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|microRNAs=
 
|microRNAs=
 
|microRNAs_nn=
 
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;11716
+
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11716
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;11716
+
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11716
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Meningeal%2520cells%252c%2520donor1.CNhs12132.11716-123C6.mm10.nobarcode.bam
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Meningeal%2520cells%252c%2520donor1.CNhs12132.11716-123C6.mm10.nobarcode.bam
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Meningeal%2520cells%252c%2520donor1.CNhs12132.11716-123C6.mm10.nobarcode.ctss.bed.gz
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Meningeal%2520cells%252c%2520donor1.CNhs12132.11716-123C6.mm10.nobarcode.ctss.bed.gz

Revision as of 07:55, 4 August 2017


Name:Mouse Meningeal cells, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs12132
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
tissuemeninges
dev stageNA
sexNA
ageNA
cell typemeningeal cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAM5762
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005064
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12132 CAGE DRX008823 DRR009695
Accession ID Mm9

Library idBAMCTSS
CNhs12132 DRZ001120 DRZ002505
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

CNhs12132

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0262
1001 --0.0749
1002 0.0145
1003 0.0194
1004 0
1005 0
1006 --0.0223
1007 --0.352
1008 0
1009 0.115
101 --0.387
1010 0
1011 --0.108
1012 0
1013 0.0264
1014 --0.0851
1015 0.337
1016 0.19
1017 0
1018 0
1019 0
102 0
1020 0.481
1021 0.127
1022 --0.124
1023 0
1024 --0.18
1025 --0.0611
1026 0
1027 0
1028 0
1029 --0.176
103 0.342
1030 0
1031 0.993
1032 0.0411
1033 0.0611
1034 0
1035 0
1036 --0.00647
1037 0
1038 --0.0736
1039 --0.0747
104 0
1040 0.545
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: CNhs12132

Jaspar motif P-value
MA0002.2 0.0993
MA0003.1 0.307
MA0004.1 0.0965
MA0006.1 0.639
MA0007.1 0.206
MA0009.1 0.471
MA0014.1 0.326
MA0017.1 0.0838
MA0018.2 0.128
MA0019.1 0.737
MA0024.1 5.32971e-4
MA0025.1 0.961
MA0027.1 0.497
MA0028.1 0.545
MA0029.1 0.869
MA0030.1 0.288
MA0031.1 0.596
MA0035.2 0.101
MA0038.1 0.0362
MA0039.2 0.0884
MA0040.1 0.627
MA0041.1 0.241
MA0042.1 0.701
MA0043.1 0.34
MA0046.1 6.51843e-6
MA0047.2 0.226
MA0048.1 0.126
MA0050.1 0.0907
MA0051.1 0.101
MA0052.1 0.0681
MA0055.1 8.40847e-4
MA0057.1 0.435
MA0058.1 0.0489
MA0059.1 0.177
MA0060.1 0.16
MA0061.1 0.338
MA0062.2 0.0929
MA0065.2 0.912
MA0066.1 0.274
MA0067.1 0.539
MA0068.1 0.788
MA0069.1 0.672
MA0070.1 0.676
MA0071.1 0.757
MA0072.1 0.685
MA0073.1 0.653
MA0074.1 0.0703
MA0076.1 0.117
MA0077.1 0.0753
MA0078.1 0.085
MA0079.2 0.123
MA0080.2 0.00622
MA0081.1 0.275
MA0083.1 2.16925e-8
MA0084.1 0.806
MA0087.1 0.933
MA0088.1 0.664
MA0090.1 3.79189e-5
MA0091.1 0.815
MA0092.1 0.0461
MA0093.1 0.141
MA0099.2 1.26425e-8
MA0100.1 0.588
MA0101.1 0.694
MA0102.2 0.135
MA0103.1 0.00127
MA0104.2 0.471
MA0105.1 0.419
MA0106.1 2.24174e-5
MA0107.1 0.9
MA0108.2 0.206
MA0111.1 0.719
MA0112.2 0.0632
MA0113.1 0.532
MA0114.1 0.366
MA0115.1 0.265
MA0116.1 0.16
MA0117.1 0.377
MA0119.1 0.243
MA0122.1 0.745
MA0124.1 0.233
MA0125.1 0.74
MA0131.1 0.386
MA0135.1 0.219
MA0136.1 0.0435
MA0137.2 0.425
MA0138.2 0.0115
MA0139.1 0.771
MA0140.1 4.85286e-4
MA0141.1 0.408
MA0142.1 0.557
MA0143.1 0.411
MA0144.1 0.728
MA0145.1 0.0352
MA0146.1 0.00837
MA0147.1 0.409
MA0148.1 0.155
MA0149.1 0.313
MA0150.1 0.663
MA0152.1 0.298
MA0153.1 7.90682e-4
MA0154.1 0.199
MA0155.1 0.343
MA0156.1 1.66572e-4
MA0157.1 0.498
MA0159.1 0.771
MA0160.1 0.796
MA0162.1 0.222
MA0163.1 0.0402
MA0164.1 0.86
MA0258.1 0.175
MA0259.1 0.698



