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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005999
|DRA_sample_Accession=CAGE@SAMD00005999
|accession_numbers=CAGE;DRX008915;DRR009789;DRZ001214;DRZ002597
|accession_numbers=CAGE;DRX008915;DRR009789;DRZ001214;DRZ002597;DRZ012564;DRZ013947
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002371,UBERON:0001474,UBERON:0000479,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0004765,UBERON:0010317,UBERON:0002204,UBERON:0001434,UBERON:0002390,UBERON:0002193,UBERON:0002405
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002371,UBERON:0001474,UBERON:0000479,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0004765,UBERON:0010317,UBERON:0002204,UBERON:0001434,UBERON:0002390,UBERON:0002193,UBERON:0002405
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0000763,CL:0002371,CL:0000766,CL:0000219,CL:0000325,CL:0000473,CL:0000234,CL:0000738,CL:0000255,CL:0000235,CL:0000864,CL:0002476
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0000763,CL:0002371,CL:0000766,CL:0000219,CL:0000325,CL:0000473,CL:0000234,CL:0000738,CL:0000255,CL:0000235,CL:0000864,CL:0002476
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|library_id=CNhs11532
|library_id=CNhs11532
|library_id_phase_based=2:CNhs11532
|library_id_phase_based=2:CNhs11532
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;3632
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;3632
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/macrophage%252c%2520bone%2520marrow%2520derived%252c%2520pool2.CNhs11532.3632-171A1.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/macrophage%252c%2520bone%2520marrow%2520derived%252c%2520pool2.CNhs11532.3632-171A1.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/macrophage%252c%2520bone%2520marrow%2520derived%252c%2520pool2.CNhs11532.3632-171A1.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/macrophage%252c%2520bone%2520marrow%2520derived%252c%2520pool2.CNhs11532.3632-171A1.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/macrophage%252c%2520bone%2520marrow%2520derived%252c%2520pool2.CNhs11532.3632-171A1.mm9.nobarcode.rdna.fa.gz
|name=macrophage, bone marrow derived
|name=macrophage, bone marrow derived
|namespace=
|namespace=
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|sample_tissue=bone marrow
|sample_tissue=bone marrow
|time=000hr
|time=000hr
|timecourse=BMM_TB_activation_IL13
|timecourse=BMM_TB_activation_IL4,BMM_TB_activation_IFNg,BMM_TB_activation_IL13,BMM_TB_activation_IL4-IL13
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:3632-171A1;search_select_hide=table117:3632-171A1
}}
}}

Latest revision as of 19:12, 4 June 2020


Name:macrophage, bone marrow derived
Species:Mouse (Mus musculus)
Library ID:CNhs11532
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :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

CAGE 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 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

CNhs11532

00
10
100
1000
10000
10010.055
1002-0.116
1003-0.123
10040
10050
1006-0.143
1007-0.277
10080
1009-0.19
101-0.0725
10100
1011-0.0175
10120
1013-0.0281
1014-0.0874
1015-0.267
1016-0.465
10170
10180
10190
1020
10200.42
10210.0839
1022-0.315
10230
1024-0.241
1025-0.0611
10260
10270
10280
1029-0.0989
103-0.0887
10300
1031-0.873
1032-0.184
10330
10340
10350
1036-0.158
10370
10380.0361
1039-0.0849
1040
1040-0.809
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: CNhs11532

