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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008676
|DRA_sample_Accession=CAGE@SAMD00005934
|accession_numbers=CAGE;DRX008786;DRR009658;DRZ001083;DRZ002468
|accession_numbers=CAGE;DRX008786;DRR009658;DRZ001083;DRZ002468
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=

Revision as of 21:05, 31 July 2014


Name:stem cell (cKit+ Sca1- lineage-) KSL, biol_rep3
Species:Mouse (Mus musculus)
Library ID:CNhs12536
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/8J
tissuebone marrow
dev stageNA
sexmale
age9-10weeks
cell typestem cell (cKit+ Sca1- lineage-)
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  SAMD00005934
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12536 CAGE DRX008786 DRR009658
Accession ID Mm9

Library idBAMCTSS
CNhs12536 DRZ001083 DRZ002468
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

CNhs12536

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.155
10040
10050.151
1006-0.13
1007-0.16
10080
1009-0.094
1010.222
10100
10110.0431
10120
1013-0.118
1014-0.0874
1015-0.00896
1016-0.332
10170
10180.0318
10190
1020.106
10200.0562
10210
1022-0.0428
10230.715
10241.013
1025-0.0611
10260
1027-0.048
10280
1029-0.0709
103-0.0887
10300
1031-0.855
1032-0.184
10330.151
10340
10350
10360.376
10370
1038-0.221
1039-0.0727
1040
1040-0.121
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: CNhs12536

Jaspar motifP-value
MA0002.23.563e-7
MA0003.10.776
MA0004.10.324
MA0006.10.794
MA0007.10.942
MA0009.10.306
MA0014.10.794
MA0017.10.203
MA0018.22.2323e-11
MA0019.10.6
MA0024.10.00103
MA0025.15.14151e-4
MA0027.10.0217
MA0028.18.72568e-8
MA0029.10.568
MA0030.10.265
MA0031.10.00274
MA0035.20.969
MA0038.10.0169
MA0039.20.123
MA0040.10.0229
MA0041.10.73
MA0042.10.565
MA0043.11.02011e-7
MA0046.17.67912e-16
MA0047.20.521
MA0048.10.0272
MA0050.11.13833e-15
MA0051.12.05586e-9
MA0052.10.803
MA0055.10.0196
MA0057.10.787
MA0058.10.212
MA0059.10.147
MA0060.10.323
MA0061.11.31364e-12
MA0062.22.23329e-21
MA0065.20.874
MA0066.10.229
MA0067.19.07477e-6
MA0068.10.0174
MA0069.10.687
MA0070.10.65
MA0071.10.857
MA0072.10.702
MA0073.10.683
MA0074.10.764
MA0076.17.95089e-8
MA0077.10.228
MA0078.10.884
MA0079.20.771
MA0080.22.70597e-14
MA0081.13.28249e-5
MA0083.10.283
MA0084.10.0656
MA0087.10.672
MA0088.10.435
MA0090.10.00539
MA0091.10.228
MA0092.10.204
MA0093.10.268
MA0099.22.41486e-21
MA0100.10.00471
MA0101.13.82229e-17
MA0102.20.014
MA0103.10.205
MA0104.20.156
MA0105.11.07413e-5
MA0106.10.68
MA0107.11.27482e-18
MA0108.20.343
MA0111.10.948
MA0112.20.924
MA0113.10.76
MA0114.10.00776
MA0115.10.917
MA0116.10.0755
MA0117.10.00802
MA0119.10.0833
MA0122.10.103
MA0124.10.928
MA0125.10.0723
MA0131.10.103
MA0135.10.589
MA0136.16.66287e-30
MA0137.20.00891
MA0138.22.33516e-5
MA0139.10.911
MA0140.10.848
MA0141.10.135
MA0142.10.783
MA0143.10.038
MA0144.10.0685
MA0145.10.772
MA0146.10.0565
MA0147.10.145
MA0148.10.963
MA0149.10.344
MA0150.13.58633e-6
MA0152.10.598
MA0153.15.20765e-6
MA0154.10.936
MA0155.10.388
MA0156.15.59777e-27
MA0157.10.0177
MA0159.10.364
MA0160.10.864
MA0162.10.61
MA0163.10.00462
MA0164.10.663
MA0258.10.338
MA0259.10.385



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: CNhs12536

Novel motifP-value
10.926
100.233
1000.988
1010.709
1020.783
1030.368
1040.694
1050.598
1060.0642
1070.63
1080.769
1090.635
110.966
1100.764
1110.936
1120.23
1130.743
1140.178
1150.82
1160.555
1171.3316e-4
1180.142
1190.69
120.545
1200.359
1210.204
1220.582
1230.207
1240.397
1250.904
1260.74
1270.942
1280.128
1290.656
130.00301
1300.67
1310.145
1320.43
1330.148
1340.811
1350.568
1360.0729
1370.00552
1380.975
1390.604
140.513
1400.757
1410.485
1420.524
1430.31
1440.926
1450.548
1460.538
1470.696
1480.173
1490.199
150.171
1500.781
1510.644
1520.154
1530.233
1540.707
1550.628
1560.0754
1570.882
1580.026
1590.724
1600.0741
1610.473
1620.441
1630.0715
1640.0502
1650.159
1660.183
1670.385
1680.183
1690.191
170.817
180.892
190.0922
20.0175
200.0217
210.77
220.936
230.437
240.0607
250.661
260.0918
270.439
280.602
290.213
30.541
300.213
310.489
320.032
330.158
340.73
350.827
360.258
370.0627
380.672
390.348
40.461
400.438
410.0732
420.559
430.899
440.931
450.739
460.967
470.672
480.728
490.959
50.91
500.642
510.665
520.732
530.78
540.58
550.918
560.906
570.568
580.273
590.802
60.87
600.491
610.301
620.324
630.56
640.529
650.949
660.375
670.841
680.614
690.601
70.72
700.51
710.347
720.431
730.0348
740.332
750.00883
760.109
770.00563
780.209
790.596
80.969
800.562
810.727
820.127
830.0114
840.621
850.101
860.157
870.0123
880.431
890.254
90.69
900.493
910.55
920.399
930.252
940.913
950.00232
960.386
970.906
980.88
990.0454



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: CNhs12536


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)
0000034 (stem cell)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000021 (hematopoietic stem cell sample)
0000103 (mouse sample)
0000001 (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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