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: CNhs12132

Novel motif P-value
1 0.922
10 0.797
100 0.764
101 0.845
102 0.159
103 0.415
104 0.656
105 0.298
106 0.0543
107 0.923
108 0.358
109 0.00195
11 0.0152
110 0.132
111 0.473
112 0.971
113 0.381
114 0.209
115 0.732
116 0.0146
117 0.332
118 0.941
119 0.402
12 0.774
120 0.602
121 0.275
122 0.269
123 0.57
124 0.0792
125 0.282
126 0.866
127 0.169
128 0.491
129 0.873
13 0.492
130 0.363
131 0.559
132 0.479
133 0.535
134 0.379
135 0.407
136 0.112
137 0.312
138 0.724
139 0.435
14 0.453
140 0.789
141 0.684
142 0.353
143 0.0448
144 0.375
145 0.105
146 0.876
147 0.537
148 0.491
149 0.112
15 0.795
150 0.227
151 0.961
152 0.0243
153 0.255
154 0.253
155 0.382
156 0.0201
157 0.295
158 0.222
159 0.199
160 0.935
161 0.57
162 0.475
163 0.256
164 0.836
165 0.719
166 0.833
167 0.0195
168 0.942
169 0.0842
17 0.0613
18 0.371
19 0.168
2 0.261
20 0.508
21 0.0851
22 0.0503
23 0.128
24 0.151
25 0.115
26 0.174
27 0.755
28 0.314
29 0.405
3 0.268
30 0.587
31 0.851
32 0.0716
33 0.831
34 0.217
35 0.124
36 0.507
37 0.0577
38 0.206
39 0.497
4 0.25
40 0.0478
41 0.329
42 0.274
43 0.25
44 0.197
45 0.495
46 0.552
47 0.189
48 0.495
49 0.561
5 0.411
50 0.0532
51 0.504
52 0.242
53 0.949
54 0.443
55 0.501
56 0.391
57 0.509
58 0.27
59 0.0121
6 0.401
60 0.299
61 0.758
62 0.821
63 0.189
64 0.301
65 0.0271
66 0.364
67 0.596
68 0.737
69 0.0839
7 0.443
70 0.0918
71 0.362
72 0.833
73 0.00353
74 0.501
75 0.2
76 0.672
77 0.00887
78 0.684
79 0.907
8 0.269
80 0.259
81 0.387
82 0.973
83 0.542
84 0.52
85 0.0473
86 0.86
87 0.00461
88 0.424
89 0.816
9 0.972
90 0.236
91 0.344
92 0.46
93 0.823
94 0.512
95 0.00574
96 0.503
97 0.869
98 0.252
99 0.986



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: CNhs12132


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)
0000151 (secretory cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000499 (stromal cell)
0000327 (extracellular matrix secreting cell)
0000255 (eukaryotic cell)
0000708 (leptomeningeal cell)

UBERON: Anatomy
0002384 (connective tissue)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)
0000119 (cell layer)
0003210 (blood-cerebrospinal fluid barrier)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000111 (mouse leptomeningeal cell 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:0000134 (mesenchymal cell)