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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0002384,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000723,CL:0000048,CL:0000988,CL:0000764,CL:0000839,CL:0000548,CL:0000034,CL:0002032,CL:0000763,CL:0000012,CL:0002320,CL:0000063,CL:0002371,CL:0000219,CL:0000004,CL:0000134,CL:0000255,CL:0000765,CL:0002031,CL:0000037,CL:0000050,CL:0000566,CL:0000049,CL:0000038,CL:0000837,CL:0000547
|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_disease_facet=DOID:4,DOID:0050686,DOID:162,DOID:2531,DOID:14566,DOID:0060083,DOID:1240
|ancestors_in_disease_facet=DOID:4,DOID:0050686,DOID:162,DOID:2531,DOID:14566,DOID:0060083,DOID:1240
|ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000101,FF:0000103,FF:0000001,FF:0100737,FF:0000401,FF:0000350,FF:0000344,FF:0000337,FF:0000403,FF:0101035,FF:0000498
|comment=
|comment=
|created_by=
|created_by=

Revision as of 23:49, 4 July 2012


Name:J2E erythroblastic leukemia response to erythropoietin, 00hr00min, biol_rep2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs12668

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.0596
10040
1005-0.771
1006-0.143
1007-0.0904
10080
1009-0.2
1010.161
10100
10110
10120
1013-0.205
1014-0.0874
10150.0483
1016-0.471
10170
10180
10190
1020
10201.353
10211.261
1022-0.0831
10230
1024-0.14
1025-0.0611
10260
1027-0.048
10280
1029-0.176
103-0.0887
10300
1031-0.911
1032-0.392
10330.725
10340
10350
10360.921
10370
1038-0.425
1039-0.282
1040
1040-0.893
10410



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12668

Jaspar motifP-value
MA0002.20.103
MA0003.10.798
MA0004.10.0159
MA0006.10.271
MA0007.10.262
MA0009.10.636
MA0014.10.955
MA0017.10.14
MA0018.20.233
MA0019.10.962
MA0024.13.67261e-5
MA0025.10.553
MA0027.10.48
MA0028.12.2894e-7
MA0029.10.431
MA0030.10.315
MA0031.10.0548
MA0035.27.04571e-14
MA0038.10.0021
MA0039.20.756
MA0040.10.622
MA0041.10.21
MA0042.10.46
MA0043.10.0652
MA0046.13.22315e-4
MA0047.20.759
MA0048.10.0186
MA0050.10.00164
MA0051.10.0143
MA0052.10.0301
MA0055.12.18866e-4
MA0057.10.579
MA0058.10.00907
MA0059.11.93555e-4
MA0060.19.32862e-4
MA0061.10.492
MA0062.25.63626e-10
MA0065.20.00555
MA0066.10.312
MA0067.10.87
MA0068.10.00515
MA0069.10.389
MA0070.10.514
MA0071.10.0451
MA0072.10.845
MA0073.10.841
MA0074.10.126
MA0076.11.61215e-9
MA0077.10.431
MA0078.10.187
MA0079.20.0429
MA0080.20.296
MA0081.10.0746
MA0083.10.0247
MA0084.10.443
MA0087.10.818
MA0088.10.00937
MA0090.10.334
MA0091.10.286
MA0092.10.651
MA0093.10.0167
MA0099.20.0521
MA0100.10.0096
MA0101.10.419
MA0102.20.0893
MA0103.10.469
MA0104.21.45087e-4
MA0105.10.00839
MA0106.10.0828
MA0107.10.716
MA0108.20.00131
MA0111.10.917
MA0112.20.0845
MA0113.10.472
MA0114.10.116
MA0115.10.015
MA0116.10.00849
MA0117.10.645
MA0119.10.7
MA0122.10.906
MA0124.10.702
MA0125.10.795
MA0131.10.394
MA0135.10.28
MA0136.13.71292e-5
MA0137.20.0267
MA0138.20.123
MA0139.10.369
MA0140.11.5309e-20
MA0141.10.00806
MA0142.10.366
MA0143.10.376
MA0144.10.279
MA0145.10.589
MA0146.10.0911
MA0147.11.94651e-5
MA0148.10.761
MA0149.10.00501
MA0150.10.0197
MA0152.10.188
MA0153.10.0718
MA0154.10.174
MA0155.10.587
MA0156.16.78612e-5
MA0157.10.02
MA0159.10.019
MA0160.10.0128
MA0162.10.952
MA0163.12.4565e-4
MA0164.10.403
MA0258.10.16
MA0259.10.0188



FANTOM5 phase1 novel unique motifs<b>Summary:</b>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 in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12668

Novel motifP-value
10.087
100.024
1000.0475
1010.481
1020.36
1030.086
1040.639
1050.898
1060.809
1070.314
1080.642
1090.0305
110.129
1100.0248
1110.00882
1120.286
1130.27
1140.366
1150.802
1160.324
1171.8708e-4
1180.354
1190.211
120.611
1200.26
1210.793
1220.697
1230.429
1240.0403
1250.00326
1260.0975
1270.0951
1280.512
1290.867
130.00763
1300.54
1310.208
1320.339
1330.414
1340.0762
1350.276
1360.301
1370.915
1380.486
1390.849
140.578
1400.939
1410.775
1420.256
1430.546
1440.944
1450.0435
1460.757
1470.829
1480.247
1490.106
150.122
1500.272
1510.996
1520.418
1530.656
1540.987
1550.636
1560.488
1570.508
1580.00253
1590.702
1600.686
1610.328
1620.753
1630.753
1640.0343
1650.936
1660.0755
1670.241
1680.776
1690.192
170.73
180.0575
190.762
20.156
200.00357
210.219
220.751
230.735
240.331
250.261
260.0135
270.787
280.921
290.00112
30.0931
300.339
310.891
320.719
330.0999
340.958
350.302
360.0106
370.245
380.451
390.763
40.433
400.112
410.0628
420.193
430.668
440.165
450.605
460.182
470.221
480.196
490.429
50.264
500.941
510.976
520.13
530.402
540.634
550.0342
560.98
570.141
580.791
590.735
60.858
600.845
610.589
620.309
630.581
640.392
650.611
660.164
670.18
680.624
690.728
70.15
700.0227
710.00366
720.659
730.258
740.549
750.0292
760.115
770.821
780.0642
790.743
80.0378
800.642
810.944
820.885
830.854
840.558
850.775
860.258
870.171
880.629
890.472
90.678
900.00967
910.794
920.939
930.19
940.234
950.0172
960.206
970.966
980.282
990.691



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs12668


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>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)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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