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FF:12124-128C9

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Name:stem cell (cKit+ Sca1- lineage-) KSL, biol_rep2
Species:Mouse (Mus musculus)
Library ID:CNhs12535
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 numberrep2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005977
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12535 CAGE DRX008785 DRR009657
Accession ID Mm9

Library idBAMCTSS
CNhs12535 DRZ001082 DRZ002467
Accession ID Mm10

Library idBAMCTSS
CNhs12535 DRZ012432 DRZ013817
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

CNhs12535

MCL coexpression id Coexpression dpi cluster scores median value
0 0
1 0
10 0
100 0
1000 --0.00703
1001 --0.0631
1002 --0.116
1003 --0.111
1004 0
1005 0.0569
1006 --0.143
1007 --0.17
1008 0
1009 --0.0804
101 0.254
1010 0
1011 0.0569
1012 0
1013 --0.169
1014 --0.0851
1015 0.00923
1016 --0.266
1017 0
1018 0.107
1019 0
102 0.107
1020 0
1021 0
1022 --0.0704
1023 0.76
1024 0.979
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.115
103 --0.0887
1030 0
1031 --0.854
1032 --0.184
1033 0.199
1034 0
1035 0
1036 0.464
1037 0
1038 --0.241
1039 --0.102
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: CNhs12535

Jaspar motif P-value
MA0002.2 1.63896e-7
MA0003.1 0.763
MA0004.1 0.211
MA0006.1 0.88
MA0007.1 0.833
MA0009.1 0.273
MA0014.1 0.871
MA0017.1 0.337
MA0018.2 1.68121e-11
MA0019.1 0.601
MA0024.1 7.39556e-4
MA0025.1 5.0228e-4
MA0027.1 0.0391
MA0028.1 2.88778e-8
MA0029.1 0.384
MA0030.1 0.247
MA0031.1 0.00385
MA0035.2 0.917
MA0038.1 0.00607
MA0039.2 0.244
MA0040.1 0.0286
MA0041.1 0.504
MA0042.1 0.532
MA0043.1 1.57493e-7
MA0046.1 5.93308e-15
MA0047.2 0.579
MA0048.1 0.0229
MA0050.1 1.3056e-15
MA0051.1 2.52363e-9
MA0052.1 0.396
MA0055.1 0.0278
MA0057.1 0.764
MA0058.1 0.087
MA0059.1 0.103
MA0060.1 0.357
MA0061.1 4.15816e-13
MA0062.2 1.93427e-22
MA0065.2 0.756
MA0066.1 0.275
MA0067.1 1.17581e-5
MA0068.1 0.0132
MA0069.1 0.628
MA0070.1 0.669
MA0071.1 0.926
MA0072.1 0.592
MA0073.1 0.647
MA0074.1 0.778
MA0076.1 3.46685e-8
MA0077.1 0.325
MA0078.1 0.947
MA0079.2 0.432
MA0080.2 2.5526e-14
MA0081.1 2.12769e-5
MA0083.1 0.515
MA0084.1 0.142
MA0087.1 0.99
MA0088.1 0.483
MA0090.1 0.00583
MA0091.1 0.285
MA0092.1 0.276
MA0093.1 0.16
MA0099.2 4.06301e-24
MA0100.1 0.00397
MA0101.1 7.08398e-18
MA0102.2 0.0197
MA0103.1 0.131
MA0104.2 0.0965
MA0105.1 2.18381e-6
MA0106.1 0.722
MA0107.1 5.45564e-20
MA0108.2 0.482
MA0111.1 0.8
MA0112.2 0.874
MA0113.1 0.762
MA0114.1 0.012
MA0115.1 0.782
MA0116.1 0.0621
MA0117.1 0.0041
MA0119.1 0.0568
MA0122.1 0.131
MA0124.1 0.994
MA0125.1 0.0686
MA0131.1 0.167
MA0135.1 0.843
MA0136.1 2.51251e-30
MA0137.2 0.00259
MA0138.2 1.8912e-5
MA0139.1 0.892
MA0140.1 0.698
MA0141.1 0.0941
MA0142.1 0.518
MA0143.1 0.0498
MA0144.1 0.0638
MA0145.1 0.461
MA0146.1 0.1
MA0147.1 0.112
MA0148.1 0.988
MA0149.1 0.339
MA0150.1 2.87117e-7
MA0152.1 0.859
MA0153.1 1.8033e-5
MA0154.1 0.833
MA0155.1 0.335
MA0156.1 1.23664e-27
MA0157.1 0.0265
MA0159.1 0.455
MA0160.1 0.746
MA0162.1 0.592
MA0163.1 0.00257
MA0164.1 0.745
MA0258.1 0.447
MA0259.1 0.358



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: CNhs12535

Novel motif P-value
1 0.872
10 0.234
100 0.969
101 0.465
102 0.84
103 0.411
104 0.582
105 0.525
106 0.0695
107 0.689
108 0.623
109 0.642
11 0.966
110 0.606
111 0.968
112 0.27
113 0.797
114 0.0998
115 0.624
116 0.631
117 2.17724e-4
118 0.176
119 0.611
12 0.472
120 0.366
121 0.263
122 0.545
123 0.163
124 0.336
125 0.945
126 0.53
127 0.876
128 0.208
129 0.892
13 0.00308
130 0.57
131 0.211
132 0.391
133 0.257
134 0.907
135 0.697
136 0.0908
137 0.00684
138 0.973
139 0.6
14 0.573
140 0.698
141 0.557
142 0.503
143 0.247
144 0.845
145 0.499
146 0.668
147 0.49
148 0.361
149 0.175
15 0.195
150 0.818
151 0.744
152 0.156
153 0.329
154 0.571
155 0.523
156 0.292
157 0.748
158 0.0336
159 0.702
160 0.0839
161 0.435
162 0.515
163 0.0437
164 0.0542
165 0.136
166 0.215
167 0.535
168 0.156
169 0.192
17 0.845
18 0.956
19 0.0758
2 0.0168
20 0.0228
21 0.957
22 0.995
23 0.402
24 0.0869
25 0.559
26 0.0935
27 0.382
28 0.687
29 0.271
3 0.638
30 0.191
31 0.444
32 0.0382
33 0.146
34 0.653
35 0.944
36 0.2
37 0.0583
38 0.676
39 0.364
4 0.488
40 0.314
41 0.114
42 0.66
43 0.871
44 0.983
45 0.7
46 0.986
47 0.642
48 0.682
49 0.949
5 0.868
50 0.62
51 0.609
52 0.606
53 0.803
54 0.551
55 0.995
56 0.963
57 0.535
58 0.342
59 0.696
6 0.786
60 0.537
61 0.368
62 0.395
63 0.552
64 0.641
65 0.97
66 0.431
67 0.779
68 0.436
69 0.574
7 0.69
70 0.562
71 0.261
72 0.453
73 0.0329
74 0.569
75 0.00883
76 0.115
77 0.00552
78 0.352
79 0.596
8 0.899
80 0.746
81 0.792
82 0.163
83 0.00591
84 0.552
85 0.087
86 0.225
87 0.0105
88 0.414
89 0.233
9 0.727
90 0.535
91 0.403
92 0.439
93 0.153
94 0.789
95 0.00349
96 0.376
97 0.92
98 0.604
99 0.026



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: CNhs12535


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