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|sample_ethnicity=
|sample_ethnicity=
|rna_rin=
|rna_rin=
|rna_od260/230=1.25000
|rna_od260/230=1.25
|rna_od260/280=1.82077
|rna_od260/280=1.820769231
|sample_cell_type=granulocyte macrophage progenitor
|sample_cell_type=granulocyte macrophage progenitor
|sample_cell_line=
|sample_cell_line=
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|rna_sample_type=total RNA
|rna_sample_type=total RNA
|rna_extraction_protocol=
|rna_extraction_protocol=
|rna_weight_ug=4.16680
|rna_weight_ug=4.1668
|rna_concentration=0.09470
|rna_concentration=0.0947
|sample_note=
|sample_note=
|profile_hcage=CNhs12202,LSID976,release010,COMPLETED
|profile_hcage=CNhs12202,LSID976,release010,COMPLETED

Revision as of 17:37, 27 February 2012


Name:granulocyte macrophage progenitor GMP, biol_rep2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/8J
tissuebone marrow
dev stageNA
sexmale
age9-10weeks
cell typegranulocyte macrophage progenitor
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
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

CNhs12202

00
10
100
1000
10000
1001-0.0749
1002-0.116
1003-0.123
10040
10050.18
1006-0.162
1007-0.307
10080
1009-0.19
1010.282
10100
1011-0.108
10120
10130.0479
1014-0.0874
1015-0.0147
1016-0.484
10170
10180
10190
1020
10200
10210
1022-0.124
10230.824
10240.358
1025-0.0611
10260
1027-0.048
10280
1029-0.176
103-0.0887
10300
1031-0.956
1032-0.556
10330.0886
10340
10350
10360.343
10370
1038-0.354
10390.00502
1040
1040-0.343
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: CNhs12202

Jaspar motifP-value
MA0002.27.5987e-6
MA0003.10.993
MA0004.10.0424
MA0006.10.939
MA0007.10.719
MA0009.10.746
MA0014.10.978
MA0017.10.109
MA0018.24.37527e-4
MA0019.10.705
MA0024.10.00149
MA0025.10.0478
MA0027.10.488
MA0028.13.83408e-8
MA0029.10.267
MA0030.10.405
MA0031.10.626
MA0035.20.887
MA0038.10.0336
MA0039.20.788
MA0040.10.115
MA0041.10.566
MA0042.10.91
MA0043.17.30284e-7
MA0046.11.55133e-10
MA0047.20.822
MA0048.10.0178
MA0050.12.49745e-4
MA0051.10.00404
MA0052.10.197
MA0055.10.0016
MA0057.10.678
MA0058.10.0152
MA0059.10.00206
MA0060.10.552
MA0061.12.16211e-4
MA0062.22.47989e-17
MA0065.20.063
MA0066.10.223
MA0067.10.0257
MA0068.10.936
MA0069.10.526
MA0070.10.0987
MA0071.10.156
MA0072.10.726
MA0073.10.632
MA0074.10.16
MA0076.11.75614e-9
MA0077.10.706
MA0078.10.533
MA0079.20.0898
MA0080.22.42269e-12
MA0081.19.0918e-5
MA0083.10.00555
MA0084.10.727
MA0087.10.933
MA0088.10.119
MA0090.10.0249
MA0091.10.851
MA0092.10.694
MA0093.10.0352
MA0099.24.58458e-11
MA0100.18.63912e-5
MA0101.18.77923e-8
MA0102.25.30246e-6
MA0103.10.483
MA0104.20.0213
MA0105.16.86915e-6
MA0106.10.188
MA0107.19.5441e-7
MA0108.20.31
MA0111.10.896
MA0112.20.0422
MA0113.10.447
MA0114.10.722
MA0115.10.486
MA0116.10.00123
MA0117.10.338
MA0119.10.638
MA0122.10.233
MA0124.10.429
MA0125.10.103
MA0131.10.163
MA0135.10.384
MA0136.15.46861e-28
MA0137.25.93632e-4
MA0138.20.00677
MA0139.10.295
MA0140.10.374
MA0141.10.151
MA0142.10.766
MA0143.10.392
MA0144.10.0766
MA0145.10.926
MA0146.10.193
MA0147.10.0124
MA0148.10.922
MA0149.10.0715
MA0150.12.90256e-5
MA0152.10.973
MA0153.10.00294
MA0154.10.175
MA0155.10.757
MA0156.17.60856e-20
MA0157.10.432
MA0159.10.00988
MA0160.10.0457
MA0162.10.286
MA0163.12.88525e-6
MA0164.10.827
MA0258.10.109
MA0259.10.147



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: CNhs12202

Novel motifP-value
10.247
100.0409
1000.806
1010.816
1020.623
1030.0674
1040.791
1050.624
1060.286
1070.8
1080.761
1090.0238
110.151
1100.0814
1110.296
1120.109
1130.536
1140.723
1150.672
1160.413
1173.18966e-4
1180.266
1190.751
120.85
1200.129
1210.434
1220.614
1230.366
1240.243
1250.386
1260.392
1270.357
1280.42
1290.428
130.00256
1300.84
1310.284
1320.57
1330.543
1340.753
1350.506
1360.265
1370.0239
1380.35
1390.17
140.555
1400.719
1410.945
1420.968
1430.111
1440.66
1450.086
1460.905
1470.826
1480.431
1490.265
150.0305
1500.678
1510.8
1520.717
1530.694
1540.929
1550.763
1560.272
1570.735
1580.0448
1590.679
1600.691
1610.207
1620.328
1630.408
1640.00425
1650.138
1660.493
1670.344
1680.6
1690.0202
170.417
180.306
190.798
20.169
200.0202
210.297
220.781
230.359
240.0458
250.216
260.00393
270.551
280.797
290.00536
30.12
300.25
310.82
320.626
330.0696
340.85
350.506
360.0292
370.0432
380.379
390.73
40.955
400.0794
410.0141
420.381
430.456
440.434
450.842
460.252
470.562
480.213
490.379
50.416
500.702
510.948
520.419
530.582
540.889
550.509
560.764
570.447
580.2
590.452
60.81
600.47
610.154
620.128
630.911
640.575
650.556
660.236
670.222
680.64
690.676
70.121
700.0284
710.00731
720.103
730.0499
740.332
750.00731
760.0904
770.487
780.0685
790.451
80.0368
800.611
810.844
820.827
830.0132
840.963
850.827
860.286
870.035
880.556
890.463
90.936
900.0139
910.927
920.7
930.0302
940.303
950.00175
960.964
970.924
980.295
990.371



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: CNhs12202


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)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000763 (myeloid cell)
0000837 (hematopoietic multipotent progenitor cell)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002032 (hematopoietic oligopotent progenitor cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

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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