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FF:12121-128C6

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Name:stem cell (cKit+ Sca1- lineage-) KSL, biol_rep1
Species:Mouse (Mus musculus)
Library ID:CNhs12534
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 numberrep1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005414
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12534 CAGE DRX008784 DRR009656
Accession ID Mm9

Library idBAMCTSS
CNhs12534 DRZ001081 DRZ002466
Accession ID Mm10

Library idBAMCTSS
CNhs12534 DRZ012431 DRZ013816
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

CNhs12534

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.00139
1001 --0.072
1002 --0.116
1003 --0.102
1004 0
1005 0
1006 --0.143
1007 --0.236
1008 0
1009 --0.0273
101 0.235
1010 0
1011 0
1012 0.0682
1013 --0.149
1014 --0.0874
1015 0.0772
1016 --0.282
1017 0
1018 0
1019 0
102 0.127
1020 0
1021 0
1022 --0.111
1023 0.81
1024 1.012
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.115
103 --0.0887
1030 0
1031 --0.911
1032 --0.28
1033 0.0682
1034 0
1035 0
1036 0.421
1037 0
1038 --0.198
1039 --0.0609
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: CNhs12534

Jaspar motif P-value
MA0002.2 2.15094e-7
MA0003.1 0.658
MA0004.1 0.244
MA0006.1 0.887
MA0007.1 0.693
MA0009.1 0.35
MA0014.1 0.529
MA0017.1 0.413
MA0018.2 1.9578e-11
MA0019.1 0.698
MA0024.1 8.48169e-4
MA0025.1 4.30764e-4
MA0027.1 0.0348
MA0028.1 3.48273e-7
MA0029.1 0.546
MA0030.1 0.215
MA0031.1 0.00288
MA0035.2 0.906
MA0038.1 0.00225
MA0039.2 0.608
MA0040.1 0.0225
MA0041.1 0.127
MA0042.1 0.341
MA0043.1 1.1927e-7
MA0046.1 2.9056e-15
MA0047.2 0.543
MA0048.1 0.0141
MA0050.1 6.6821e-15
MA0051.1 4.66319e-8
MA0052.1 0.295
MA0055.1 0.0163
MA0057.1 0.784
MA0058.1 0.152
MA0059.1 0.0586
MA0060.1 0.914
MA0061.1 1.09498e-14
MA0062.2 3.20628e-20
MA0065.2 0.886
MA0066.1 0.143
MA0067.1 1.46181e-5
MA0068.1 0.00419
MA0069.1 0.612
MA0070.1 0.537
MA0071.1 0.702
MA0072.1 0.881
MA0073.1 0.705
MA0074.1 0.644
MA0076.1 4.80143e-7
MA0077.1 0.256
MA0078.1 0.891
MA0079.2 0.166
MA0080.2 4.66137e-14
MA0081.1 7.14077e-5
MA0083.1 0.4
MA0084.1 0.0502
MA0087.1 0.74
MA0088.1 0.615
MA0090.1 0.00925
MA0091.1 0.311
MA0092.1 0.379
MA0093.1 0.207
MA0099.2 4.9867e-27
MA0100.1 0.00452
MA0101.1 9.89916e-20
MA0102.2 0.0494
MA0103.1 0.197
MA0104.2 0.0794
MA0105.1 2.26708e-7
MA0106.1 0.839
MA0107.1 1.89918e-21
MA0108.2 0.831
MA0111.1 0.859
MA0112.2 0.476
MA0113.1 0.858
MA0114.1 0.0123
MA0115.1 0.914
MA0116.1 0.0328
MA0117.1 0.00965
MA0119.1 0.164
MA0122.1 0.0873
MA0124.1 0.947
MA0125.1 0.0939
MA0131.1 0.106
MA0135.1 0.399
MA0136.1 1.64025e-29
MA0137.2 0.00164
MA0138.2 1.63499e-5
MA0139.1 0.772
MA0140.1 0.617
MA0141.1 0.264
MA0142.1 0.344
MA0143.1 0.0966
MA0144.1 0.0489
MA0145.1 0.64
MA0146.1 0.133
MA0147.1 0.0792
MA0148.1 0.97
MA0149.1 0.185
MA0150.1 8.09947e-8
MA0152.1 0.75
MA0153.1 3.48843e-5
MA0154.1 0.908
MA0155.1 0.423
MA0156.1 2.15946e-26
MA0157.1 0.0154
MA0159.1 0.247
MA0160.1 0.954
MA0162.1 0.631
MA0163.1 7.87149e-4
MA0164.1 0.656
MA0258.1 0.166
MA0259.1 0.342



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: CNhs12534

Novel motif P-value
1 0.936
10 0.174
100 0.884
101 0.554
102 0.917
103 0.532
104 0.564
105 0.624
106 0.0562
107 0.843
108 0.669
109 0.588
11 0.926
110 0.651
111 0.898
112 0.211
113 0.827
114 0.164
115 0.57
116 0.599
117 2.82009e-4
118 0.132
119 0.691
12 0.548
120 0.372
121 0.208
122 0.563
123 0.205
124 0.542
125 0.99
126 0.535
127 0.954
128 0.067
129 0.581
13 0.0017
130 0.507
131 0.212
132 0.339
133 0.336
134 0.879
135 0.689
136 0.14
137 0.00463
138 0.996
139 0.838
14 0.524
140 0.701
141 0.489
142 0.585
143 0.297
144 0.906
145 0.427
146 0.583
147 0.625
148 0.229
149 0.244
15 0.0956
150 0.776
151 0.717
152 0.27
153 0.211
154 0.503
155 0.666
156 0.0863
157 0.825
158 0.0308
159 0.787
160 0.11
161 0.323
162 0.337
163 0.0782
164 0.0384
165 0.0958
166 0.24
167 0.297
168 0.272
169 0.178
17 0.828
18 0.87
19 0.101
2 0.0187
20 0.0218
21 0.883
22 0.958
23 0.482
24 0.0402
25 0.59
26 0.0542
27 0.431
28 0.716
29 0.173
3 0.508
30 0.175
31 0.491
32 0.0403
33 0.156
34 0.677
35 0.997
36 0.152
37 0.0547
38 0.711
39 0.482
4 0.48
40 0.241
41 0.0859
42 0.608
43 0.975
44 0.953
45 0.709
46 0.814
47 0.588
48 0.749
49 0.847
5 0.806
50 0.663
51 0.743
52 0.78
53 0.78
54 0.594
55 0.957
56 0.969
57 0.665
58 0.267
59 0.814
6 0.829
60 0.451
61 0.394
62 0.277
63 0.692
64 0.603
65 0.923
66 0.472
67 0.8
68 0.367
69 0.588
7 0.584
70 0.427
71 0.201
72 0.514
73 0.0507
74 0.81
75 0.00732
76 0.0822
77 0.00899
78 0.261
79 0.547
8 0.965
80 0.81
81 0.769
82 0.166
83 0.0174
84 0.501
85 0.149
86 0.199
87 0.0316
88 0.423
89 0.33
9 0.689
90 0.262
91 0.518
92 0.731
93 0.166
94 0.886
95 0.00628
96 0.555
97 0.966
98 0.776
99 0.0421



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: CNhs12534


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