Personal tools

FF:3560-170A1: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(6 intermediate revisions by 2 users not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005517
|DRA_sample_Accession=CAGE@SAMD00005517
|accession_numbers=CAGE;DRX008914;DRR009788;DRZ001213;DRZ002596
|accession_numbers=CAGE;DRX008914;DRR009788;DRZ001213;DRZ002596;DRZ012563;DRZ013946
|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
Line 47: Line 47:
|library_id=CNhs11457
|library_id=CNhs11457
|library_id_phase_based=2:CNhs11457
|library_id_phase_based=2:CNhs11457
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;3560
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;3560
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/macrophage%252c%2520bone%2520marrow%2520derived%252c%2520pool1.CNhs11457.3560-170A1.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/macrophage%252c%2520bone%2520marrow%2520derived%252c%2520pool1.CNhs11457.3560-170A1.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/macrophage%252c%2520bone%2520marrow%2520derived%252c%2520pool1.CNhs11457.3560-170A1.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/macrophage%252c%2520bone%2520marrow%2520derived%252c%2520pool1.CNhs11457.3560-170A1.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/macrophage%252c%2520bone%2520marrow%2520derived%252c%2520pool1.CNhs11457.3560-170A1.mm9.nobarcode.rdna.fa.gz
|name=macrophage, bone marrow derived
|name=macrophage, bone marrow derived
|namespace=
|namespace=
Line 88: Line 97:
|sample_tissue=bone marrow
|sample_tissue=bone marrow
|time=000hr
|time=000hr
|timecourse=BMM_TB_activation_IL4
|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=table111:3560-170A1;search_select_hide=table117:3560-170A1
}}
}}

Latest revision as of 19:10, 4 June 2020


Name:macrophage, bone marrow derived
Species:Mouse (Mus musculus)
Library ID:CNhs11457
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  SAMD00005517
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11457 CAGE DRX008914 DRR009788
Accession ID Mm9

Library idBAMCTSS
CNhs11457 DRZ001213 DRZ002596
Accession ID Mm10

Library idBAMCTSS
CNhs11457 DRZ012563 DRZ013946
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

CNhs11457

00
10
100
1000
10000
1001-0.0631
1002-0.116
1003-0.123
10040
10050
1006-0.0364
1007-0.142
10080
1009-0.2
101-0.0739
10100
1011-0.177
10120
1013-0.0294
1014-0.0874
1015-0.303
1016-0.465
10170
10180
10190
1020
10200.604
10210
1022-0.141
10230.399
1024-0.14
1025-0.0611
10260
10270
10280
1029-0.148
103-0.0887
10300
1031-0.832
1032-0.288
1033-0.0665
10340
10350
10360.0565
10370
10380.00805
1039-0.107
1040
1040-0.536
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: CNhs11457

Jaspar motifP-value
MA0002.26.07125e-5
MA0003.10.498
MA0004.10.239
MA0006.10.517
MA0007.10.322
MA0009.10.191
MA0014.10.878
MA0017.10.142
MA0018.20.0377
MA0019.10.807
MA0024.10.0146
MA0025.10.721
MA0027.10.583
MA0028.10.14
MA0029.10.834
MA0030.10.285
MA0031.10.459
MA0035.20.276
MA0038.10.00315
MA0039.20.694
MA0040.10.701
MA0041.10.0732
MA0042.10.488
MA0043.10.0582
MA0046.11.48625e-8
MA0047.20.342
MA0048.10.728
MA0050.11.20175e-17
MA0051.11.31145e-12
MA0052.10.00135
MA0055.10.972
MA0057.10.841
MA0058.10.096
MA0059.10.101
MA0060.12.39358e-15
MA0061.10.00789
MA0062.23.3426e-4
MA0065.20.047
MA0066.10.0245
MA0067.10.466
MA0068.10.418
MA0069.10.807
MA0070.10.0958
MA0071.10.255
MA0072.10.343
MA0073.10.907
MA0074.10.131
MA0076.10.288
MA0077.10.137
MA0078.10.835
MA0079.20.157
MA0080.23.11114e-12
MA0081.10.00324
MA0083.10.00405
MA0084.10.256
MA0087.10.966
MA0088.10.127
MA0090.10.0701
MA0091.10.229
MA0092.10.66
MA0093.10.237
MA0099.20.0076
MA0100.10.475
MA0101.10.0152
MA0102.20.192
MA0103.10.83
MA0104.20.803
MA0105.11.23552e-4
MA0106.10.348
MA0107.10.0197
MA0108.21.34588e-9
MA0111.10.412
MA0112.28.82154e-5
MA0113.10.409
MA0114.10.354
MA0115.10.983
MA0116.10.00357
MA0117.10.758
MA0119.10.247
MA0122.10.374
MA0124.10.434
MA0125.10.121
MA0131.10.462
MA0135.10.0043
MA0136.14.61506e-14
MA0137.20.443
MA0138.20.979
MA0139.10.373
MA0140.10.6
MA0141.10.0559
MA0142.10.663
MA0143.10.179
MA0144.10.491
MA0145.10.183
MA0146.10.0215
MA0147.10.845
MA0148.10.565
MA0149.10.148
MA0150.10.0389
MA0152.10.986
MA0153.11.36817e-5
MA0154.10.00812
MA0155.10.959
MA0156.14.75709e-8
MA0157.10.623
MA0159.17.80757e-4
MA0160.10.255
MA0162.10.3
MA0163.11.07252e-5
MA0164.10.55
MA0258.10.00461
MA0259.10.941



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: CNhs11457

Novel motifP-value
10.0434
100.0174
1000.955
1010.866
1020.854
1030.0312
1040.859
1050.722
1060.13
1070.671
1080.91
1090.0443
110.0755
1100.114
1110.00336
1120.0108
1130.602
1140.00568
1150.687
1160.476
1174.88335e-4
1180.0996
1190.147
120.505
1200.173
1210.0758
1220.561
1230.824
1240.699
1250.415
1260.296
1270.252
1280.207
1290.119
130.0145
1300.702
1310.736
1320.955
1330.817
1340.533
1350.911
1360.913
1370.288
1380.871
1390.0871
140.594
1400.0226
1410.174
1420.863
1430.103
1440.861
1450.197
1460.641
1470.742
1480.0456
1490.038
150.0436
1500.206
1510.259
1520.468
1530.953
1540.88
1550.492
1560.555
1570.674
1580.194
1591
1600.268
1610.289
1620.748
1630.695
1640.0492
1650.0284
1660.876
1670.307
1680.832
1690.00485
170.22
180.132
190.148
20.715
200.118
210.393
220.219
230.625
240.192
250.456
260.00367
270.845
280.375
290.0726
30.00989
300.527
310.659
320.567
330.251
340.799
350.177
360.0192
370.0229
380.208
390.667
40.478
400.181
410.384
420.182
430.0363
440.196
450.742
460.0386
470.159
480.232
490.054
50.106
500.867
510.739
520.995
530.46
540.684
550.996
560.324
570.344
580.336
590.128
60.612
600.189
610.157
620.108
630.258
640.452
650.117
660.477
670.0867
680.0166
690.495
70.13
700.00369
710.0284
720.13
730.0355
740.862
750.00957
760.0604
770.383
780.122
790.496
80.0582
800.846
810.27
820.257
830.764
840.799
850.209
860.185
870.513
880.587
890.0862
90.507
900.0318
910.592
920.0823
930.119
940.345
950.11
960.734
970.789
980.159
990.97



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: CNhs11457


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)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:3560-170A1&oldid=4578246"