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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000065,UBERON:0000072,UBERON:0000077,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000915,UBERON:0000922,UBERON:0000923,UBERON:0000925,UBERON:0000926,UBERON:0001004,UBERON:0001005,UBERON:0001007,UBERON:0001041,UBERON:0001048,UBERON:0001062,UBERON:0001555,UBERON:0001558,UBERON:0002050,UBERON:0002224,UBERON:0002532,UBERON:0003104,UBERON:0003126,UBERON:0003258,UBERON:0004119,UBERON:0004120,UBERON:0004185,UBERON:0004921,UBERON:0005423,UBERON:0007026,UBERON:0007196,UBERON:0008947,UBERON:0009142
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0003126,UBERON:0002100,UBERON:0000926,UBERON:0000479,UBERON:0001007,UBERON:0000064,UBERON:0000077,UBERON:0000466,UBERON:0000062,UBERON:0000475,UBERON:0004120,UBERON:0004119,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0004921,UBERON:0005423,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0003103,UBERON:0009569,UBERON:0005291,UBERON:0005178,UBERON:0000072,UBERON:0005177,UBERON:0003104,UBERON:0000464,UBERON:0001048,UBERON:0001005,UBERON:0000925,UBERON:0005181,UBERON:0006598,UBERON:0004185,UBERON:0002532,UBERON:0007196,UBERON:0001555,UBERON:0000065,UBERON:0001558,UBERON:0001004,UBERON:0007026,UBERON:0001041,UBERON:0002224,UBERON:0000915,UBERON:0009142,UBERON:0008947,UBERON:0003258,UBERON:0006595,UBERON:0006603
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000068,CL:0000069,CL:0000144,CL:0000220,CL:0000223,CL:0000255,CL:0000307,CL:0000377,CL:0000548,CL:0002076,CL:0002202,CL:0002321,CL:0002368,CL:0002371,CL:0002632
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000548,CL:0000012,CL:0002321,CL:0000063,CL:0000066,CL:0002371,CL:0000068,CL:0000220,CL:0000004,CL:0002202,CL:0000069,CL:0000255,CL:0002076,CL:0002632,CL:0002368,CL:0000307,CL:0000223,CL:0000377
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|comment=
|comment=

Revision as of 18:08, 8 June 2012


Name:Tracheal epithelial cells, differentiation to ciliated epithelial cells, 000hr, biol_rep2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM: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 number0-2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
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

CNhs13740

00
10
100
1000
10000
1001-0.0668
1002-0.116
1003-0.113
10040
10050.245
1006-0.378
1007-0.329
10080
1009-0.0572
1010.0479
10100
1011-0.2
10120
1013-0.047
10140
1015-0.0623
1016-0.239
10170
10180.783
10190
1020
10200.178
10210.255
1022-0.0974
10230
1024-0.14
10250
10260
1027-0.048
10280.246
1029-0.115
103-0.0887
10300
1031-0.554
1032-0.1
10330.0144
10340
10350
10360.16
10370
1038-0.22
1039-0.15
1040
1040-0.118
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 no result for this sample


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: CNhs13740

Jaspar motifP-value
MA0002.20.368
MA0003.10.435
MA0004.10.808
MA0006.10.267
MA0007.10.459
MA0009.10.184
MA0014.10.0977
MA0017.10.855
MA0018.20.0404
MA0019.10.108
MA0024.10.313
MA0025.10.195
MA0027.10.966
MA0028.14.37321e-6
MA0029.10.444
MA0030.10.94
MA0031.10.989
MA0035.24.87796e-4
MA0038.10.017
MA0039.20.00998
MA0040.10.72
MA0041.10.883
MA0042.10.894
MA0043.10.376
MA0046.15.6182e-5
MA0047.20.0294
MA0048.10.00519
MA0050.10.337
MA0051.10.47
MA0052.10.00988
MA0055.17.31898e-5
MA0057.10.099
MA0058.10.903
MA0059.10.109
MA0060.10.0164
MA0061.10.133
MA0062.22.10292e-8
MA0065.20.235
MA0066.10.313
MA0067.10.327
MA0068.10.966
MA0069.10.36
MA0070.10.0694
MA0071.10.319
MA0072.10.505
MA0073.10.764
MA0074.10.565
MA0076.12.42787e-5
MA0077.10.175
MA0078.10.315
MA0079.20.261
MA0080.20.327
MA0081.10.644
MA0083.10.0508
MA0084.10.361
MA0087.10.342
MA0088.10.168
MA0090.13.72587e-4
MA0091.10.511
MA0092.10.64
MA0093.10.949
MA0099.21.80316e-21
MA0100.10.51
MA0101.13.4387e-4
MA0102.20.34
MA0103.13.54246e-6
MA0104.20.715
MA0105.10.342
MA0106.11.28857e-4
MA0107.10.00655
MA0108.20.533
MA0111.10.575
MA0112.20.00892
MA0113.10.301
MA0114.10.719
MA0115.10.312
MA0116.10.174
MA0117.10.619
MA0119.10.579
MA0122.10.726
MA0124.10.325
MA0125.10.0504
MA0131.10.274
MA0135.10.0789
MA0136.10.00143
MA0137.20.00721
MA0138.20.0176
MA0139.10.575
MA0140.13.63295e-5
MA0141.10.679
MA0142.10.362
MA0143.10.556
MA0144.10.0554
MA0145.10.119
MA0146.10.168
MA0147.10.4
MA0148.10.284
MA0149.10.00584
MA0150.10.00117
MA0152.10.188
MA0153.10.009
MA0154.10.862
MA0155.10.399
MA0156.10.00157
MA0157.10.561
MA0159.14.25351e-4
MA0160.10.932
MA0162.10.321
MA0163.10.0684
MA0164.10.248
MA0258.10.064
MA0259.10.596



