142.10.8
MA0143.10.827
MA0144.10.203
MA0145.10.136
MA0146.10.0408
MA0147.10.473
MA0148.10.0258
MA0149.10.191
MA0150.10.23
MA0152.10.076
MA0153.14.93809e-4
MA0154.10.205
MA0155.10.085
MA0156.16.7189e-5
MA0157.10.478
MA0159.10.776
MA0160.10.141
MA0162.10.351
MA0163.10.114
MA0164.10.823
MA0258.10.975
MA0259.10.132



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: CNhs12634

Novel motifP-value
10.318
100.471
1000.996
1010.984
1020.75
1030.222
1040.94
1050.893
1060.098
1070.947
1080.29
1090.266
110.814
1100.738
1110.594
1120.407
1130.411
1140.88
1150.801
1160.126
1170.14
1180.675
1190.126
120.917
1200.316
1210.591
1220.567
1230.728
1240.952
1250.114
1260.42
1270.97
1280.592
1290.119
130.101
1300.837
1310.771
1320.109
1330.826
1340.744
1350.103
1360.0506
1370.423
1380.525
1390.039
140.326
1400.0583
1410.257
1420.0231
1430.855
1440.837
1450.118
1460.631
1470.94
1480.861
1490.148
150.205
1500.307
1510.312
1520.0404
1530.13
1540.0611
1550.816
1560.0164
1570.335
1580.0168
1590.218
1600.622
1610.559
1620.584
1630.152
1643.20609e-4
1650.992
1660.981
1670.0431
1680.605
1690.268
170.653
180.804
190.619
20.0258
200.76
210.44
220.175
230.129
240.592
250.167
260.729
270.528
280.314
290.127
30.696
300.105
310.315
320.00711
330.7
340.0296
350.492
360.55
370.576
380.55
390.434
40.862
400.544
410.815
420.665
430.51
440.313
450.179
460.41
470.872
480.918
490.366
50.0567
500.179
510.777
520.0736
530.762
540.635
550.366
560.391
570.549
580.182
590.00895
60.993
600.371
610.418
620.398
630.174
640.762
650.0785
660.626
670.663
680.254
690.0994
70.0476
700.984
710.593
720.785
730.0762
740.348
750.64
760.116
770.00817
780.00452
790.865
80.596
800.547
810.369
820.421
830.481
840.417
850.468
860.86
870.00126
880.266
890.685
90.735
900.191
910.815
920.396
930.0887
940.0157
950.197
960.11
970.895
980.2
990.204



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: CNhs12634


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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