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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005570
 
|DRA_sample_Accession=CAGE@SAMD00005570
|accession_numbers=CAGE;DRX008826;DRR009698;DRZ001123;DRZ002508
+
|accession_numbers=CAGE;DRX008826;DRR009698;DRZ001123;DRZ002508;DRZ012473;DRZ013858
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002371,UBERON:0001474,UBERON:0002384,UBERON:0000479,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0004765,UBERON:0010317,UBERON:0002204,UBERON:0001434,UBERON:0002390,UBERON:0002193,UBERON:0002405
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002371,UBERON:0001474,UBERON:0002384,UBERON:0000479,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0004765,UBERON:0010317,UBERON:0002204,UBERON:0001434,UBERON:0002390,UBERON:0002193,UBERON:0002405
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0000048,CL:0000548,CL:0002320,CL:0002371,CL:0000219,CL:0000134,CL:0000255,CL:0000034,CL:0002092,CL:0002540
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0000048,CL:0000548,CL:0002320,CL:0002371,CL:0000219,CL:0000134,CL:0000255,CL:0000034,CL:0002092,CL:0002540
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|library_id=CNhs12633
 
|library_id=CNhs12633
 
|library_id_phase_based=2:CNhs12633
 
|library_id_phase_based=2:CNhs12633
 +
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11735
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11735
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Mesenchymal%2520stem%2520cells%2520-%2520bone%2520marrow%2520derived%252c%2520donor2.CNhs12633.11735-123E7.mm10.nobarcode.bam
 
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Mesenchymal%2520stem%2520cells%2520-%2520bone%2520marrow%2520derived%252c%2520donor2.CNhs12633.11735-123E7.mm10.nobarcode.bam
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Mesenchymal%2520stem%2520cells%2520-%2520bone%2520marrow%2520derived%252c%2520donor2.CNhs12633.11735-123E7.mm10.nobarcode.ctss.bed.gz
 
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Mesenchymal%2520stem%2520cells%2520-%2520bone%2520marrow%2520derived%252c%2520donor2.CNhs12633.11735-123E7.mm10.nobarcode.ctss.bed.gz

Latest revision as of 12:04, 10 August 2017


Name:Mouse Mesenchymal stem cells - bone marrow derived, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12633
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
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typemesenchymal stem cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMCS2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005570
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12633 CAGE DRX008826 DRR009698
Accession ID Mm9

Library idBAMCTSS
CNhs12633 DRZ001123 DRZ002508
Accession ID Mm10

Library idBAMCTSS
CNhs12633 DRZ012473 DRZ013858
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

CNhs12633

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0777
1001 --0.0631
1002 0.00981
1003 --0.102
1004 0
1005 0
1006 0.145
1007 --0.406
1008 0
1009 --0.19
101 --0.472
1010 0
1011 0.119
1012 0
1013 0.187
1014 --0.0874
1015 --0.0653
1016 --0.321
1017 0
1018 0
1019 0
102 0
1020 0.695
1021 0
1022 --0.124
1023 0
1024 --0.14
1025 --0.0611
1026 0
1027 0
1028 0
1029 --0.176
103 0
1030 0
1031 --0.111
1032 --0.177
1033 0
1034 0
1035 0
1036 --0.0393
1037 0
1038 --0.298
1039 --0.0323
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: CNhs12633

