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FF:12127-128D3

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Name:stem cell (cKit+ Sca1- lineage-) KSL, biol_rep3
Species:Mouse (Mus musculus)
Library ID:CNhs12536
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 typestem cell (cKit+ Sca1- lineage-)
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  SAMD00005934
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12536 CAGE DRX008786 DRR009658
Accession ID Mm9

Library idBAMCTSS
CNhs12536 DRZ001083 DRZ002468
Accession ID Mm10

Library idBAMCTSS
CNhs12536 DRZ012433 DRZ013818
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

CNhs12536

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.0355
1001 --0.0749
1002 --0.116
1003 --0.155
1004 0
1005 0.151
1006 --0.13
1007 --0.16
1008 0
1009 --0.094
101 0.222
1010 0
1011 0.0431
1012 0
1013 --0.118
1014 --0.0874
1015 --0.00896
1016 --0.332
1017 0
1018 0.0318
1019 0
102 0.106
1020 0.0562
1021 0
1022 --0.0428
1023 0.715
1024 1.013
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.0709
103 --0.0887
1030 0
1031 --0.855
1032 --0.184
1033 0.151
1034 0
1035 0
1036 0.376
1037 0
1038 --0.221
1039 --0.0727
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: CNhs12536

Jaspar motif P-value
MA0002.2 3.563e-7
MA0003.1 0.776
MA0004.1 0.324
MA0006.1 0.794
MA0007.1 0.942
MA0009.1 0.306
MA0014.1 0.794
MA0017.1 0.203
MA0018.2 2.2323e-11
MA0019.1 0.6
MA0024.1 0.00103
MA0025.1 5.14151e-4
MA0027.1 0.0217
MA0028.1 8.72568e-8
MA0029.1 0.568
MA0030.1 0.265
MA0031.1 0.00274
MA0035.2 0.969
MA0038.1 0.0169
MA0039.2 0.123
MA0040.1 0.0229
MA0041.1 0.73
MA0042.1 0.565
MA0043.1 1.02011e-7
MA0046.1 7.67912e-16
MA0047.2 0.521
MA0048.1 0.0272
MA0050.1 1.13833e-15
MA0051.1 2.05586e-9
MA0052.1 0.803
MA0055.1 0.0196
MA0057.1 0.787
MA0058.1 0.212
MA0059.1 0.147
MA0060.1 0.323
MA0061.1 1.31364e-12
MA0062.2 2.23329e-21
MA0065.2 0.874
MA0066.1 0.229
MA0067.1 9.07477e-6
MA0068.1 0.0174
MA0069.1 0.687
MA0070.1 0.65
MA0071.1 0.857
MA0072.1 0.702
MA0073.1 0.683
MA0074.1 0.764
MA0076.1 7.95089e-8
MA0077.1 0.228
MA0078.1 0.884
MA0079.2 0.771
MA0080.2 2.70597e-14
MA0081.1 3.28249e-5
MA0083.1 0.283
MA0084.1 0.0656
MA0087.1 0.672
MA0088.1 0.435
MA0090.1 0.00539
MA0091.1 0.228
MA0092.1 0.204
MA0093.1 0.268
MA0099.2 2.41486e-21
MA0100.1 0.00471
MA0101.1 3.82229e-17
MA0102.2 0.014
MA0103.1 0.205
MA0104.2 0.156
MA0105.1 1.07413e-5
MA0106.1 0.68
MA0107.1 1.27482e-18
MA0108.2 0.343
MA0111.1 0.948
MA0112.2 0.924
MA0113.1 0.76
MA0114.1 0.00776
MA0115.1 0.917
MA0116.1 0.0755
MA0117.1 0.00802
MA0119.1 0.0833
MA0122.1 0.103
MA0124.1 0.928
MA0125.1 0.0723
MA0131.1 0.103
MA0135.1 0.589
MA0136.1 6.66287e-30
MA0137.2 0.00891
MA0138.2 2.33516e-5
MA0139.1 0.911
MA0140.1 0.848
MA0141.1 0.135
MA0142.1 0.783
MA0143.1 0.038
MA0144.1 0.0685
MA0145.1 0.772
MA0146.1 0.0565
MA0147.1 0.145
MA0148.1 0.963
MA0149.1 0.344
MA0150.1 3.58633e-6
MA0152.1 0.598
MA0153.1 5.20765e-6
MA0154.1 0.936
MA0155.1 0.388
MA0156.1 5.59777e-27
MA0157.1 0.0177
MA0159.1 0.364
MA0160.1 0.864
MA0162.1 0.61
MA0163.1 0.00462
MA0164.1 0.663
MA0258.1 0.338
MA0259.1 0.385



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: CNhs12536

Novel motif P-value
1 0.926
10 0.233
100 0.988
101 0.709
102 0.783
103 0.368
104 0.694
105 0.598
106 0.0642
107 0.63
108 0.769
109 0.635
11 0.966
110 0.764
111 0.936
112 0.23
113 0.743
114 0.178
115 0.82
116 0.555
117 1.3316e-4
118 0.142
119 0.69
12 0.545
120 0.359
121 0.204
122 0.582
123 0.207
124 0.397
125 0.904
126 0.74
127 0.942
128 0.128
129 0.656
13 0.00301
130 0.67
131 0.145
132 0.43
133 0.148
134 0.811
135 0.568
136 0.0729
137 0.00552
138 0.975
139 0.604
14 0.513
140 0.757
141 0.485
142 0.524
143 0.31
144 0.926
145 0.548
146 0.538
147 0.696
148 0.173
149 0.199
15 0.171
150 0.781
151 0.644
152 0.154
153 0.233
154 0.707
155 0.628
156 0.0754
157 0.882
158 0.026
159 0.724
160 0.0741
161 0.473
162 0.441
163 0.0715
164 0.0502
165 0.159
166 0.183
167 0.385
168 0.183
169 0.191
17 0.817
18 0.892
19 0.0922
2 0.0175
20 0.0217
21 0.77
22 0.936
23 0.437
24 0.0607
25 0.661
26 0.0918
27 0.439
28 0.602
29 0.213
3 0.541
30 0.213
31 0.489
32 0.032
33 0.158
34 0.73
35 0.827
36 0.258
37 0.0627
38 0.672
39 0.348
4 0.461
40 0.438
41 0.0732
42 0.559
43 0.899
44 0.931
45 0.739
46 0.967
47 0.672
48 0.728
49 0.959
5 0.91
50 0.642
51 0.665
52 0.732
53 0.78
54 0.58
55 0.918
56 0.906
57 0.568
58 0.273
59 0.802
6 0.87
60 0.491
61 0.301
62 0.324
63 0.56
64 0.529
65 0.949
66 0.375
67 0.841
68 0.614
69 0.601
7 0.72
70 0.51
71 0.347
72 0.431
73 0.0348
74 0.332
75 0.00883
76 0.109
77 0.00563
78 0.209
79 0.596
8 0.969
80 0.562
81 0.727
82 0.127
83 0.0114
84 0.621
85 0.101
86 0.157
87 0.0123
88 0.431
89 0.254
9 0.69
90 0.493
91 0.55
92 0.399
93 0.252
94 0.913
95 0.00232
96 0.386
97 0.906
98 0.88
99 0.0454



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: CNhs12536


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)
0000034 (stem cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000021 (hematopoietic stem cell sample)
0000103 (mouse sample)
0000001 (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

NA