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FF:12129-128D5

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Name:granulocyte macrophage progenitor GMP, biol_rep3
Species:Mouse (Mus musculus)
Library ID:CNhs11928
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :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 numberrep3
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005059
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11928 CAGE DRX008861 DRR009733
Accession ID Mm9

Library idBAMCTSS
CNhs11928 DRZ001158 DRZ002543
Accession ID Mm10

Library idBAMCTSS
CNhs11928 DRZ012508 DRZ013893
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. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs11928

00
10
100
1000
10000
1001-0.0749
1002-0.116
1003-0.0999
10040
10050.345
1006-0.271
1007-0.403
10080
1009-0.179
1010.232
10100
10110
10120
10130.115
1014-0.0874
1015-0.038
1016-0.465
10170
10180
10190
1020
10200
10210.0599
1022-0.0704
10230.515
10240.244
1025-0.0611
10260
1027-0.048
10280
1029-0.176
103-0.0887
10300
1031-0.911
1032-0.561
10330.0671
10340
10350
10360.442
10370
1038-0.582
1039-0.00482
1040
1040-0.268
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



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: CNhs11928

Jaspar motifP-value
MA0002.26.0637e-5
MA0003.10.548
MA0004.10.0743
MA0006.10.916
MA0007.10.613
MA0009.10.728
MA0014.10.801
MA0017.10.0832
MA0018.20.0123
MA0019.10.551
MA0024.10.00102
MA0025.10.0821
MA0027.10.739
MA0028.16.04536e-7
MA0029.10.455
MA0030.10.0583
MA0031.10.846
MA0035.20.876
MA0038.10.00621
MA0039.20.96
MA0040.10.481
MA0041.10.0731
MA0042.10.334
MA0043.13.71601e-4
MA0046.18.11007e-16
MA0047.20.969
MA0048.10.0104
MA0050.12.81403e-6
MA0051.10.00181
MA0052.10.037
MA0055.10.00451
MA0057.10.67
MA0058.10.0342
MA0059.10.00122
MA0060.10.981
MA0061.10.00128
MA0062.25.83428e-14
MA0065.20.0999
MA0066.10.241
MA0067.10.0385
MA0068.10.0768
MA0069.10.225
MA0070.10.086
MA0071.10.109
MA0072.10.562
MA0073.10.857
MA0074.10.134
MA0076.13.11674e-7
MA0077.10.678
MA0078.10.384
MA0079.20.0673
MA0080.24.02874e-12
MA0081.14.55652e-4
MA0083.14.24347e-4
MA0084.10.468
MA0087.10.599
MA0088.10.256
MA0090.10.0121
MA0091.10.614
MA0092.10.765
MA0093.10.0714
MA0099.25.12809e-8
MA0100.13.14477e-4
MA0101.11.72041e-6
MA0102.25.18562e-5
MA0103.10.499
MA0104.20.0347
MA0105.11.50879e-5
MA0106.10.219
MA0107.12.61519e-5
MA0108.20.0321
MA0111.10.896
MA0112.20.0209
MA0113.10.59
MA0114.10.792
MA0115.10.473
MA0116.10.00186
MA0117.10.315
MA0119.10.697
MA0122.10.256
MA0124.10.568
MA0125.10.0243
MA0131.10.288
MA0135.10.0144
MA0136.11.42392e-26
MA0137.20.0139
MA0138.20.00687
MA0139.10.338
MA0140.10.41
MA0141.10.0994
MA0142.10.704
MA0143.10.516
MA0144.10.19
MA0145.10.904
MA0146.10.154
MA0147.10.0178
MA0148.10.537
MA0149.10.0499
MA0150.11.4761e-4
MA0152.10.794
MA0153.11.61018e-5
MA0154.10.228
MA0155.10.794
MA0156.15.87286e-18
MA0157.10.676
MA0159.10.0113
MA0160.10.0629
MA0162.10.352
MA0163.11.48558e-5
MA0164.10.41
MA0258.10.0509
MA0259.10.186



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: CNhs11928

Novel motifP-value
10.195
100.0347
1000.648
1010.994
1020.56
1030.0745
1040.771
1050.492
1060.144
1070.73
1080.645
1090.0416
110.129
1100.0983
1110.0868
1120.147
1130.62
1140.784
1150.467
1160.424
1173.34158e-4
1180.244
1190.523
120.68
1200.308
1210.289
1220.482
1230.349
1240.669
1250.177
1260.275
1270.546
1280.132
1290.253
130.00522
1300.642
1310.377
1320.792
1330.243
1340.623
1350.885
1360.284
1370.0263
1380.672
1390.246
140.475
1400.156
1410.74
1420.574
1430.065
1440.651
1450.0186
1460.711
1470.891
1480.414
1490.258
150.0197
1500.432
1510.78
1520.75
1530.392
1540.596
1550.759
1560.504
1570.959
1580.0893
1590.447
1600.896
1610.199
1620.404
1630.593
1640.0123
1650.299
1660.476
1670.266
1680.336
1690.0336
170.549
180.233
190.789
20.0911
200.0188
210.248
220.722
230.388
240.0789
250.285
260.00206
270.485
280.648
290.00758
30.109
300.242
310.897
320.591
330.08
340.702
350.301
360.031
370.0429
380.454
390.735
40.938
400.152
410.0536
420.292
430.327
440.412
450.773
460.189
470.456
480.253
490.218
50.343
500.689
510.952
520.601
530.458
540.82
550.59
560.672
570.229
580.23
590.776
60.737
600.402
610.19
620.117
630.86
640.594
650.569
660.445
670.119
680.851
690.895
70.188
700.0709
710.00877
720.249
730.0502
740.362
750.0087
760.0421
770.409
780.0906
790.665
80.0336
800.839
810.866
820.681
830.0718
840.507
850.996
860.227
870.0779
880.576
890.943
90.909
900.00861
910.951
920.68
930.0699
940.272
950.0141
960.778
970.939
980.374
990.575



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: CNhs11928


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)
0000548 (animal cell)
0002032 (hematopoietic oligopotent progenitor cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000557 (granulocyte monocyte progenitor cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002371 (bone marrow)
0001474 (bone element)
0000479 (tissue)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0004765 (skeletal element)
0010317 (germ layer / neural crest derived structure)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0002390 (hematopoietic system)
0002193 (hemolymphoid system)
0002405 (immune system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000070 (granulocyte macrophage progenitor cell 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
CL:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)

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