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FF:13368-143G2

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Name:Tracheal epithelial cells, differentiation to ciliated epithelial cells
Species:Mouse (Mus musculus)
Library ID:CNhs13740
Sample type:time courses
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
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

Accession numbers
MethodSample accession id
CAGE  SAMD00005464
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13740 CAGE DRX008912 DRR009786
Accession ID Mm9

Library idBAMCTSS
CNhs13740 DRZ001211 DRZ002594
Accession ID Mm10

Library idBAMCTSS
CNhs13740 DRZ012561 DRZ013944
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.
Analyst:NA

link to dataset.
data

CNhs13740

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0668
1002 --0.116
1003 --0.113
1004 0
1005 0.245
1006 --0.378
1007 --0.329
1008 0
1009 --0.0572
101 0.0479
1010 0
1011 --0.2
1012 0
1013 --0.047
1014 0
1015 --0.0623
1016 --0.239
1017 0
1018 0.783
1019 0
102 0
1020 0.178
1021 0.255
1022 --0.0974
1023 0
1024 --0.14
1025 0
1026 0
1027 --0.048
1028 0.246
1029 --0.115
103 --0.0887
1030 0
1031 --0.554
1032 --0.1
1033 0.0144
1034 0
1035 0
1036 0.16
1037 0
1038 --0.22
1039 --0.15
104 0
1040 --0.118
1041 0



Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs13740

Jaspar motif P-value
MA0002.2 0.368
MA0003.1 0.435
MA0004.1 0.808
MA0006.1 0.267
MA0007.1 0.459
MA0009.1 0.184
MA0014.1 0.0977
MA0017.1 0.855
MA0018.2 0.0404
MA0019.1 0.108
MA0024.1 0.313
MA0025.1 0.195
MA0027.1 0.966
MA0028.1 4.37321e-6
MA0029.1 0.444
MA0030.1 0.94
MA0031.1 0.989
MA0035.2 4.87796e-4
MA0038.1 0.017
MA0039.2 0.00998
MA0040.1 0.72
MA0041.1 0.883
MA0042.1 0.894
MA0043.1 0.376
MA0046.1 5.6182e-5
MA0047.2 0.0294
MA0048.1 0.00519
MA0050.1 0.337
MA0051.1 0.47
MA0052.1 0.00988
MA0055.1 7.31898e-5
MA0057.1 0.099
MA0058.1 0.903
MA0059.1 0.109
MA0060.1 0.0164
MA0061.1 0.133
MA0062.2 2.10292e-8
MA0065.2 0.235
MA0066.1 0.313
MA0067.1 0.327
MA0068.1 0.966
MA0069.1 0.36
MA0070.1 0.0694
MA0071.1 0.319
MA0072.1 0.505
MA0073.1 0.764
MA0074.1 0.565
MA0076.1 2.42787e-5
MA0077.1 0.175
MA0078.1 0.315
MA0079.2 0.261
MA0080.2 0.327
MA0081.1 0.644
MA0083.1 0.0508
MA0084.1 0.361
MA0087.1 0.342
MA0088.1 0.168
MA0090.1 3.72587e-4
MA0091.1 0.511
MA0092.1 0.64
MA0093.1 0.949
MA0099.2 1.80316e-21
MA0100.1 0.51
MA0101.1 3.4387e-4
MA0102.2 0.34
MA0103.1 3.54246e-6
MA0104.2 0.715
MA0105.1 0.342
MA0106.1 1.28857e-4
MA0107.1 0.00655
MA0108.2 0.533
MA0111.1 0.575
MA0112.2 0.00892
MA0113.1 0.301
MA0114.1 0.719
MA0115.1 0.312
MA0116.1 0.174
MA0117.1 0.619
MA0119.1 0.579
MA0122.1 0.726
MA0124.1 0.325
MA0125.1 0.0504
MA0131.1 0.274
MA0135.1 0.0789
MA0136.1 0.00143
MA0137.2 0.00721
MA0138.2 0.0176
MA0139.1 0.575
MA0140.1 3.63295e-5
MA0141.1 0.679
MA0142.1 0.362
MA0143.1 0.556
MA0144.1 0.0554
MA0145.1 0.119
MA0146.1 0.168
MA0147.1 0.4
MA0148.1 0.284
MA0149.1 0.00584
MA0150.1 0.00117
MA0152.1 0.188
MA0153.1 0.009
MA0154.1 0.862
MA0155.1 0.399
MA0156.1 0.00157
MA0157.1 0.561
MA0159.1 4.25351e-4
MA0160.1 0.932
MA0162.1 0.321
MA0163.1 0.0684
MA0164.1 0.248
MA0258.1 0.064
MA0259.1 0.596



FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs13740

Novel motif P-value
1 0.484
10 0.0336
100 0.355
101 0.0499
102 0.264
103 0.0565
104 0.862
105 0.569
106 0.128
107 0.95
108 0.543
109 0.0087
11 0.284
110 0.188
111 0.141
112 0.914
113 0.304
114 0.623
115 0.749
116 0.101
117 0.00226
118 0.821
119 0.308
12 0.537
120 0.593
121 0.992
122 0.12
123 0.0574
124 0.771
125 0.0528
126 0.884
127 0.914
128 0.157
129 0.681
13 5.0794e-7
130 0.493
131 0.0771
132 0.251
133 0.0293
134 0.188
135 0.0601
136 0.0097
137 0.97
138 0.211
139 0.184
14 0.634
140 0.327
141 0.329
142 0.886
143 0.484
144 0.234
145 0.0302
146 0.598
147 0.622
148 0.639
149 0.115
15 0.257
150 0.329
151 0.7
152 0.0128
153 0.299
154 0.306
155 0.185
156 0.00413
157 0.386
158 0.532
159 0.262
160 0.897
161 0.726
162 0.409
163 0.875
164 0.0445
165 0.18
166 0.937
167 0.52
168 0.323
169 0.0472
17 0.102
18 0.634
19 0.743
2 0.153
20 0.0484
21 0.278
22 0.539
23 0.995
24 0.0978
25 0.984
26 0.011
27 0.581
28 0.755
29 5.91018e-4
3 0.106
30 0.564
31 0.4
32 0.142
33 0.0655
34 0.292
35 0.933
36 0.0607
37 0.0272
38 0.761
39 0.0693
4 0.144
40 0.0338
41 0.109
42 0.409
43 0.593
44 0.356
45 0.898
46 0.215
47 0.403
48 0.424
49 0.693
5 0.95
50 0.58
51 0.842
52 0.73
53 0.168
54 0.828
55 0.812
56 0.838
57 0.181
58 0.536
59 0.757
6 0.747
60 0.239
61 0.111
62 0.404
63 0.239
64 0.654
65 0.696
66 0.226
67 0.196
68 0.401
69 0.478
7 0.211
70 0.0181
71 0.00884
72 0.76
73 1.95606e-4
74 0.19
75 0.0131
76 0.244
77 0.455
78 0.00216
79 0.287
8 0.264
80 0.0301
81 0.539
82 0.94
83 0.585
84 0.968
85 0.904
86 0.268
87 0.019
88 0.891
89 0.861
9 0.932
90 0.551
91 0.325
92 0.973
93 0.643
94 0.298
95 0.00109
96 0.734
97 0.857
98 0.258
99 0.575



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs13740


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
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)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

CL:0000223 (endodermal cell)
CL:0000377 (tracheoblast)