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{{f5samples
 
{{f5samples
|DRA_sample_Accession=CAGE@DRS008715
+
|DRA_sample_Accession=CAGE@SAMD00005198
 
|accession_numbers=CAGE;DRX008825;DRR009697;DRZ001122;DRZ002507
 
|accession_numbers=CAGE;DRX008825;DRR009697;DRZ001122;DRZ002507
 
|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

Revision as of 11:20, 31 July 2014


Name:Mouse Mesenchymal stem cells - bone marrow derived, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs12628
Sample type:primary cells
Genomic View: UCSC
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 numberRNAMCS1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00005198
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12628 CAGE DRX008825 DRR009697
Accession ID Mm9

Library idBAMCTSS
CNhs12628 DRZ001122 DRZ002507
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs12628

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0.0678
1001 --0.0749
1002 0.168
1003 --0.0137
1004 0
1005 0
1006 0.304
1007 --0.451
1008 0
1009 --0.00295
101 --0.507
1010 0
1011 0.00323
1012 0
1013 0.175
1014 --0.0874
1015 0.0682
1016 --0.187
1017 0
1018 0
1019 0
102 0
1020 0.447
1021 0.279
1022 --0.124
1023 0
1024 --0.14
1025 --0.0611
1026 0
1027 0
1028 0
1029 --0.176
103 0.0455
1030 0
1031 --0.18
1032 --0.177
1033 --0.0382
1034 0
1035 0
1036 --0.0244
1037 0
1038 --0.0333
1039 -5.195984e-4
104 0
1040 --0.0413
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: CNhs12628

Jaspar motif P-value
MA0002.2 8.47186e-6
MA0003.1 0.135
MA0004.1 0.302
MA0006.1 0.528
MA0007.1 0.609
MA0009.1 0.385
MA0014.1 0.704
MA0017.1 0.248
MA0018.2 0.0973
MA0019.1 0.592
MA0024.1 0.00552
MA0025.1 0.694
MA0027.1 0.703
MA0028.1 0.846
MA0029.1 0.821
MA0030.1 0.335
MA0031.1 0.84
MA0035.2 0.232
MA0038.1 7.88839e-5
MA0039.2 0.812
MA0040.1 0.606
MA0041.1 0.466
MA0042.1 0.92
MA0043.1 0.141
MA0046.1 1.94943e-7
MA0047.2 0.939
MA0048.1 0.536
MA0050.1 1.72552e-7
MA0051.1 6.99951e-5
MA0052.1 0.051
MA0055.1 0.729
MA0057.1 0.23
MA0058.1 0.139
MA0059.1 0.232
MA0060.1 9.6513e-14
MA0061.1 0.0305
MA0062.2 0.097
MA0065.2 0.0102
MA0066.1 0.0164
MA0067.1 0.816
MA0068.1 0.483
MA0069.1 0.986
MA0070.1 0.237
MA0071.1 0.0996
MA0072.1 0.271
MA0073.1 0.683
MA0074.1 0.0346
MA0076.1 0.502
MA0077.1 0.581
MA0078.1 0.601
MA0079.2 0.689
MA0080.2 2.26373e-13
MA0081.1 8.84382e-4
MA0083.1 0.342
MA0084.1 0.75
MA0087.1 0.54
MA0088.1 0.317
MA0090.1 0.815
MA0091.1 0.327
MA0092.1 0.453
MA0093.1 0.295
MA0099.2 1.76179e-4
MA0100.1 0.884
MA0101.1 0.0935
MA0102.2 0.549
MA0103.1 0.968
MA0104.2 0.806
MA0105.1 0.00866
MA0106.1 0.21
MA0107.1 0.0671
MA0108.2 0.0673
MA0111.1 0.308
MA0112.2 7.36373e-5
MA0113.1 0.331
MA0114.1 0.334
MA0115.1 0.573
MA0116.1 0.0026
MA0117.1 0.719
MA0119.1 0.295
MA0122.1 0.5
MA0124.1 0.76
MA0125.1 0.0698
MA0131.1 0.153
MA0135.1 0.219
MA0136.1 2.53605e-12
MA0137.2 0.973
MA0138.2 0.644
MA0139.1 0.123
MA0140.1 0.18
MA0141.1 0.0159
MA0142.1 0.818
MA0143.1 0.0965
MA0144.1 0.448
MA0145.1 0.0367
MA0146.1 0.00674
MA0147.1 0.793
MA0148.1 0.667
MA0149.1 0.232
MA0150.1 0.00547
MA0152.1 0.363
MA0153.1 4.37683e-5
MA0154.1 0.00494
MA0155.1 0.403
MA0156.1 1.76814e-4
MA0157.1 0.535
MA0159.1 0.00733
MA0160.1 0.0992
MA0162.1 0.182
MA0163.1 6.19654e-6
MA0164.1 0.863
MA0258.1 0.00814
MA0259.1 0.599



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: CNhs12628

Novel motif P-value
1 0.103
10 0.0593
100 0.787
101 0.803
102 0.591
103 0.113
104 0.916
105 0.444
106 0.0215
107 0.352
108 0.561
109 0.0204
11 0.055
110 0.1
111 0.0211
112 0.0711
113 0.759
114 0.0176
115 0.388
116 0.146
117 0.0289
118 0.297
119 0.229
12 0.674
120 0.0439
121 0.383
122 0.911
123 0.644
124 0.824
125 0.174
126 0.526
127 0.276
128 0.0501
129 0.192
13 0.0926
130 0.509
131 0.0933
132 0.535
133 0.129
134 0.722
135 0.923
136 0.604
137 0.462
138 0.379
139 0.188
14 0.568
140 0.0653
141 0.191
142 0.327
143 0.0108
144 0.89
145 0.151
146 0.673
147 0.801
148 0.15
149 0.0146
15 0.0894
150 0.136
151 0.237
152 0.0951
153 0.854
154 0.519
155 0.396
156 0.314
157 0.588
158 0.391
159 0.739
160 0.468
161 0.0826
162 0.825
163 0.913
164 0.139
165 0.101
166 0.629
167 0.392
168 0.51
169 0.00462
17 0.0319
18 0.117
19 0.134
2 0.693
20 0.268
21 0.34
22 0.114
23 0.113
24 0.124
25 0.849
26 0.00947
27 0.656
28 0.734
29 0.0855
3 0.0204
30 0.725
31 0.298
32 0.119
33 0.313
34 0.403
35 0.62
36 0.0173
37 0.0401
38 0.15
39 0.669
4 0.316
40 0.0641
41 0.276
42 0.238
43 0.0444
44 0.0475
45 0.504
46 0.0695
47 0.252
48 0.234
49 0.075
5 0.206
50 0.454
51 0.738
52 0.446
53 0.945
54 0.695
55 0.589
56 0.145
57 0.551
58 0.385
59 0.00514
6 1
60 0.114
61 0.331
62 0.123
63 0.105
64 0.324
65 0.0472
66 0.779
67 0.179
68 0.0536
69 0.208
7 0.469
70 2.89002e-4
71 0.0313
72 0.11
73 0.034
74 0.837
75 0.074
76 0.337
77 0.117
78 0.0305
79 0.729
8 0.0625
80 0.852
81 0.166
82 0.213
83 0.936
84 0.539
85 0.06
86 0.442
87 0.143
88 0.954
89 0.0809
9 0.479
90 0.51
91 0.2
92 0.0753
93 0.239
94 0.894
95 0.039
96 0.888
97 0.876
98 0.123
99 0.747



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: CNhs12628


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)