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|sample_ethnicity=
|sample_ethnicity=
|rna_rin=
|rna_rin=
|rna_od260/230=2.15000
|rna_od260/230=2.15
|rna_od260/280=2.08000
|rna_od260/280=2.08
|sample_cell_type=erythroblast
|sample_cell_type=erythroblast
|sample_cell_line=J2E
|sample_cell_line=J2E
Line 29: Line 29:
|rna_sample_type=
|rna_sample_type=
|rna_extraction_protocol=Repurified by minelute
|rna_extraction_protocol=Repurified by minelute
|rna_weight_ug=29.13100
|rna_weight_ug=29.13
|rna_concentration=2.91310
|rna_concentration=2.91
|sample_note=
|sample_note=
|profile_hcage=CNhs12770,LSID971,release012,MAPPING
|profile_hcage=CNhs12770,LSID971,release012,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:39, 27 February 2012


Name:J2E erythroblastic leukemia response to erythropoietin, 00hr00min, biol_rep3
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]





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

CNhs12770

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.175
10040
1005-0.771
1006-0.143
1007-0.472
10080
1009-0.2
101-0.104
10100
1011-0.108
10120
1013-0.4
1014-0.0874
1015-0.87
1016-0.664
10170
10180
10190
1020
10200
1021-0.0487
1022-0.124
10230
1024-0.307
1025-0.0611
10260
1027-0.048
10280
1029-0.176
103-0.0829
10300
1031-1.193
1032-0.655
1033-0.0752
10340
10350
10360.724
10370
1038-0.892
1039-0.348
1040
1040-1.06
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: CNhs12770

Jaspar motifP-value
MA0002.20.00212
MA0003.10.549
MA0004.10.801
MA0006.10.931
MA0007.10.25
MA0009.10.578
MA0014.10.235
MA0017.10.023
MA0018.20.0256
MA0019.10.446
MA0024.10.429
MA0025.10.129
MA0027.10.785
MA0028.10.0272
MA0029.10.771
MA0030.10.171
MA0031.10.564
MA0035.20.00738
MA0038.10.00455
MA0039.20.0314
MA0040.10.952
MA0041.10.671
MA0042.10.359
MA0043.10.00131
MA0046.10.624
MA0047.20.31
MA0048.10.907
MA0050.10.00342
MA0051.17.33573e-4
MA0052.10.514
MA0055.10.679
MA0057.10.657
MA0058.10.976
MA0059.10.0607
MA0060.14.79492e-11
MA0061.10.118
MA0062.20.00129
MA0065.20.0049
MA0066.10.00827
MA0067.10.255
MA0068.10.343
MA0069.10.603
MA0070.10.0266
MA0071.10.0782
MA0072.10.397
MA0073.10.945
MA0074.10.216
MA0076.10.0052
MA0077.10.789
MA0078.10.0689
MA0079.20.0288
MA0080.20.709
MA0081.10.452
MA0083.10.725
MA0084.10.76
MA0087.10.829
MA0088.10.584
MA0090.10.371
MA0091.10.0262
MA0092.10.245
MA0093.10.959
MA0099.20.076
MA0100.10.245
MA0101.10.818
MA0102.20.23
MA0103.10.071
MA0104.20.14
MA0105.11.22382e-6
MA0106.10.175
MA0107.10.737
MA0108.20.335
MA0111.10.295
MA0112.22.26161e-5
MA0113.10.313
MA0114.10.0665
MA0115.10.0328
MA0116.13.43634e-4
MA0117.10.76
MA0119.10.0262
MA0122.10.8
MA0124.10.953
MA0125.10.11
MA0131.10.306
MA0135.10.00187
MA0136.10.344
MA0137.20.307
MA0138.20.445
MA0139.10.193
MA0140.11.26144e-4
MA0141.10.00478
MA0142.10.0172
MA0143.10.122
MA0144.10.655
MA0145.10.277
MA0146.10.767
MA0147.10.0986
MA0148.10.124
MA0149.10.0318
MA0150.10.0822
MA0152.10.841
MA0153.10.731
MA0154.10.00331
MA0155.10.567
MA0156.10.077
MA0157.10.96
MA0159.10.00571
MA0160.10.0908
MA0162.10.25
MA0163.11.44161e-4
MA0164.10.73
MA0258.12.29138e-4
MA0259.10.823



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: CNhs12770

Novel motifP-value
10.0521
100.047
1000.673
1010.541
1020.857
1030.0863
1040.497
1050.43
1060.0279
1070.0337
1080.638
1090.119
110.0558
1100.0541
1110.051
1120.0909
1130.661
1140.0206
1150.921
1160.433
1170.133
1180.385
1190.0516
120.71
1200.303
1210.822
1220.605
1230.337
1240.29
1250.034
1260.471
1270.257
1280.024
1290.066
130.37
1300.93
1310.609
1320.599
1330.224
1340.738
1350.129
1360.115
1370.991
1380.328
1390.029
140.638
1400.0754
1410.163
1420.125
1430.0432
1440.881
1450.091
1460.643
1470.602
1480.237
1490.28
150.0725
1500.361
1510.266
1520.949
1530.4
1540.69
1550.835
1560.38
1570.235
1580.0928
1590.14
1600.118
1610.453
1620.402
1630.869
1640.199
1650.183
1660.883
1670.141
1680.322
1690.0145
170.162
180.145
190.186
20.69
200.936
210.436
220.31
230.033
240.431
250.617
260.0307
270.3
280.717
290.136
30.0802
300.874
310.458
320.175
330.619
340.629
350.0546
360.0182
370.274
380.324
390.67
40.538
400.425
410.138
420.177
430.124
440.137
450.782
460.0476
470.162
480.266
490.091
50.0819
500.957
510.335
520.524
530.66
540.521
550.26
560.392
570.121
580.278
590.0832
60.749
600.189
610.526
620.077
630.165
640.182
650.109
660.616
670.273
680.0381
690.396
70.272
700.0165
710.0334
720.653
730.585
740.353
750.114
760.576
770.177
780.229
790.304
80.0374
800.236
810.371
820.0556
830.592
840.351
850.0313
860.649
870.226
880.888
890.119
90.517
900.0266
910.0483
920.0468
930.0238
940.00962
950.757
960.065
970.939
980.144
990.399



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: CNhs12770


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000038 (erythroid progenitor cell)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000050 (megakaryocyte-erythroid progenitor cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000547 (proerythroblast)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000763 (myeloid cell)
0000764 (erythroid lineage cell)
0000765 (erythroblast)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

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

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

FF: FANTOM5
NA

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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