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FF:12157-128G6

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Name:Sox2+ Supporting cells - organ of corti, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs12532
Sample type:primary cells
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samples)
Excluding candidate novel miRNAs(CAGE samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueorgan of corti
dev stageNA
sexmixed
ageNA
cell typeSELECT CELL TYPE
cell lineNA
companyNA
collaborationAlbert Edge (Department of Otolaryngology, Harvard Medical School)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005538
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12532 CAGE DRX008778 DRR009650
Accession ID Mm9

Library idBAMCTSS
CNhs12532 DRZ001075 DRZ002460
Accession ID Mm10

Library idBAMCTSS
CNhs12532 DRZ012425 DRZ013810
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

CNhs12532

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0.0637
10 0
100 0
1000 0
1001 --0.0749
1002 0.464
1003 --0.132
1004 0
1005 --0.0389
1006 0.0334
1007 0.205
1008 0
1009 0.0414
101 --0.0684
1010 0
1011 0.0866
1012 0
1013 0.0777
1014 --0.0874
1015 0.223
1016 0.296
1017 0
1018 0
1019 0
102 0
1020 0
1021 0
1022 0.0125
1023 0
1024 0
1025 0
1026 0
1027 0.517
1028 0
1029 --0.12
103 --0.0721
1030 0
1031 0
1032 0.325
1033 0.0572
1034 0
1035 0.0572
1036 0.0124
1037 0.0572
1038 0.0456
1039 --0.0717
104 0
1040 --0.121
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: CNhs12532

Jaspar motif P-value
MA0002.2 0.00452
MA0003.1 0.519
MA0004.1 0.589
MA0006.1 0.968
MA0007.1 0.454
MA0009.1 0.279
MA0014.1 0.0981
MA0017.1 2.11564e-9
MA0018.2 3.08379e-4
MA0019.1 0.499
MA0024.1 0.88
MA0025.1 0.868
MA0027.1 0.846
MA0028.1 0.472
MA0029.1 0.335
MA0030.1 0.678
MA0031.1 0.429
MA0035.2 0.0626
MA0038.1 0.245
MA0039.2 0.192
MA0040.1 0.241
MA0041.1 0.142
MA0042.1 0.909
MA0043.1 0.00496
MA0046.1 5.32088e-11
MA0047.2 0.00932
MA0048.1 0.509
MA0050.1 0.016
MA0051.1 0.0497
MA0052.1 0.138
MA0055.1 0.955
MA0057.1 0.475
MA0058.1 0.845
MA0059.1 0.152
MA0060.1 6.62129e-10
MA0061.1 0.0128
MA0062.2 0.868
MA0065.2 2.22353e-4
MA0066.1 0.0269
MA0067.1 0.148
MA0068.1 0.0987
MA0069.1 0.303
MA0070.1 0.508
MA0071.1 0.0929
MA0072.1 0.584
MA0073.1 0.88
MA0074.1 0.08
MA0076.1 0.289
MA0077.1 0.0131
MA0078.1 0.803
MA0079.2 0.0789
MA0080.2 3.95037e-10
MA0081.1 0.252
MA0083.1 0.0592
MA0084.1 0.0888
MA0087.1 0.0555
MA0088.1 0.259
MA0090.1 0.216
MA0091.1 0.31
MA0092.1 0.413
MA0093.1 0.709
MA0099.2 0.0164
MA0100.1 0.835
MA0101.1 0.105
MA0102.2 0.696
MA0103.1 0.975
MA0104.2 0.292
MA0105.1 1.30973e-6
MA0106.1 0.0487
MA0107.1 0.0395
MA0108.2 0.855
MA0111.1 0.905
MA0112.2 1.69995e-5
MA0113.1 0.795
MA0114.1 8.47883e-6
MA0115.1 7.88156e-5
MA0116.1 5.11268e-5
MA0117.1 0.97
MA0119.1 0.14
MA0122.1 0.93
MA0124.1 0.412
MA0125.1 0.0233
MA0131.1 0.711
MA0135.1 0.155
MA0136.1 1.90304e-7
MA0137.2 0.612
MA0138.2 0.204
MA0139.1 0.186
MA0140.1 0.00195
MA0141.1 0.00473
MA0142.1 0.782
MA0143.1 0.0607
MA0144.1 0.214
MA0145.1 0.123
MA0146.1 0.897
MA0147.1 0.185
MA0148.1 0.00202
MA0149.1 0.783
MA0150.1 0.0272
MA0152.1 0.81
MA0153.1 6.33411e-8
MA0154.1 0.00328
MA0155.1 0.843
MA0156.1 1.57498e-4
MA0157.1 0.326
MA0159.1 6.00836e-4
MA0160.1 0.0112
MA0162.1 0.204
MA0163.1 2.04606e-4
MA0164.1 0.47
MA0258.1 0.00148
MA0259.1 0.569



