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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005952
 
|DRA_sample_Accession=CAGE@SAMD00005952
 +
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00005952
 
|accession_numbers=CAGE;DRX008902;DRR009774,DRR009775,DRR009776;DRZ001199,DRZ001200,DRZ001201;DRZ002584;DRZ012549,DRZ012550,DRZ012551;DRZ013934
 
|accession_numbers=CAGE;DRX008902;DRR009774,DRR009775,DRR009776;DRZ001199,DRZ001200,DRZ001201;DRZ002584;DRZ012549,DRZ012550,DRZ012551;DRZ013934
 +
|accession_numbers_RNASeq=sRNA-Seq;DRX037390;DRR041756;DRZ007365
 
|ancestors_in_anatomy_facet=
 
|ancestors_in_anatomy_facet=
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000764,CL:0000548,CL:0000763,CL:0002371,CL:0002242,CL:0000255,CL:0000765
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000764,CL:0000548,CL:0000763,CL:0002371,CL:0002242,CL:0000255,CL:0000765
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|rna_tube_id=139I3
 
|rna_tube_id=139I3
 
|rna_weight_ug=8.03
 
|rna_weight_ug=8.03
 +
|rnaseq_library_id=SRhi10062.ATCACG
 
|sample_age=
 
|sample_age=
 
|sample_category=time courses
 
|sample_category=time courses

Latest revision as of 06:59, 17 October 2017


Name:J2E erythroblastic leukemia response to erythropoietin
Species:Mouse (Mus musculus)
Library ID:CNhs12449
Sample type:time courses
Genomic View: UCSC
MicroRNAs:Including candidate novel miRNAs(CAGE samplessRNA samples)
Excluding candidate novel miRNAs(CAGE samplessRNA samples)
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexNA
ageNA
cell typeerythroblast
cell lineJ2E
companyNA
collaborationPeter Klinken (Western Australian Institute of Medical Research)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)Repurified by minelute

Accession numbers
MethodSample accession id
CAGE  SAMD00005952
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12449 CAGE DRX008902 DRR009774
DRR009775
DRR009776
Accession ID Mm9

Library idBAMCTSS
CNhs12449 DRZ001199
DRZ001200
DRZ001201
DRZ002584
Accession ID Mm10

Library idBAMCTSS
CNhs12449 DRZ012549
DRZ012550
DRZ012551
DRZ013934
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00005952
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10062.ATCACG sRNA-Seq DRX037390 DRR041756
Accession ID Mm9

Library idBAMCTSS
SRhi10062.ATCACG DRZ007365


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

CNhs12449

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 --0.0174
1004 0
1005 --0.409
1006 --0.143
1007 --0.188
1008 0
1009 --0.19
101 0.177
1010 0
1011 0.165
1012 0
1013 --0.0989
1014 --0.0874
1015 0.128
1016 --0.664
1017 0
1018 0
1019 0
102 0
1020 0.827
1021 0.613
1022 --0.0704
1023 0
1024 --0.14
1025 --0.0611
1026 0
1027 --0.048
1028 0
1029 --0.176
103 --0.0887
1030 0
1031 --0.941
1032 --0.32
1033 0.717
1034 0
1035 0
1036 1.059
1037 0
1038 --0.336
1039 --0.222
104 0
1040 --0.989
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: CNhs12449

Jaspar motif P-value
MA0002.2 0.206
MA0003.1 0.656
MA0004.1 0.0157
MA0006.1 0.226
MA0007.1 0.472
MA0009.1 0.798
MA0014.1 0.956
MA0017.1 0.198
MA0018.2 0.0826
MA0019.1 0.617
MA0024.1 1.41368e-5
MA0025.1 0.156
MA0027.1 0.433
MA0028.1 4.07751e-8
MA0029.1 0.716
MA0030.1 0.385
MA0031.1 0.0491
MA0035.2 2.19245e-13
MA0038.1 0.00232
MA0039.2 0.821
MA0040.1 0.366
MA0041.1 0.208
MA0042.1 0.496
MA0043.1 0.0265
MA0046.1 5.41426e-5
MA0047.2 0.197
MA0048.1 0.0174
MA0050.1 9.97103e-4
MA0051.1 0.0317
MA0052.1 0.116
MA0055.1 9.71852e-5
MA0057.1 0.61
MA0058.1 0.00554
MA0059.1 1.37022e-4
MA0060.1 8.73182e-6
MA0061.1 0.595
MA0062.2 1.10015e-10
MA0065.2 0.0177
MA0066.1 0.47
MA0067.1 0.594
MA0068.1 0.0969
MA0069.1 0.566
MA0070.1 0.709
MA0071.1 0.0817
MA0072.1 0.797
MA0073.1 0.9
MA0074.1 0.316
MA0076.1 1.64026e-10
MA0077.1 0.254
MA0078.1 0.328
MA0079.2 0.0406
MA0080.2 0.384
MA0081.1 0.0344
MA0083.1 0.0157
MA0084.1 0.738
MA0087.1 0.775
MA0088.1 0.0217
MA0090.1 0.288
MA0091.1 0.327
MA0092.1 0.525
MA0093.1 0.0172
MA0099.2 0.0609
MA0100.1 0.0192
MA0101.1 0.355
MA0102.2 0.291
MA0103.1 0.681
MA0104.2 9.99737e-5
MA0105.1 0.0229
MA0106.1 0.111
MA0107.1 0.604
MA0108.2 0.0231
MA0111.1 0.803
MA0112.2 0.134
MA0113.1 0.82
MA0114.1 0.212
MA0115.1 0.0154
MA0116.1 0.0181
MA0117.1 0.494
MA0119.1 0.988
MA0122.1 0.813
MA0124.1 0.375
MA0125.1 0.468
MA0131.1 0.293
MA0135.1 0.411
MA0136.1 1.01374e-5
MA0137.2 0.161
MA0138.2 0.11
MA0139.1 0.285
MA0140.1 2.4696e-22
MA0141.1 0.0159
MA0142.1 0.413
MA0143.1 0.195
MA0144.1 0.593
MA0145.1 0.531
MA0146.1 0.195
MA0147.1 1.50097e-5
MA0148.1 0.419
MA0149.1 0.00813
MA0150.1 0.0424
MA0152.1 0.334
MA0153.1 0.128
MA0154.1 0.395
MA0155.1 0.438
MA0156.1 4.8328e-5
MA0157.1 0.0175
MA0159.1 0.0183
MA0160.1 0.0546
MA0162.1 0.892
MA0163.1 3.63783e-4
MA0164.1 0.467
MA0258.1 0.266
MA0259.1 0.0096