Jaspar motif P-value
MA0002.2 4.88808e-6
MA0003.1 0.125
MA0004.1 0.426
MA0006.1 0.493
MA0007.1 0.639
MA0009.1 0.669
MA0014.1 0.816
MA0017.1 0.234
MA0018.2 0.0802
MA0019.1 0.965
MA0024.1 0.0051
MA0025.1 0.765
MA0027.1 0.539
MA0028.1 0.485
MA0029.1 0.728
MA0030.1 0.204
MA0031.1 0.771
MA0035.2 0.244
MA0038.1 4.23469e-5
MA0039.2 0.995
MA0040.1 0.589
MA0041.1 0.541
MA0042.1 0.712
MA0043.1 0.0782
MA0046.1 6.88112e-6
MA0047.2 0.715
MA0048.1 0.723
MA0050.1 2.07149e-5
MA0051.1 4.77704e-4
MA0052.1 0.0562
MA0055.1 0.912
MA0057.1 0.314
MA0058.1 0.255
MA0059.1 0.156
MA0060.1 1.20161e-12
MA0061.1 0.0274
MA0062.2 0.537
MA0065.2 0.00696
MA0066.1 0.0124
MA0067.1 0.658
MA0068.1 0.285
MA0069.1 0.912
MA0070.1 0.172
MA0071.1 0.149
MA0072.1 0.43
MA0073.1 0.643
MA0074.1 0.029
MA0076.1 0.23
MA0077.1 0.728
MA0078.1 0.66
MA0079.2 0.461
MA0080.2 9.69998e-14
MA0081.1 0.00374
MA0083.1 0.384
MA0084.1 0.76
MA0087.1 0.942
MA0088.1 0.294
MA0090.1 0.665
MA0091.1 0.226
MA0092.1 0.392
MA0093.1 0.457
MA0099.2 0.00109
MA0100.1 0.928
MA0101.1 0.172
MA0102.2 0.513
MA0103.1 0.6
MA0104.2 0.841
MA0105.1 0.00166
MA0106.1 0.23
MA0107.1 0.164
MA0108.2 0.0922
MA0111.1 0.324
MA0112.2 7.3374e-5
MA0113.1 0.313
MA0114.1 0.321
MA0115.1 0.519
MA0116.1 0.00101
MA0117.1 0.777
MA0119.1 0.206
MA0122.1 0.718
MA0124.1 0.222
MA0125.1 0.0659
MA0131.1 0.12
MA0135.1 0.232
MA0136.1 5.07696e-10
MA0137.2 0.879
MA0138.2 0.526
MA0139.1 0.0593
MA0140.1 0.32
MA0141.1 0.0299
MA0142.1 0.318
MA0143.1 0.39
MA0144.1 0.405
MA0145.1 0.0392
MA0146.1 0.0121
MA0147.1 0.83
MA0148.1 0.777
MA0149.1 0.159
MA0150.1 0.01
MA0152.1 0.305
MA0153.1 5.91161e-4
MA0154.1 0.00461
MA0155.1 0.378
MA0156.1 0.00275
MA0157.1 0.538
MA0159.1 0.00245
MA0160.1 0.148
MA0162.1 0.184
MA0163.1 6.16997e-5
MA0164.1 0.943
MA0258.1 0.00576
MA0259.1 0.541



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: CNhs12633

Novel motif P-value
1 0.126
10 0.0714
100 0.78
101 0.936
102 0.63
103 0.0842
104 0.949
105 0.756
106 0.0244
107 0.201
108 0.5
109 0.0281
11 0.059
110 0.0881
111 0.0105
112 0.061
113 0.891
114 0.0248
115 0.267
116 0.141
117 0.0914
118 0.297
119 0.192
12 0.779
120 0.0301
121 0.503
122 0.868
123 0.848
124 0.663
125 0.115
126 0.417
127 0.379
128 0.0332
129 0.118
13 0.109
130 0.994
131 0.0348
132 0.563
133 0.068
134 0.655
135 0.928
136 0.846
137 0.275
138 0.393
139 0.0821
14 0.599
140 0.313
141 0.187
142 0.672
143 0.00713
144 0.971
145 0.248
146 0.7
147 0.827
148 0.0845
149 0.0129
15 0.0913
150 0.179
151 0.223
152 0.182
153 0.809
154 0.72
155 0.411
156 0.422
157 0.505
158 0.599
159 0.923
160 0.478
161 0.0706
162 0.842
163 0.892
164 0.159
165 0.0588
166 0.835
167 0.42
168 0.711
169 0.00484
17 0.0371
18 0.0877
19 0.135
2 0.521
20 0.526
21 0.442
22 0.141
23 0.0929
24 0.142
25 0.752
26 0.0134
27 0.357
28 0.674
29 0.0968
3 0.0361
30 0.78
31 0.297
32 0.117
33 0.409
34 0.388
35 0.516
36 0.00894
37 0.0533
38 0.193
39 0.549
4 0.281
40 0.0735
41 0.292
42 0.295
43 0.0508
44 0.0521
45 0.486
46 0.0725
47 0.178
48 0.2
49 0.07
5 0.185
50 0.491
51 0.702
52 0.38
53 0.888
54 0.671
55 0.397
56 0.18
57 0.54
58 0.346
59 0.00906
6 0.667
60 0.134
61 0.484
62 0.117
63 0.117
64 0.251
65 0.0494
66 0.734
67 0.271
68 0.105
69 0.273
7 0.462
70 3.23278e-4
71 0.0341
72 0.186
73 0.0726
74 0.827
75 0.0681
76 0.401
77 0.139
78 0.0862
79 0.593
8 0.0691
80 0.678
81 0.168
82 0.093
83 0.802
84 0.608
85 0.0856
86 0.471
87 0.325
88 0.836
89 0.0523
9 0.448
90 0.286
91 0.174
92 0.0958
93 0.118
94 0.664
95 0.0721
96 0.669
97 0.832
98 0.0962
99 0.59



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: CNhs12633


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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000219 (motile cell)
0000134 (mesenchymal cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0002092 (bone marrow cell)
0002540 (mesenchymal stem cell of the bone marrow)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002371 (bone marrow)
0001474 (bone element)
0002384 (connective tissue)
0000479 (tissue)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0004765 (skeletal element)
0010317 (germ layer / neural crest derived structure)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0002390 (hematopoietic system)
0002193 (hemolymphoid system)
0002405 (immune system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000112 (mouse mesenchymal stem cell of bone marrow 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)