Personal tools

FF:12163-128H3

From FANTOM5_SSTAR

Revision as of 21:36, 10 August 2017 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:MC1+Gr1+ myeloid-derived suppressor cells cancer, donor3 (0128 3LL)
Species:Mouse (Mus musculus)
Library ID:CNhs12542
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typestem cell
cell lineNA
companyNA
collaborationHozumi Motohashi (Tohoku University Graduate School of Medicine)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005808
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12542 CAGE DRX008774 DRR009646
Accession ID Mm9

Library idBAMCTSS
CNhs12542 DRZ001071 DRZ002456
Accession ID Mm10

Library idBAMCTSS
CNhs12542 DRZ012421 DRZ013806
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

CNhs12542

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.123
10040
10051.244
1006-0.3
1007-0.186
10080
1009-0.2
101-0.235
10100
1011-0.115
10120
1013-0.0868
1014-0.0874
1015-0.12
1016-0.594
10170
10180
10190
1020
10200
10210
1022-0.315
10230.617
1024-0.14
1025-0.0611
10260
1027-0.048
10280
10290.00687
103-0.0887
10300
1031-0.911
1032-0.768
10330.148
10340
10350
10360.214
10370
1038-0.585
1039-0.638
1040
1040-0.315
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: CNhs12542

Jaspar motifP-value
MA0002.24.57167e-12
MA0003.10.905
MA0004.10.582
MA0006.10.218
MA0007.10.47
MA0009.10.925
MA0014.10.177
MA0017.10.258
MA0018.20.545
MA0019.10.855
MA0024.10.875
MA0025.10.143
MA0027.10.518
MA0028.12.21434e-6
MA0029.10.576
MA0030.10.671
MA0031.10.135
MA0035.20.724
MA0038.10.237
MA0039.20.0478
MA0040.10.135
MA0041.10.562
MA0042.10.852
MA0043.10.00122
MA0046.11.37792e-10
MA0047.20.154
MA0048.10.115
MA0050.12.23317e-6
MA0051.18.33824e-5
MA0052.14.88255e-4
MA0055.10.0816
MA0057.10.884
MA0058.10.828
MA0059.10.587
MA0060.10.753
MA0061.10.0272
MA0062.25.33287e-20
MA0065.20.175
MA0066.10.2
MA0067.10.0237
MA0068.10.83
MA0069.10.535
MA0070.10.488
MA0071.10.4
MA0072.10.145
MA0073.10.697
MA0074.10.451
MA0076.11.95043e-7
MA0077.10.111
MA0078.10.844
MA0079.20.377
MA0080.22.72352e-15
MA0081.12.40404e-4
MA0083.10.146
MA0084.10.799
MA0087.10.566
MA0088.10.579
MA0090.10.0252
MA0091.10.996
MA0092.10.601
MA0093.10.57
MA0099.20.0306
MA0100.10.0125
MA0101.10.0211
MA0102.22.13315e-8
MA0103.10.824
MA0104.20.172
MA0105.11.4307e-4
MA0106.10.531
MA0107.10.0361
MA0108.20.00838
MA0111.10.647
MA0112.20.00109
MA0113.10.467
MA0114.10.607
MA0115.10.563
MA0116.16.86261e-4
MA0117.10.284
MA0119.10.498
MA0122.10.502
MA0124.10.599
MA0125.10.0447
MA0131.10.438
MA0135.10.78
MA0136.14.0494e-32
MA0137.20.00669
MA0138.20.0876
MA0139.10.361
MA0140.10.893
MA0141.10.282
MA0142.10.185
MA0143.10.116
MA0144.10.0243
MA0145.10.304
MA0146.10.0746
MA0147.10.157
MA0148.10.322
MA0149.10.297
MA0150.11.2134e-4
MA0152.10.421
MA0153.10.00616
MA0154.10.0363
MA0155.10.804
MA0156.11.73228e-29
MA0157.10.254
MA0159.10.0188
MA0160.10.301
MA0162.10.349
MA0163.10.00517
MA0164.10.495
MA0258.10.00848
MA0259.10.645



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: CNhs12542

Novel motifP-value
10.148
100.0491
1000.727
1010.698
1020.383
1030.102
1040.918
1050.514
1060.112
1070.8
1080.82
1090.0426
110.0842
1100.181
1110.52
1120.0378
1130.91
1140.146
1150.706
1160.843
1174.89974e-4
1180.485
1190.485
120.69
1200.0727
1210.667
1220.502
1230.319
1240.909
1250.2
1260.406
1270.209
1280.266
1290.337
130.049
1300.468
1310.681
1320.92
1330.195
1340.836
1350.258
1360.338
1370.0481
1380.358
1390.0699
140.385
1400.834
1410.594
1420.0472
1430.00159
1440.965
1450.102
1460.896
1470.691
1480.298
1490.946
150.0427
1500.35
1510.243
1520.329
1530.39
1540.897
1550.591
1560.247
1570.87
1580.0906
1590.674
1600.946
1610.0996
1620.513
1630.435
1640.0132
1650.17
1660.547
1670.726
1680.327
1690.00864
170.237
180.0888
190.576
20.325
200.0352
210.374
220.421
230.413
240.0913
250.174
260.135
270.767
280.128
290.012
30.0525
300.436
310.747
320.665
330.186
340.776
350.538
360.148
370.0653
380.281
390.786
40.702
400.234
410.0181
420.251
430.159
440.791
450.955
460.335
470.203
480.162
490.123
50.142
500.698
510.658
520.668
530.485
540.648
550.455
560.277
570.633
580.189
590.409
60.606
600.302
610.253
620.117
630.632
640.625
650.306
660.569
670.141
680.842
690.591
70.126
700.0928
710.0415
720.176
730.0507
740.121
750.00638
760.151
770.865
780.101
790.51
80.287
800.0315
810.578
820.579
830.679
840.872
850.328
860.122
870.165
880.47
890.739
90.43
900.088
910.592
920.55
930.679
940.0512
950.00657
960.822
970.86
980.419
990.264



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: CNhs12542


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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0002371 (somatic cell)
0000034 (stem cell)
0000355 (multi-potent skeletal muscle stem cell)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
0060100 (musculoskeletal system cancer)
4045 (muscle cancer)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001134 (skeletal muscle tissue)
0000479 (tissue)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002036 (striated muscle tissue)
0002385 (muscle tissue)
0010317 (germ layer / neural crest derived structure)
0001015 (musculature)
0002204 (musculoskeletal system)
0000383 (musculature of body)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000267 (mouse muscle derived stem cell sample)
0000268 (cancer related muscle derived stem cell (Mouse) 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:0000355 (multi-potent skeletal muscle stem cell)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:12163-128H3&oldid=4344280"