Personal tools

FF:13369-143G3

From FANTOM5_SSTAR

Revision as of 13:08, 10 August 2017 by Autoedit (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Name:Tracheal epithelial cells, differentiation to ciliated epithelial cells
Species:Mouse (Mus musculus)
Library ID:CNhs13741
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 number0-3
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

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.
Analyst:NA

link to dataset.
data

CNhs13741

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0356
1002 --0.116
1003 --0.102
1004 0
1005 0.0457
1006 --0.362
1007 --0.306
1008 0
1009 --0.19
101 0.0376
1010 0
1011 --0.12
1012 0
1013 0.0241
1014 0
1015 --0.0805
1016 --0.486
1017 0
1018 0.744
1019 0
102 0
1020 0.178
1021 0.178
1022 --0.138
1023 0
1024 --0.14
1025 0
1026 0
1027 --0.048
1028 0
1029 --0.148
103 --0.0861
1030 0
1031 --0.627
1032 --0.162
1033 0
1034 0
1035 0
1036 0.255
1037 0
1038 --0.159
1039 --0.0104
104 0
1040 0.0568
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: CNhs13741

Jaspar motif P-value
MA0002.2 0.225
MA0003.1 0.479
MA0004.1 0.651
MA0006.1 0.247
MA0007.1 0.622
MA0009.1 0.175
MA0014.1 0.106
MA0017.1 0.914
MA0018.2 0.051
MA0019.1 0.124
MA0024.1 0.886
MA0025.1 0.425
MA0027.1 0.877
MA0028.1 6.10034e-5
MA0029.1 0.47
MA0030.1 0.916
MA0031.1 0.824
MA0035.2 3.79235e-4
MA0038.1 0.0213
MA0039.2 0.0236
MA0040.1 0.91
MA0041.1 0.596
MA0042.1 0.728
MA0043.1 0.546
MA0046.1 4.84586e-5
MA0047.2 0.0274
MA0048.1 0.00607
MA0050.1 0.202
MA0051.1 0.136
MA0052.1 0.0243
MA0055.1 6.45399e-5
MA0057.1 0.0987
MA0058.1 0.756
MA0059.1 0.0448
MA0060.1 0.00189
MA0061.1 0.102
MA0062.2 5.39378e-7
MA0065.2 0.16
MA0066.1 0.231
MA0067.1 0.29
MA0068.1 0.716
MA0069.1 0.343
MA0070.1 0.0705
MA0071.1 0.26
MA0072.1 0.671
MA0073.1 0.605
MA0074.1 0.484
MA0076.1 9.5507e-4
MA0077.1 0.521
MA0078.1 0.306
MA0079.2 0.246
MA0080.2 0.444
MA0081.1 0.715
MA0083.1 0.0238
MA0084.1 0.698
MA0087.1 0.183
MA0088.1 0.138
MA0090.1 4.73441e-4
MA0091.1 0.641
MA0092.1 0.456
MA0093.1 0.812
MA0099.2 1.03311e-19
MA0100.1 0.265
MA0101.1 8.01223e-4
MA0102.2 0.332
MA0103.1 2.61764e-6
MA0104.2 0.572
MA0105.1 0.24
MA0106.1 9.58631e-4
MA0107.1 0.012
MA0108.2 0.528
MA0111.1 0.701
MA0112.2 0.0048
MA0113.1 0.305
MA0114.1 0.926
MA0115.1 0.488
MA0116.1 0.0987
MA0117.1 0.878
MA0119.1 0.318
MA0122.1 0.763
MA0124.1 0.0888
MA0125.1 0.0756
MA0131.1 0.278
MA0135.1 0.098
MA0136.1 0.00285
MA0137.2 0.0575
MA0138.2 0.039
MA0139.1 0.4
MA0140.1 6.64163e-4
MA0141.1 0.491
MA0142.1 0.53
MA0143.1 0.578
MA0144.1 0.128
MA0145.1 0.0841
MA0146.1 0.114
MA0147.1 0.28
MA0148.1 0.385
MA0149.1 0.00532
MA0150.1 0.00345
MA0152.1 0.311
MA0153.1 0.0169
MA0154.1 0.615
MA0155.1 0.444
MA0156.1 0.00824
MA0157.1 0.725
MA0159.1 3.48039e-4
MA0160.1 0.572
MA0162.1 0.343
MA0163.1 0.05
MA0164.1 0.161
MA0258.1 0.0346
MA0259.1 0.575



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: CNhs13741

Novel motif P-value
1 0.521
10 0.0388
100 0.392
101 0.0837
102 0.308
103 0.0405
104 0.905
105 0.68
106 0.126
107 0.682
108 0.575
109 0.0132
11 0.252
110 0.132
111 0.0767
112 0.875
113 0.359
114 0.266
115 0.477
116 0.0612
117 0.00209
118 0.525
119 0.197
12 0.516
120 0.552
121 0.785
122 0.134
123 0.0856
124 0.709
125 0.0372
126 0.809
127 0.963
128 0.0737
129 0.881
13 2.09184e-6
130 0.401
131 0.0632
132 0.596
133 0.0709
134 0.269
135 0.025
136 0.0186
137 0.816
138 0.221
139 0.209
14 0.639
140 0.295
141 0.135
142 0.846
143 0.187
144 0.112
145 0.0335
146 0.368
147 0.477
148 0.745
149 0.172
15 0.168
150 0.352
151 0.656
152 0.0174
153 0.536
154 0.323
155 0.273
156 0.00778
157 0.705
158 0.329
159 0.295
160 0.934
161 0.684
162 0.418
163 0.771
164 0.0574
165 0.22
166 0.996
167 0.659
168 0.479
169 0.0309
17 0.151
18 0.929
19 0.515
2 0.185
20 0.067
21 0.295
22 0.468
23 0.779
24 0.104
25 0.972
26 0.00698
27 0.686
28 0.683
29 0.00143
3 0.0725
30 0.719
31 0.613
32 0.127
33 0.0837
34 0.384
35 0.825
36 0.0421
37 0.0301
38 0.559
39 0.0562
4 0.284
40 0.0484
41 0.101
42 0.486
43 0.431
44 0.148
45 0.963
46 0.189
47 0.498
48 0.479
49 0.516
5 0.619
50 0.566
51 0.712
52 0.68
53 0.151
54 0.691
55 0.95
56 0.972
57 0.208
58 0.578
59 0.743
6 0.887
60 0.289
61 0.0904
62 0.441
63 0.172
64 0.907
65 0.321
66 0.477
67 0.25
68 0.225
69 0.388
7 0.226
70 0.00433
71 0.00741
72 0.818
73 5.88387e-4
74 0.46
75 0.00999
76 0.302
77 0.386
78 0.00103
79 0.163
8 0.165
80 0.0712
81 0.765
82 0.99
83 0.468
84 0.724
85 0.937
86 0.24
87 0.0548
88 0.962
89 0.698
9 0.781
90 0.663
91 0.337
92 0.846
93 0.525
94 0.278
95 0.00261
96 0.457
97 0.884
98 0.314
99 0.3



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: CNhs13741


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)