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: CNhs12532

Novel motif P-value
1 0.0367
10 0.0255
100 0.894
101 0.642
102 0.593
103 0.106
104 0.646
105 0.641
106 0.158
107 0.219
108 0.653
109 0.163
11 0.154
110 0.0227
111 6.99748e-4
112 0.0122
113 0.984
114 0.00894
115 0.89
116 0.571
117 0.0453
118 0.617
119 0.0613
12 0.995
120 0.497
121 0.589
122 0.934
123 0.895
124 0.817
125 0.143
126 0.588
127 0.333
128 0.105
129 0.0973
13 0.0771
130 0.267
131 0.858
132 0.536
133 0.845
134 0.29
135 0.249
136 0.331
137 0.195
138 0.657
139 0.0567
14 0.991
140 0.2
141 0.733
142 0.238
143 0.355
144 0.693
145 0.113
146 0.364
147 0.566
148 0.254
149 0.515
15 0.113
150 0.423
151 0.388
152 0.977
153 0.161
154 0.452
155 0.579
156 0.0133
157 0.507
158 0.421
159 0.0137
160 0.195
161 0.66
162 0.64
163 0.313
164 0.00284
165 0.944
166 0.795
167 0.163
168 0.957
169 0.00501
17 0.16
18 0.176
19 0.0922
2 0.811
20 0.548
21 0.207
22 0.418
23 0.115
24 0.951
25 0.453
26 0.0134
27 0.876
28 0.624
29 0.0573
3 0.0537
30 0.94
31 0.584
32 0.0435
33 0.586
34 0.931
35 0.161
36 0.104
37 0.149
38 0.269
39 0.825
4 0.28
40 0.811
41 0.678
42 0.0696
43 0.0928
44 0.618
45 0.927
46 0.0207
47 0.272
48 0.26
49 0.0939
5 0.198
50 0.664
51 0.518
52 0.901
53 0.854
54 0.697
55 0.847
56 0.257
57 0.502
58 0.287
59 0.0423
6 0.891
60 0.4
61 0.317
62 0.118
63 0.107
64 0.301
65 0.144
66 0.268
67 0.648
68 0.00706
69 0.661
7 0.177
70 0.0177
71 0.0148
72 0.578
73 0.541
74 0.227
75 0.0597
76 0.428
77 0.344
78 0.00275
79 0.833
8 0.101
80 0.842
81 0.505
82 0.0987
83 0.476
84 0.615
85 0.0506
86 0.622
87 0.0253
88 0.944
89 0.128
9 0.345
90 0.0573
91 0.219
92 0.185
93 0.231
94 0.32
95 0.385
96 0.226
97 0.795
98 0.373
99 0.339



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: CNhs12532


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)
0000197 (receptor cell)
0000003 (native cell)
0000548 (animal cell)
0000075 (columnar/cuboidal epithelial cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000710 (neurecto-epithelial cell)
0002491 (auditory epithelial cell)
0000630 (supportive cell)
0000255 (eukaryotic cell)
0002077 (ecto-epithelial cell)
0000098 (sensory epithelial cell)
0005014 (auditory epithelial support cell)
0002315 (supporting cell of cochlea)
0002490 (organ of Corti supporting cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001474 (bone element)
0000033 (head)
0000058 (duct)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0000075 (subdivision of skeletal system)
0004765 (skeletal element)
0004766 (cranial bone)
0008193 (pneumatized bone)
0005913 (zone of bone organ)
0005744 (cranial conduit)
0001032 (sensory system)
0003457 (head bone)
0008001 (irregular bone)
0007914 (head or neck bone)
0010317 (germ layer / neural crest derived structure)
0002227 (spiral organ of cochlea)
0001846 (internal ear)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0004456 (entire sense organ system)
0004339 (calvarium)
0002105 (vestibulo-auditory system)
0001678 (temporal bone)
0003128 (cranium)
0001694 (petrous part of temporal bone)
0004681 (vestibular system)
0001839 (bony labyrinth)
0001690 (ear)
0001844 (cochlea)
0001849 (membranous labyrinth)
0002499 (cochlear labyrinth)
0001855 (cochlear duct of membranous labyrinth)
0011137 (axial skeletal system)
0010323 (cranial skeletal system)
0003129 (skull)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000279 (mouse Sox2-positive supporting cell- organ of corti 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:0000133 (neurectodermal cell)
CL:0000221 (ectodermal cell)