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: CNhs12449

Novel motif P-value
1 0.166
10 0.0213
100 0.0586
101 0.38
102 0.239
103 0.0686
104 0.55
105 0.867
106 0.61
107 0.242
108 0.619
109 0.0484
11 0.189
110 0.0498
111 0.0046
112 0.4
113 0.242
114 0.837
115 0.681
116 0.166
117 3.09957e-4
118 0.408
119 0.396
12 0.564
120 0.283
121 0.456
122 0.54
123 0.414
124 0.0349
125 0.0106
126 0.061
127 0.166
128 0.577
129 0.815
13 0.00211
130 0.613
131 0.458
132 0.254
133 0.553
134 0.0188
135 0.075
136 0.197
137 0.805
138 0.464
139 0.987
14 0.578
140 0.888
141 0.815
142 0.227
143 0.658
144 0.923
145 0.103
146 0.863
147 0.867
148 0.131
149 0.0552
15 0.224
150 0.372
151 0.851
152 0.315
153 0.638
154 0.898
155 0.702
156 0.262
157 0.911
158 0.015
159 0.944
160 0.552
161 0.718
162 0.721
163 0.446
164 0.041
165 0.883
166 0.028
167 0.33
168 0.803
169 0.321
17 0.963
18 0.114
19 0.681
2 0.12
20 0.00316
21 0.195
22 0.907
23 0.426
24 0.28
25 0.201
26 0.00992
27 0.476
28 0.976
29 0.0029
3 0.0876
30 0.359
31 0.722
32 0.656
33 0.117
34 0.675
35 0.49
36 0.00929
37 0.283
38 0.627
39 0.495
4 0.318
40 0.0719
41 0.104
42 0.139
43 0.853
44 0.357
45 0.436
46 0.28
47 0.352
48 0.294
49 0.694
5 0.439
50 0.845
51 0.773
52 0.098
53 0.352
54 0.558
55 0.0193
56 0.994
57 0.158
58 0.985
59 0.88
6 0.801
60 0.948
61 0.564
62 0.422
63 0.826
64 0.573
65 0.894
66 0.151
67 0.0599
68 0.596
69 0.922
7 0.156
70 0.0868
71 0.00181
72 0.899
73 0.286
74 0.344
75 0.0332
76 0.16
77 0.935
78 0.102
79 0.873
8 0.0642
80 0.849
81 0.862
82 0.548
83 0.992
84 0.641
85 0.792
86 0.266
87 0.0894
88 0.612
89 0.228
9 0.523
90 0.0378
91 0.683
92 0.892
93 0.267
94 0.527
95 0.0679
96 0.445
97 0.987
98 0.382
99 0.411



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: CNhs12449


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)
0000764 (erythroid lineage cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0000765 (erythroblast)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
2531 (hematologic cancer)
14566 (disease of cellular proliferation)
0060083 (immune system cancer)
1240 (leukemia)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0100737 (leukemia cell line sample)
0000401 (erythroblastic leukemia cell line sample)
0000350 (experimentally modified sample)
0000344 (0 minute sample)
0000337 (erythropoietin treatment sample)
0000403 (mouse J2E erythroblastic leukemia cell line sample)
0101035 (hematopoietic cell line sample)
0000498 (mouse J2E erythroblastic leukemia line 0min after treatment with erythropoietin 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)