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FF:12128-128D4

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Name:common myeloid progenitor CMP, biol_rep3
Species:Mouse (Mus musculus)
Library ID:CNhs12551
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
strainC57BL/8J
tissuebone marrow
dev stageNA
sexmale
age9-10weeks
cell typecommon myeloid progenitor
cell lineNA
companyNA
collaborationKitamura/Nakahara
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberrep3
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00004862
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12551 CAGE DRX008781 DRR009653
Accession ID Mm9

Library idBAMCTSS
CNhs12551 DRZ001078 DRZ002463
Accession ID Mm10

Library idBAMCTSS
CNhs12551 DRZ012428 DRZ013813
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

CNhs12551

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 0
1001 --0.0749
1002 --0.116
1003 --0.0786
1004 0
1005 0.0413
1006 --0.2
1007 --0.288
1008 0
1009 --0.161
101 0.259
1010 0
1011 0
1012 0
1013 --0.16
1014 --0.0874
1015 --0.0554
1016 --0.496
1017 0
1018 0
1019 0
102 0.052
1020 0.0983
1021 0
1022 --0.221
1023 0.634
1024 0.457
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.131
103 --0.0887
1030 0
1031 --0.911
1032 --0.436
1033 0.103
1034 0
1035 0
1036 0.544
1037 0
1038 --0.283
1039 0.0315
104 0
1040 --0.23
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: CNhs12551

Jaspar motif P-value
MA0002.2 1.01348e-5
MA0003.1 0.606
MA0004.1 0.0749
MA0006.1 0.93
MA0007.1 0.54
MA0009.1 0.519
MA0014.1 0.845
MA0017.1 0.411
MA0018.2 5.50289e-6
MA0019.1 0.842
MA0024.1 7.82816e-5
MA0025.1 0.109
MA0027.1 0.329
MA0028.1 3.98595e-8
MA0029.1 0.188
MA0030.1 0.187
MA0031.1 0.62
MA0035.2 0.821
MA0038.1 0.059
MA0039.2 0.884
MA0040.1 0.071
MA0041.1 0.143
MA0042.1 0.373
MA0043.1 2.77667e-6
MA0046.1 1.43527e-15
MA0047.2 0.832
MA0048.1 0.00771
MA0050.1 5.0758e-8
MA0051.1 7.93014e-5
MA0052.1 0.453
MA0055.1 0.00272
MA0057.1 0.722
MA0058.1 0.0271
MA0059.1 0.00155
MA0060.1 0.519
MA0061.1 4.96743e-6
MA0062.2 1.23665e-17
MA0065.2 0.27
MA0066.1 0.176
MA0067.1 0.00454
MA0068.1 0.00676
MA0069.1 0.424
MA0070.1 0.141
MA0071.1 0.323
MA0072.1 0.892
MA0073.1 0.713
MA0074.1 0.344
MA0076.1 2.69709e-9
MA0077.1 0.275
MA0078.1 0.734
MA0079.2 0.0814
MA0080.2 1.5801e-12
MA0081.1 5.36974e-5
MA0083.1 0.00622
MA0084.1 0.625
MA0087.1 0.923
MA0088.1 0.209
MA0090.1 0.00592
MA0091.1 0.961
MA0092.1 0.585
MA0093.1 0.0636
MA0099.2 5.22816e-14
MA0100.1 3.48636e-4
MA0101.1 1.80075e-9
MA0102.2 9.73841e-5
MA0103.1 0.177
MA0104.2 0.0283
MA0105.1 1.61349e-6
MA0106.1 0.156
MA0107.1 1.76886e-8
MA0108.2 0.207
MA0111.1 0.838
MA0112.2 0.0669
MA0113.1 0.57
MA0114.1 0.56
MA0115.1 0.914
MA0116.1 0.00121
MA0117.1 0.267
MA0119.1 0.373
MA0122.1 0.162
MA0124.1 0.816
MA0125.1 0.0343
MA0131.1 0.114
MA0135.1 0.0285
MA0136.1 1.95447e-28
MA0137.2 0.00159
MA0138.2 4.2564e-4
MA0139.1 0.388
MA0140.1 0.541
MA0141.1 0.594
MA0142.1 0.791
MA0143.1 0.202
MA0144.1 0.103
MA0145.1 0.655
MA0146.1 0.191
MA0147.1 0.0165
MA0148.1 0.592
MA0149.1 0.111
MA0150.1 2.7925e-5
MA0152.1 0.837
MA0153.1 1.52204e-4
MA0154.1 0.261
MA0155.1 0.71
MA0156.1 4.52944e-22
MA0157.1 0.348
MA0159.1 0.0473
MA0160.1 0.264
MA0162.1 0.431
MA0163.1 2.561e-5
MA0164.1 0.603
MA0258.1 0.0828
MA0259.1 0.187



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: CNhs12551

Novel motif P-value
1 0.392
10 0.0457
100 0.637
101 0.905
102 0.674
103 0.27
104 0.81
105 0.544
106 0.17
107 0.912
108 0.499
109 0.0889
11 0.236
110 0.148
111 0.257
112 0.144
113 0.544
114 0.493
115 0.571
116 0.777
117 2.68768e-4
118 0.215
119 1
12 0.685
120 0.306
121 0.431
122 0.435
123 0.162
124 0.412
125 0.423
126 0.512
127 0.611
128 0.244
129 0.302
13 0.00129
130 0.529
131 0.338
132 0.405
133 0.353
134 0.683
135 0.713
136 0.233
137 0.00671
138 0.793
139 0.521
14 0.492
140 0.481
141 0.519
142 0.861
143 0.194
144 0.89
145 0.0553
146 0.684
147 0.576
148 0.24
149 0.151
15 0.034
150 0.573
151 0.811
152 0.802
153 0.411
154 0.663
155 0.947
156 0.372
157 0.937
158 0.0595
159 0.465
160 0.567
161 0.152
162 0.396
163 0.261
164 0.0109
165 0.158
166 0.382
167 0.224
168 0.673
169 0.0396
17 0.683
18 0.374
19 0.623
2 0.0711
20 0.0123
21 0.389
22 0.83
23 0.201
24 0.037
25 0.294
26 0.0043
27 0.354
28 0.694
29 0.0103
3 0.144
30 0.173
31 0.708
32 0.313
33 0.0919
34 0.613
35 0.525
36 0.0486
37 0.0477
38 0.518
39 0.641
4 0.594
40 0.156
41 0.0767
42 0.366
43 0.519
44 0.7
45 0.693
46 0.317
47 0.674
48 0.333
49 0.462
5 0.561
50 0.682
51 0.978
52 0.531
53 0.606
54 0.743
55 0.593
56 0.788
57 0.413
58 0.265
59 0.929
6 0.785
60 0.527
61 0.212
62 0.189
63 0.93
64 0.81
65 0.885
66 0.32
67 0.339
68 0.685
69 0.704
7 0.265
70 0.168
71 0.0155
72 0.117
73 0.0509
74 0.655
75 0.00647
76 0.049
77 0.132
78 0.143
79 0.691
8 0.0949
80 0.711
81 0.938
82 0.345
83 0.0703
84 0.38
85 0.52
86 0.213
87 0.0452
88 0.508
89 0.994
9 0.882
90 0.0306
91 0.843
92 0.991
93 0.167
94 0.458
95 0.003
96 0.998
97 0.938
98 0.523
99 0.231



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: CNhs12551


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)
0002032 (hematopoietic oligopotent progenitor cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000049 (common myeloid progenitor)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000041 (common myeloid progenitor 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)