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|is_obsolete=
|is_obsolete=
|library_id=CNhs12206
|library_id=CNhs12206
|library_ids=CNhs12206
|name=granulocyte macrophage progenitor GMP, biol_rep1
|name=granulocyte macrophage progenitor GMP, biol_rep1
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 17:05, 25 October 2013


Name:granulocyte macrophage progenitor GMP, biol_rep1
Species:Mouse (Mus musculus)
Library ID:CNhs12206
Sample type:primary cells
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 numberrep1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008672
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12206 CAGE DRX008782 DRR009654
Accession ID Mm9

Library idBAMCTSS
CNhs12206 DRZ001079 DRZ002464
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

CNhs12206

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.175
10040
10050.168
1006-0.241
1007-0.375
10080
1009-0.19
1010.301
10100
1011-0.108
10120
1013-0.161
1014-0.0874
1015-0.0718
1016-0.594
10170
10180
10190
1020
10200
1021-0.0487
1022-0.309
10230.904
10240.402
1025-0.0611
10260
1027-0.048
10280
1029-0.176
103-0.0887
10300
1031-0.917
1032-0.391
10330
10340
10350
10360.393
10370
1038-0.506
1039-0.117
1040
1040-0.532
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: CNhs12206

Jaspar motifP-value
MA0002.22.34478e-7
MA0003.10.833
MA0004.10.0689
MA0006.10.955
MA0007.10.73
MA0009.10.957
MA0014.10.92
MA0017.10.0587
MA0018.20.00661
MA0019.10.496
MA0024.10.00271
MA0025.10.242
MA0027.10.387
MA0028.12.3887e-5
MA0029.10.237
MA0030.10.188
MA0031.10.992
MA0035.20.882
MA0038.10.0219
MA0039.20.85
MA0040.10.0485
MA0041.10.745
MA0042.10.63
MA0043.15.36064e-4
MA0046.17.22477e-9
MA0047.20.826
MA0048.10.0623
MA0050.10.00243
MA0051.10.0175
MA0052.10.349
MA0055.10.0257
MA0057.10.489
MA0058.10.0407
MA0059.10.00109
MA0060.10.0554
MA0061.18.79012e-4
MA0062.21.75276e-12
MA0065.20.0248
MA0066.10.052
MA0067.10.0847
MA0068.10.793
MA0069.10.427
MA0070.10.137
MA0071.10.0836
MA0072.10.499
MA0073.10.737
MA0074.10.183
MA0076.11.46395e-5
MA0077.10.636
MA0078.10.297
MA0079.20.0623
MA0080.27.65085e-12
MA0081.15.88254e-4
MA0083.10.0038
MA0084.10.708
MA0087.10.642
MA0088.10.14
MA0090.10.0333
MA0091.10.732
MA0092.10.911
MA0093.10.0697
MA0099.29.26632e-8
MA0100.12.62428e-4
MA0101.14.79263e-6
MA0102.23.13114e-4
MA0103.10.826
MA0104.20.0189
MA0105.18.86864e-7
MA0106.10.119
MA0107.13.24543e-5
MA0108.20.0938
MA0111.10.73
MA0112.20.00931
MA0113.10.397
MA0114.10.408
MA0115.10.423
MA0116.13.35907e-4
MA0117.10.394
MA0119.10.882
MA0122.10.09
MA0124.10.36
MA0125.10.0298
MA0131.10.405
MA0135.10.0834
MA0136.15.53065e-25
MA0137.20.00327
MA0138.20.0397
MA0139.10.351
MA0140.10.606
MA0141.10.0564
MA0142.10.588
MA0143.10.686
MA0144.10.0945
MA0145.10.913
MA0146.10.163
MA0147.10.00915
MA0148.10.963
MA0149.10.0358
MA0150.12.56621e-4
MA0152.10.971
MA0153.10.00173
MA0154.10.0701
MA0155.10.985
MA0156.16.91019e-15
MA0157.10.638
MA0159.10.00682
MA0160.10.0124
MA0162.10.256
MA0163.12.22617e-6
MA0164.10.863
MA0258.10.0294
MA0259.10.165



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: CNhs12206

Novel motifP-value
10.113
100.0314
1000.808
1010.662
1020.572
1030.025
1040.575
1050.868
1060.243
1070.891
1080.906
1090.0133
110.092
1100.0932
1110.0953
1120.0457
1130.933
1140.7
1150.452
1160.492
1170.00109
1180.161
1190.409
120.82
1200.0927
1210.295
1220.627
1230.833
1240.729
1250.259
1260.47
1270.261
1280.357
1290.237
130.0119
1300.651
1310.724
1320.587
1330.788
1340.592
1350.568
1360.684
1370.0237
1380.149
1390.0637
140.729
1400.337
1410.495
1420.959
1430.0521
1440.704
1450.0647
1460.994
1470.878
1480.436
1490.588
150.0205
1500.828
1510.481
1520.865
1530.48
1540.756
1550.57
1560.397
1570.629
1580.0157
1590.832
1600.753
1610.0384
1620.581
1630.316
1640.0118
1650.173
1660.627
1670.26
1680.947
1690.0126
170.352
180.227
190.995
20.34
200.071
210.275
220.601
230.735
240.0975
250.24
260.00264
270.78
280.687
290.00818
30.0901
300.333
310.951
320.935
330.0557
340.973
350.278
360.0169
370.0612
380.312
390.899
40.92
400.0986
410.025
420.269
430.237
440.472
450.957
460.134
470.355
480.174
490.177
50.204
500.682
510.741
520.621
530.709
540.819
550.326
560.535
570.225
580.12
590.316
60.815
600.356
610.155
620.0624
630.687
640.382
650.29
660.543
670.181
680.791
690.97
70.116
700.022
710.00796
720.154
730.104
740.45
750.0191
760.142
770.911
780.112
790.488
80.0108
800.375
810.669
820.465
830.0624
840.857
850.524
860.266
870.173
880.676
890.241
90.896
900.0126
910.93
920.346
930.0381
940.206
950.00699
960.453
970.961
980.134
990.652



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: CNhs12206


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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