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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005581
|DRA_sample_Accession=CAGE@SAMD00005581
|accession_numbers=CAGE;DRX008913;DRR009787;DRZ001212;DRZ002595
|accession_numbers=CAGE;DRX008913;DRR009787;DRZ001212;DRZ002595;DRZ012562;DRZ013945
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0003126,UBERON:0002100,UBERON:0000064,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0009569,UBERON:0005178,UBERON:0000072,UBERON:0005177,UBERON:0000464,UBERON:0001005,UBERON:0005181,UBERON:0010317,UBERON:0007196,UBERON:0000065,UBERON:0001558,UBERON:0001004,UBERON:0002224,UBERON:0000915
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0003126,UBERON:0002100,UBERON:0000064,UBERON:0004119,UBERON:0000466,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0009569,UBERON:0005178,UBERON:0000072,UBERON:0005177,UBERON:0000464,UBERON:0001005,UBERON:0005181,UBERON:0010317,UBERON:0007196,UBERON:0000065,UBERON:0001558,UBERON:0001004,UBERON:0002224,UBERON:0000915
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002202,CL:0000255,CL:0002076,CL:0002632,CL:0002368,CL:0000307
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002202,CL:0000255,CL:0002076,CL:0002632,CL:0002368,CL:0000307
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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;13369
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;13369
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;13369
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;13369
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/Tracheal%2520epithelial%2520cells%252c%2520differentiation%2520to%2520ciliated%2520epithelial%2520cells%252c%2520000hr%252c%2520biol_rep3.CNhs13741.13369-143G3.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/Tracheal%2520epithelial%2520cells%252c%2520differentiation%2520to%2520ciliated%2520epithelial%2520cells%252c%2520000hr%252c%2520biol_rep3.CNhs13741.13369-143G3.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/Tracheal%2520epithelial%2520cells%252c%2520differentiation%2520to%2520ciliated%2520epithelial%2520cells%252c%2520000hr%252c%2520biol_rep3.CNhs13741.13369-143G3.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/Tracheal%2520epithelial%2520cells%252c%2520differentiation%2520to%2520ciliated%2520epithelial%2520cells%252c%2520000hr%252c%2520biol_rep3.CNhs13741.13369-143G3.mm10.nobarcode.ctss.bed.gz
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|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:13369-143G3;search_select_hide=table117:13369-143G3
}}
}}

Latest revision as of 18:57, 4 June 2020


Name:Tracheal epithelial cells, differentiation to ciliated epithelial cells
Species:Mouse (Mus musculus)
Library ID:CNhs13741
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissueNA
dev stageNA
sexfemale
ageNA
cell typeSELECT CELL TYPE
cell lineNA
companyNA
collaborationMitsuru Morimoto
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number0-3
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005581
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13741 CAGE DRX008913 DRR009787
Accession ID Mm9

Library idBAMCTSS
CNhs13741 DRZ001212 DRZ002595
Accession ID Mm10

Library idBAMCTSS
CNhs13741 DRZ012562 DRZ013945
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

CNhs13741

00
10
100
1000
10000
1001-0.0356
1002-0.116
1003-0.102
10040
10050.0457
1006-0.362
1007-0.306
10080
1009-0.19
1010.0376
10100
1011-0.12
10120
10130.0241
10140
1015-0.0805
1016-0.486
10170
10180.744
10190
1020
10200.178
10210.178
1022-0.138
10230
1024-0.14
10250
10260
1027-0.048
10280
1029-0.148
103-0.0861
10300
1031-0.627
1032-0.162
10330
10340
10350
10360.255
10370
1038-0.159
1039-0.0104
1040
10400.0568
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: CNhs13741