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: CNhs13740

Novel motifP-value
10.484
100.0336
1000.355
1010.0499
1020.264
1030.0565
1040.862
1050.569
1060.128
1070.95
1080.543
1090.0087
110.284
1100.188
1110.141
1120.914
1130.304
1140.623
1150.749
1160.101
1170.00226
1180.821
1190.308
120.537
1200.593
1210.992
1220.12
1230.0574
1240.771
1250.0528
1260.884
1270.914
1280.157
1290.681
135.0794e-7
1300.493
1310.0771
1320.251
1330.0293
1340.188
1350.0601
1360.0097
1370.97
1380.211
1390.184
140.634
1400.327
1410.329
1420.886
1430.484
1440.234
1450.0302
1460.598
1470.622
1480.639
1490.115
150.257
1500.329
1510.7
1520.0128
1530.299
1540.306
1550.185
1560.00413
1570.386
1580.532
1590.262
1600.897
1610.726
1620.409
1630.875
1640.0445
1650.18
1660.937
1670.52
1680.323
1690.0472
170.102
180.634
190.743
20.153
200.0484
210.278
220.539
230.995
240.0978
250.984
260.011
270.581
280.755
295.91018e-4
30.106
300.564
310.4
320.142
330.0655
340.292
350.933
360.0607
370.0272
380.761
390.0693
40.144
400.0338
410.109
420.409
430.593
440.356
450.898
460.215
470.403
480.424
490.693
50.95
500.58
510.842
520.73
530.168
540.828
550.812
560.838
570.181
580.536
590.757
60.747
600.239
610.111
620.404
630.239
640.654
650.696
660.226
670.196
680.401
690.478
70.211
700.0181
710.00884
720.76
731.95606e-4
740.19
750.0131
760.244
770.455
780.00216
790.287
80.264
800.0301
810.539
820.94
830.585
840.968
850.904
860.268
870.019
880.891
890.861
90.932
900.551
910.325
920.973
930.643
940.298
950.00109
960.734
970.857
980.258
990.575



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: CNhs13740


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)
0002321 (embryonic cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000068 (duct epithelial cell)
0002202 (epithelial cell of tracheobronchial tree)
0000069 (branched duct epithelial cell)
0000255 (eukaryotic cell)
0002076 (endo-epithelial cell)
0002632 (epithelial cell of lower respiratory tract)
0002368 (respiratory epithelial cell)
0000307 (tracheal epithelial cell)
0000223 (endodermal cell)
0000377 (tracheoblast)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0003126 (trachea)
0002100 (trunk)
0000926 (mesoderm)
0000479 (tissue)
0001007 (digestive system)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0004119 (endoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0004921 (subdivision of digestive tract)
0005423 (developing anatomical structure)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0003103 (compound organ)
0009569 (subdivision of trunk)
0005291 (embryonic tissue)
0005178 (thoracic cavity element)
0000072 (segment of respiratory tract)
0005177 (trunk region element)
0003104 (mesenchyme)
0000464 (anatomical space)
0001048 (primordium)
0001005 (respiratory airway)
0000925 (endoderm)
0005181 (thoracic segment organ)
0006598 (presumptive structure)
0004185 (endodermal part of digestive tract)
0002532 (epiblast (generic))
0007196 (tracheobronchial tree)
0001555 (digestive tract)
0000065 (respiratory tract)
0001558 (lower respiratory tract)
0001004 (respiratory system)
0007026 (primitive gut)
0001041 (foregut)
0002224 (thoracic cavity)
0000915 (thoracic segment of trunk)
0009142 (entire embryonic mesenchyme)
0008947 (respiratory primordium)
0003258 (endoderm of foregut)
0006595 (presumptive endoderm)
0006603 (presumptive mesoderm)

FF: FANTOM5
NA

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
NA

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