Jaspar motifP-value
MA0002.22.18394e-5
MA0003.10.392
MA0004.10.243
MA0006.10.509
MA0007.10.594
MA0009.10.192
MA0014.10.493
MA0017.10.0566
MA0018.20.0181
MA0019.10.629
MA0024.10.0511
MA0025.10.99
MA0027.10.665
MA0028.10.0345
MA0029.10.804
MA0030.10.139
MA0031.10.457
MA0035.20.134
MA0038.10.00399
MA0039.20.707
MA0040.10.437
MA0041.10.0918
MA0042.10.66
MA0043.10.178
MA0046.16.38582e-11
MA0047.20.377
MA0048.10.482
MA0050.12.17068e-24
MA0051.11.62823e-17
MA0052.11.95666e-4
MA0055.10.583
MA0057.10.698
MA0058.10.0881
MA0059.10.0553
MA0060.16.76966e-12
MA0061.10.00167
MA0062.26.96372e-6
MA0065.20.0242
MA0066.10.00903
MA0067.10.436
MA0068.10.626
MA0069.10.936
MA0070.10.0595
MA0071.10.299
MA0072.10.374
MA0073.10.893
MA0074.10.138
MA0076.10.0977
MA0077.10.2
MA0078.10.895
MA0079.20.173
MA0080.29.78586e-13
MA0081.10.00255
MA0083.10.00374
MA0084.10.345
MA0087.10.849
MA0088.10.197
MA0090.10.0438
MA0091.10.341
MA0092.10.618
MA0093.10.217
MA0099.20.00299
MA0100.10.409
MA0101.10.00152
MA0102.20.0147
MA0103.10.829
MA0104.20.728
MA0105.12.79239e-4
MA0106.10.151
MA0107.10.00106
MA0108.23.45002e-9
MA0111.10.378
MA0112.27.75125e-5
MA0113.10.477
MA0114.10.194
MA0115.10.441
MA0116.10.0016
MA0117.10.877
MA0119.10.321
MA0122.10.212
MA0124.10.869
MA0125.10.0792
MA0131.10.777
MA0135.10.00157
MA0136.13.10862e-15
MA0137.20.162
MA0138.20.769
MA0139.10.24
MA0140.10.135
MA0141.10.0603
MA0142.10.685
MA0143.10.0861
MA0144.10.368
MA0145.10.165
MA0146.10.00856
MA0147.10.716
MA0148.10.626
MA0149.10.107
MA0150.10.00916
MA0152.10.75
MA0153.11.94603e-6
MA0154.10.0151
MA0155.10.853
MA0156.11.04402e-9
MA0157.10.644
MA0159.10.00106
MA0160.10.209
MA0162.10.273
MA0163.13.34615e-5
MA0164.10.9
MA0258.10.00475
MA0259.10.775



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: CNhs11532

Novel motifP-value
10.039
100.0233
1000.947
1010.824
1020.571
1030.0251
1040.892
1050.843
1060.101
1070.487
1080.826
1090.0345
110.0604
1100.0493
1110.00274
1120.00894
1130.63
1140.0126
1150.675
1160.522
1176.5589e-4
1180.263
1190.175
120.823
1200.174
1210.183
1220.673
1230.675
1240.764
1250.179
1260.292
1270.45
1280.0546
1290.0758
130.0118
1300.865
1310.423
1320.662
1330.823
1340.526
1350.908
1360.995
1370.103
1380.998
1390.0546
140.843
1400.047
1410.088
1420.606
1430.0309
1440.881
1450.0737
1460.708
1470.678
1480.0546
1490.0927
150.0615
1500.206
1510.282
1520.267
1530.536
1540.729
1550.6
1560.308
1570.866
1580.222
1590.895
1600.377
1610.17
1620.775
1630.783
1640.0689
1650.0589
1660.783
1670.391
1680.955
1690.00335
170.126
180.175
190.159
20.575
200.116
210.51
220.224
230.667
240.281
250.311
260.00461
270.975
280.417
290.0549
30.0179
300.537
310.649
320.836
330.123
340.955
350.46
360.0247
370.0243
380.292
390.731
40.428
400.124
410.373
420.234
430.041
440.309
450.9
460.0593
470.112
480.204
490.0546
50.178
500.987
510.864
520.888
530.571
540.75
550.95
560.476
570.43
580.311
590.161
60.885
600.203
610.151
620.0996
630.313
640.574
650.263
660.519
670.104
680.00381
690.651
70.119
700.0054
710.0284
720.178
730.0279
740.831
750.012
760.0674
770.553
780.0843
790.549
80.0329
800.692
810.243
820.276
830.879
840.687
850.355
860.226
870.62
880.699
890.154
90.518
900.0348
910.553
920.093
930.118
940.279
950.0476
960.5
970.819
980.283
991



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: CNhs11532


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)
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)<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:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)

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