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|is_a=EFO:0002091;;FF:0000103;;FF:0011232
|is_a=EFO:0002091;;FF:0011232
|is_obsolete=
|name=Tracheal epithelial cells, differentiation to ciliated epithelial cells, 000hr, biol_rep1
|name=Tracheal epithelial cells, differentiation to ciliated epithelial cells, 000hr, biol_rep1
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Revision as of 02:36, 28 June 2012


Name:Tracheal epithelial cells, differentiation to ciliated epithelial cells, 000hr, biol_rep1
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 number0-1
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

CNhs13739

00
10
100
1000
10000.0426
1001-0.0749
1002-0.116
1003-0.001
10040
10050.233
1006-0.341
1007-0.255
10080
1009-0.157
1010.0637
10100
1011-0.227
10120
10130.0459
10140
1015-0.0842
1016-0.289
10170
10180.849
10190
1020
10200.217
10210.156
1022-0.124
10230
1024-0.0899
10250
10260
1027-0.048
10280.0851
1029-0.0977
103-0.0887
10300
1031-0.581
1032-0.0914
10330.0537
10340
10350
10360.223
10370
1038-0.202
1039-0.133
1040
1040-0.00144
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: CNhs13739

Jaspar motifP-value
MA0002.20.31
MA0003.10.486
MA0004.10.735
MA0006.10.286
MA0007.10.584
MA0009.10.109
MA0014.10.0802
MA0017.10.724
MA0018.20.0389
MA0019.10.0686
MA0024.10.252
MA0025.10.372
MA0027.10.994
MA0028.11.93526e-6
MA0029.10.543
MA0030.10.656
MA0031.10.992
MA0035.22.26598e-4
MA0038.10.0289
MA0039.20.00851
MA0040.10.737
MA0041.10.572
MA0042.10.662
MA0043.10.591
MA0046.15.91984e-5
MA0047.20.0697
MA0048.10.00623
MA0050.10.293
MA0051.10.406
MA0052.10.0116
MA0055.14.67238e-5
MA0057.10.163
MA0058.10.792
MA0059.10.0823
MA0060.10.0474
MA0061.10.12
MA0062.22.00983e-8
MA0065.20.174
MA0066.10.293
MA0067.10.216
MA0068.10.941
MA0069.10.586
MA0070.10.0756
MA0071.10.313
MA0072.10.548
MA0073.10.641
MA0074.10.5
MA0076.12.93977e-5
MA0077.10.444
MA0078.10.315
MA0079.20.283
MA0080.20.66
MA0081.10.961
MA0083.10.0276
MA0084.10.381
MA0087.10.339
MA0088.10.171
MA0090.16.74659e-4
MA0091.10.495
MA0092.10.552
MA0093.10.853
MA0099.21.41547e-22
MA0100.10.343
MA0101.15.37731e-4
MA0102.20.342
MA0103.13.46132e-6
MA0104.20.73
MA0105.10.329
MA0106.11.30737e-4
MA0107.10.00866
MA0108.20.398
MA0111.10.693
MA0112.20.00813
MA0113.10.341
MA0114.10.906
MA0115.10.418
MA0116.10.178
MA0117.10.697
MA0119.10.616
MA0122.10.798
MA0124.10.261
MA0125.10.0311
MA0131.10.194
MA0135.10.0675
MA0136.10.00671
MA0137.20.0254
MA0138.20.0238
MA0139.10.514
MA0140.12.98616e-5
MA0141.10.759
MA0142.10.238
MA0143.10.278
MA0144.10.113
MA0145.10.0964
MA0146.10.194
MA0147.10.45
MA0148.10.332
MA0149.10.00402
MA0150.10.00147
MA0152.10.171
MA0153.10.00797
MA0154.10.617
MA0155.10.432
MA0156.10.00183
MA0157.10.754
MA0159.10.0012
MA0160.10.858
MA0162.10.405
MA0163.10.0414
MA0164.10.179
MA0258.10.0528
MA0259.10.608



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: CNhs13739

Novel motifP-value
10.383
100.0294
1000.314
1010.0334
1020.193
1030.0572
1040.841
1050.488
1060.18
1070.95
1080.56
1090.0127
110.294
1100.119
1110.143
1120.977
1130.277
1140.552
1150.668
1160.0606
1170.002
1180.706
1190.369
120.542
1200.543
1210.743
1220.126
1230.0673
1240.798
1250.0481
1260.835
1270.931
1280.306
1290.993
135.31053e-7
1300.468
1310.12
1320.419
1330.0339
1340.291
1350.0516
1360.0147
1370.811
1380.178
1390.361
140.624
1400.434
1410.479
1420.89
1430.386
1440.232
1450.0233
1460.401
1470.446
1480.481
1490.142
150.201
1500.342
1510.657
1520.0266
1530.3
1540.365
1550.418
1560.00329
1570.598
1580.555
1590.305
1600.925
1610.742
1620.247
1630.713
1640.0437
1650.225
1660.891
1670.732
1680.46
1690.0523
170.143
180.665
190.604
20.129
200.0435
210.162
220.611
230.758
240.15
250.972
260.00927
270.566
280.665
294.71433e-4
30.146
300.457
310.438
320.0844
330.0536
340.263
350.918
360.0642
370.0395
380.767
390.062
40.149
400.0401
410.126
420.412
430.67
440.281
450.803
460.25
470.533
480.471
490.669
50.86
500.629
510.808
520.914
530.163
540.825
550.905
560.937
570.23
580.685
590.817
60.876
600.401
610.154
620.518
630.228
640.762
650.603
660.301
670.252
680.304
690.496
70.184
700.00866
710.00986
720.849
736.04833e-4
740.243
750.0158
760.289
770.508
780.00199
790.233
80.196
800.0383
810.692
820.771
830.431
840.916
850.926
860.326
870.0274
880.852
890.712
90.827
900.337
910.306
920.898
930.844
940.46
950.00183
960.663
970.893
980.318
990.672



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: CNhs13739


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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