Personal tools

FF:11775-124A2

From FANTOM5_SSTAR

Revision as of 12:10, 10 August 2017 by Autoedit (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Name:CD41+ megakaryocyte control, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs13212
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 typemegakaryocyte
cell lineNA
companyNA
collaborationHozumi Motohashi (Tohoku University Graduate School of Medicine)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberPBS-1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

Accession numbers
MethodSample accession id
CAGE  SAMD00004730
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13212 CAGE DRX008800 DRR009672
Accession ID Mm9

Library idBAMCTSS
CNhs13212 DRZ001097 DRZ002482
Accession ID Mm10

Library idBAMCTSS
CNhs13212 DRZ012447 DRZ013832
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

CNhs13212

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.00367
1001 --0.00378
1002 --0.116
1003 --0.166
1004 0
1005 0.212
1006 --0.143
1007 --0.198
1008 0
1009 --0.19
101 0.158
1010 0
1011 0.105
1012 0
1013 --0.126
1014 --0.0874
1015 --0.0904
1016 --0.594
1017 0
1018 0
1019 0
102 0.212
1020 0.0953
1021 0.212
1022 --0.227
1023 0.0294
1024 --0.14
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.119
103 --0.0887
1030 0.619
1031 --0.848
1032 --0.536
1033 0.0526
1034 0
1035 0
1036 0.22
1037 0
1038 --0.258
1039 --0.0403
104 0
1040 --0.172
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: CNhs13212

Jaspar motif P-value
MA0002.2 2.70599e-6
MA0003.1 0.451
MA0004.1 0.112
MA0006.1 0.804
MA0007.1 0.776
MA0009.1 0.704
MA0014.1 0.747
MA0017.1 0.341
MA0018.2 0.738
MA0019.1 0.417
MA0024.1 0.979
MA0025.1 0.294
MA0027.1 0.838
MA0028.1 1.87225e-5
MA0029.1 0.214
MA0030.1 0.191
MA0031.1 0.76
MA0035.2 0.7
MA0038.1 0.437
MA0039.2 0.787
MA0040.1 0.694
MA0041.1 0.123
MA0042.1 0.717
MA0043.1 0.487
MA0046.1 6.81692e-10
MA0047.2 0.9
MA0048.1 0.421
MA0050.1 4.13943e-13
MA0051.1 2.93988e-8
MA0052.1 0.0123
MA0055.1 0.53
MA0057.1 0.986
MA0058.1 0.129
MA0059.1 0.0381
MA0060.1 0.0125
MA0061.1 1.21889e-6
MA0062.2 1.22846e-16
MA0065.2 0.26
MA0066.1 0.0418
MA0067.1 0.277
MA0068.1 0.0399
MA0069.1 0.499
MA0070.1 0.591
MA0071.1 0.495
MA0072.1 0.537
MA0073.1 0.705
MA0074.1 0.561
MA0076.1 2.53513e-6
MA0077.1 0.16
MA0078.1 0.756
MA0079.2 0.0694
MA0080.2 2.63883e-14
MA0081.1 0.001
MA0083.1 0.0432
MA0084.1 0.693
MA0087.1 0.825
MA0088.1 0.649
MA0090.1 0.00826
MA0091.1 0.304
MA0092.1 0.804
MA0093.1 0.128
MA0099.2 0.309
MA0100.1 0.358
MA0101.1 2.13392e-6
MA0102.2 0.805
MA0103.1 0.127
MA0104.2 0.14
MA0105.1 1.01321e-8
MA0106.1 0.836
MA0107.1 9.22729e-7
MA0108.2 5.49013e-5
MA0111.1 0.436
MA0112.2 0.00486
MA0113.1 0.238
MA0114.1 0.71
MA0115.1 0.785
MA0116.1 6.71082e-4
MA0117.1 0.769
MA0119.1 0.684
MA0122.1 0.979
MA0124.1 0.618
MA0125.1 0.0315
MA0131.1 0.457
MA0135.1 0.9
MA0136.1 1.60766e-19
MA0137.2 0.245
MA0138.2 0.0701
MA0139.1 0.12
MA0140.1 0.542
MA0141.1 0.685
MA0142.1 1.87284e-4
MA0143.1 0.217
MA0144.1 0.423
MA0145.1 0.647
MA0146.1 0.351
MA0147.1 0.0986
MA0148.1 0.885
MA0149.1 0.177
MA0150.1 0.638
MA0152.1 0.327
MA0153.1 4.76015e-7
MA0154.1 0.00128
MA0155.1 0.774
MA0156.1 4.03382e-23
MA0157.1 0.383
MA0159.1 0.0201
MA0160.1 0.736
MA0162.1 0.434
MA0163.1 1.47283e-4
MA0164.1 0.5
MA0258.1 0.0136
MA0259.1 0.458



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: CNhs13212

Novel motif P-value
1 0.13
10 0.0316
100 0.829
101 0.989
102 0.59
103 0.0689
104 0.714
105 0.749
106 0.297
107 0.852
108 0.558
109 0.124
11 0.167
110 0.0575
111 0.0665
112 0.0435
113 0.291
114 0.154
115 0.652
116 0.922
117 6.26559e-4
118 0.113
119 0.639
12 0.467
120 0.432
121 0.415
122 0.847
123 0.8
124 0.878
125 0.161
126 0.239
127 0.453
128 0.145
129 0.128
13 0.079
130 0.904
131 0.841
132 0.696
133 0.989
134 0.949
135 0.974
136 0.888
137 0.132
138 0.789
139 0.274
14 0.968
140 0.843
141 0.159
142 0.661
143 0.0123
144 0.535
145 0.119
146 0.845
147 0.805
148 0.0892
149 0.579
15 0.0869
150 0.328
151 0.16
152 0.696
153 0.188
154 0.422
155 0.249
156 1.17834e-25
157 0.839
158 0.128
159 0.745
160 0.996
161 0.0521
162 0.322
163 0.269
164 0.0905
165 0.316
166 0.506
167 0.136
168 0.92
169 0.0635
17 0.425
18 0.273
19 0.892
2 0.161
20 0.0328
21 0.329
22 0.826
23 0.348
24 0.464
25 0.189
26 0.0281
27 0.708
28 0.221
29 0.0192
3 0.051
30 0.233
31 0.931
32 0.802
33 0.217
34 0.717
35 0.0888
36 0.045
37 0.0684
38 0.716
39 0.533
4 0.768
40 0.204
41 0.361
42 0.121
43 0.139
44 0.276
45 0.753
46 0.165
47 0.215
48 0.163
49 0.108
5 0.0424
50 0.642
51 0.884
52 0.334
53 0.447
54 0.829
55 0.482
56 0.702
57 0.7
58 0.128
59 0.287
6 0.613
60 0.662
61 0.106
62 0.0526
63 0.715
64 0.614
65 0.711
66 0.981
67 0.711
68 0.0743
69 0.785
7 0.186
70 0.0121
71 0.0429
72 0.227
73 0.107
74 0.869
75 0.0033
76 0.0168
77 0.432
78 0.0933
79 0.723
8 0.0566
80 0.0148
81 0.531
82 0.202
83 0.148
84 0.513
85 0.509
86 0.157
87 0.515
88 0.518
89 0.561
9 0.873
90 0.0211
91 0.659
92 0.207
93 0.306
94 0.174
95 0.16
96 0.313
97 0.804
98 0.137
99 0.342



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: CNhs13212


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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000556 (megakaryocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002371 (bone marrow)
0001474 (bone element)
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)
0000343 (control treatment sample)
0011468 (mouse CD41-positive megakaryocyte control 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:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)