Jaspar motifP-value
MA0002.20.225
MA0003.10.479
MA0004.10.651
MA0006.10.247
MA0007.10.622
MA0009.10.175
MA0014.10.106
MA0017.10.914
MA0018.20.051
MA0019.10.124
MA0024.10.886
MA0025.10.425
MA0027.10.877
MA0028.16.10034e-5
MA0029.10.47
MA0030.10.916
MA0031.10.824
MA0035.23.79235e-4
MA0038.10.0213
MA0039.20.0236
MA0040.10.91
MA0041.10.596
MA0042.10.728
MA0043.10.546
MA0046.14.84586e-5
MA0047.20.0274
MA0048.10.00607
MA0050.10.202
MA0051.10.136
MA0052.10.0243
MA0055.16.45399e-5
MA0057.10.0987
MA0058.10.756
MA0059.10.0448
MA0060.10.00189
MA0061.10.102
MA0062.25.39378e-7
MA0065.20.16
MA0066.10.231
MA0067.10.29
MA0068.10.716
MA0069.10.343
MA0070.10.0705
MA0071.10.26
MA0072.10.671
MA0073.10.605
MA0074.10.484
MA0076.19.5507e-4
MA0077.10.521
MA0078.10.306
MA0079.20.246
MA0080.20.444
MA0081.10.715
MA0083.10.0238
MA0084.10.698
MA0087.10.183
MA0088.10.138
MA0090.14.73441e-4
MA0091.10.641
MA0092.10.456
MA0093.10.812
MA0099.21.03311e-19
MA0100.10.265
MA0101.18.01223e-4
MA0102.20.332
MA0103.12.61764e-6
MA0104.20.572
MA0105.10.24
MA0106.19.58631e-4
MA0107.10.012
MA0108.20.528
MA0111.10.701
MA0112.20.0048
MA0113.10.305
MA0114.10.926
MA0115.10.488
MA0116.10.0987
MA0117.10.878
MA0119.10.318
MA0122.10.763
MA0124.10.0888
MA0125.10.0756
MA0131.10.278
MA0135.10.098
MA0136.10.00285
MA0137.20.0575
MA0138.20.039
MA0139.10.4
MA0140.16.64163e-4
MA0141.10.491
MA0142.10.53
MA0143.10.578
MA0144.10.128
MA0145.10.0841
MA0146.10.114
MA0147.10.28
MA0148.10.385
MA0149.10.00532
MA0150.10.00345
MA0152.10.311
MA0153.10.0169
MA0154.10.615
MA0155.10.444
MA0156.10.00824
MA0157.10.725
MA0159.13.48039e-4
MA0160.10.572
MA0162.10.343
MA0163.10.05
MA0164.10.161
MA0258.10.0346
MA0259.10.575



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: CNhs13741

Novel motifP-value
10.521
100.0388
1000.392
1010.0837
1020.308
1030.0405
1040.905
1050.68
1060.126
1070.682
1080.575
1090.0132
110.252
1100.132
1110.0767
1120.875
1130.359
1140.266
1150.477
1160.0612
1170.00209
1180.525
1190.197
120.516
1200.552
1210.785
1220.134
1230.0856
1240.709
1250.0372
1260.809
1270.963
1280.0737
1290.881
132.09184e-6
1300.401
1310.0632
1320.596
1330.0709
1340.269
1350.025
1360.0186
1370.816
1380.221
1390.209
140.639
1400.295
1410.135
1420.846
1430.187
1440.112
1450.0335
1460.368
1470.477
1480.745
1490.172
150.168
1500.352
1510.656
1520.0174
1530.536
1540.323
1550.273
1560.00778
1570.705
1580.329
1590.295
1600.934
1610.684
1620.418
1630.771
1640.0574
1650.22
1660.996
1670.659
1680.479
1690.0309
170.151
180.929
190.515
20.185
200.067
210.295
220.468
230.779
240.104
250.972
260.00698
270.686
280.683
290.00143
30.0725
300.719
310.613
320.127
330.0837
340.384
350.825
360.0421
370.0301
380.559
390.0562
40.284
400.0484
410.101
420.486
430.431
440.148
450.963
460.189
470.498
480.479
490.516
50.619
500.566
510.712
520.68
530.151
540.691
550.95
560.972
570.208
580.578
590.743
60.887
600.289
610.0904
620.441
630.172
640.907
650.321
660.477
670.25
680.225
690.388
70.226
700.00433
710.00741
720.818
735.88387e-4
740.46
750.00999
760.302
770.386
780.00103
790.163
80.165
800.0712
810.765
820.99
830.468
840.724
850.937
860.24
870.0548
880.962
890.698
90.781
900.663
910.337
920.846
930.525
940.278
950.00261
960.457
970.884
980.314
990.3



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: CNhs13741


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)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002202 (epithelial cell of tracheobronchial tree)
0000255 (eukaryotic cell)
0002076 (endo-epithelial cell)
0002632 (epithelial cell of lower respiratory tract)
0002368 (respiratory epithelial cell)
0000307 (tracheal epithelial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0003126 (trachea)
0002100 (trunk)
0000064 (organ part)
0004119 (endoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0009569 (subdivision of trunk)
0005178 (thoracic cavity element)
0000072 (segment of respiratory tract)
0005177 (trunk region element)
0000464 (anatomical space)
0001005 (respiratory airway)
0005181 (thoracic segment organ)
0010317 (germ layer / neural crest derived structure)
0007196 (tracheobronchial tree)
0000065 (respiratory tract)
0001558 (lower respiratory tract)
0001004 (respiratory system)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000357 (0 hr sample)
0000645 (tracheal ciliated cell differentiation sample)
0000652 (tracheal ciliated cell line sample)
0011232 (mouse tracheal ciliated cells differentiation after 0hr 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:0000223 (endodermal cell)
CL:0000377 (tracheoblast)

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