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FF:13367-143G1

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Name:Tracheal epithelial cells, differentiation to ciliated epithelial cells
Species:Mouse (Mus musculus)
Library ID:CNhs13739
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 number0-1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004953
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13739 CAGE DRX008911 DRR009785
Accession ID Mm9

Library idBAMCTSS
CNhs13739 DRZ001210 DRZ002593
Accession ID Mm10

Library idBAMCTSS
CNhs13739 DRZ012560 DRZ013943
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

CNhs13739

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0426
1001 --0.0749
1002 --0.116
1003 --0.001
1004 0
1005 0.233
1006 --0.341
1007 --0.255
1008 0
1009 --0.157
101 0.0637
1010 0
1011 --0.227
1012 0
1013 0.0459
1014 0
1015 --0.0842
1016 --0.289
1017 0
1018 0.849
1019 0
102 0
1020 0.217
1021 0.156
1022 --0.124
1023 0
1024 --0.0899
1025 0
1026 0
1027 --0.048
1028 0.0851
1029 --0.0977
103 --0.0887
1030 0
1031 --0.581
1032 --0.0914
1033 0.0537
1034 0
1035 0
1036 0.223
1037 0
1038 --0.202
1039 --0.133
104 0
1040 --0.00144
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: CNhs13739

Jaspar motif P-value
MA0002.2 0.31
MA0003.1 0.486
MA0004.1 0.735
MA0006.1 0.286
MA0007.1 0.584
MA0009.1 0.109
MA0014.1 0.0802
MA0017.1 0.724
MA0018.2 0.0389
MA0019.1 0.0686
MA0024.1 0.252
MA0025.1 0.372
MA0027.1 0.994
MA0028.1 1.93526e-6
MA0029.1 0.543
MA0030.1 0.656
MA0031.1 0.992
MA0035.2 2.26598e-4
MA0038.1 0.0289
MA0039.2 0.00851
MA0040.1 0.737
MA0041.1 0.572
MA0042.1 0.662
MA0043.1 0.591
MA0046.1 5.91984e-5
MA0047.2 0.0697
MA0048.1 0.00623
MA0050.1 0.293
MA0051.1 0.406
MA0052.1 0.0116
MA0055.1 4.67238e-5
MA0057.1 0.163
MA0058.1 0.792
MA0059.1 0.0823
MA0060.1 0.0474
MA0061.1 0.12
MA0062.2 2.00983e-8
MA0065.2 0.174
MA0066.1 0.293
MA0067.1 0.216
MA0068.1 0.941
MA0069.1 0.586
MA0070.1 0.0756
MA0071.1 0.313
MA0072.1 0.548
MA0073.1 0.641
MA0074.1 0.5
MA0076.1 2.93977e-5
MA0077.1 0.444
MA0078.1 0.315
MA0079.2 0.283
MA0080.2 0.66
MA0081.1 0.961
MA0083.1 0.0276
MA0084.1 0.381
MA0087.1 0.339
MA0088.1 0.171
MA0090.1 6.74659e-4
MA0091.1 0.495
MA0092.1 0.552
MA0093.1 0.853
MA0099.2 1.41547e-22
MA0100.1 0.343
MA0101.1 5.37731e-4
MA0102.2 0.342
MA0103.1 3.46132e-6
MA0104.2 0.73
MA0105.1 0.329
MA0106.1 1.30737e-4
MA0107.1 0.00866
MA0108.2 0.398
MA0111.1 0.693
MA0112.2 0.00813
MA0113.1 0.341
MA0114.1 0.906
MA0115.1 0.418
MA0116.1 0.178
MA0117.1 0.697
MA0119.1 0.616
MA0122.1 0.798
MA0124.1 0.261
MA0125.1 0.0311
MA0131.1 0.194
MA0135.1 0.0675
MA0136.1 0.00671
MA0137.2 0.0254
MA0138.2 0.0238
MA0139.1 0.514
MA0140.1 2.98616e-5
MA0141.1 0.759
MA0142.1 0.238
MA0143.1 0.278
MA0144.1 0.113
MA0145.1 0.0964
MA0146.1 0.194
MA0147.1 0.45
MA0148.1 0.332
MA0149.1 0.00402
MA0150.1 0.00147
MA0152.1 0.171
MA0153.1 0.00797
MA0154.1 0.617
MA0155.1 0.432
MA0156.1 0.00183
MA0157.1 0.754
MA0159.1 0.0012
MA0160.1 0.858
MA0162.1 0.405
MA0163.1 0.0414
MA0164.1 0.179
MA0258.1 0.0528
MA0259.1 0.608



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: CNhs13739

Novel motif P-value
1 0.383
10 0.0294
100 0.314
101 0.0334
102 0.193
103 0.0572
104 0.841
105 0.488
106 0.18
107 0.95
108 0.56
109 0.0127
11 0.294
110 0.119
111 0.143
112 0.977
113 0.277
114 0.552
115 0.668
116 0.0606
117 0.002
118 0.706
119 0.369
12 0.542
120 0.543
121 0.743
122 0.126
123 0.0673
124 0.798
125 0.0481
126 0.835
127 0.931
128 0.306
129 0.993
13 5.31053e-7
130 0.468
131 0.12
132 0.419
133 0.0339
134 0.291
135 0.0516
136 0.0147
137 0.811
138 0.178
139 0.361
14 0.624
140 0.434
141 0.479
142 0.89
143 0.386
144 0.232
145 0.0233
146 0.401
147 0.446
148 0.481
149 0.142
15 0.201
150 0.342
151 0.657
152 0.0266
153 0.3
154 0.365
155 0.418
156 0.00329
157 0.598
158 0.555
159 0.305
160 0.925
161 0.742
162 0.247
163 0.713
164 0.0437
165 0.225
166 0.891
167 0.732
168 0.46
169 0.0523
17 0.143
18 0.665
19 0.604
2 0.129
20 0.0435
21 0.162
22 0.611
23 0.758
24 0.15
25 0.972
26 0.00927
27 0.566
28 0.665
29 4.71433e-4
3 0.146
30 0.457
31 0.438
32 0.0844
33 0.0536
34 0.263
35 0.918
36 0.0642
37 0.0395
38 0.767
39 0.062
4 0.149
40 0.0401
41 0.126
42 0.412
43 0.67
44 0.281
45 0.803
46 0.25
47 0.533
48 0.471
49 0.669
5 0.86
50 0.629
51 0.808
52 0.914
53 0.163
54 0.825
55 0.905
56 0.937
57 0.23
58 0.685
59 0.817
6 0.876
60 0.401
61 0.154
62 0.518
63 0.228
64 0.762
65 0.603
66 0.301
67 0.252
68 0.304
69 0.496
7 0.184
70 0.00866
71 0.00986
72 0.849
73 6.04833e-4
74 0.243
75 0.0158
76 0.289
77 0.508
78 0.00199
79 0.233
8 0.196
80 0.0383
81 0.692
82 0.771
83 0.431
84 0.916
85 0.926
86 0.326
87 0.0274
88 0.852
89 0.712
9 0.827
90 0.337
91 0.306
92 0.898
93 0.844
94 0.46
95 0.00183
96 0.663
97 0.893
98 0.318
99 0.672



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: CNhs13739


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)