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|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001
|comment=Previously. MDSC (MC1-positiveGr1-positive) control, rep1 (4,5,6PBS). TODO: full classification
|comment=Previously. MDSC (MC1-positiveGr1-positive) control, rep1 (4,5,6PBS). TODO: full classification
|created_by=
|created_by=

Revision as of 22:40, 4 July 2012


Name:MC1+Gr1+ myeloid-derived suppressor cells control, donor1 (4,5,6PBS)
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
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
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

CNhs12540

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.175
10040
10051.111
10060
1007-0.182
10080
1009-0.2
101-0.349
10100
1011-0.211
10120.103
1013-0.199
1014-0.0874
1015-0.319
1016-0.594
10170
10180
10190
1020
10200
1021-0.0487
1022-0.315
10230.525
1024-0.22
1025-0.0611
10260
1027-0.048
10280
1029-0.0989
103-0.0887
10300
1031-0.911
1032-0.802
10330.392
10340
10350
10360.183
10370
1038-0.58
1039-0.53
1040
1040-0.342
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: CNhs12540

Jaspar motifP-value
MA0002.29.02178e-12
MA0003.10.885
MA0004.10.704
MA0006.10.193
MA0007.10.459
MA0009.10.71
MA0014.10.18
MA0017.10.435
MA0018.20.002
MA0019.10.979
MA0024.10.125
MA0025.17.31685e-4
MA0027.10.536
MA0028.16.01563e-5
MA0029.10.675
MA0030.10.861
MA0031.10.0133
MA0035.20.647
MA0038.10.0598
MA0039.20.0303
MA0040.10.0602
MA0041.10.975
MA0042.10.907
MA0043.11.51686e-7
MA0046.11.39389e-9
MA0047.20.0371
MA0048.10.236
MA0050.11.07405e-4
MA0051.10.00159
MA0052.10.883
MA0055.10.184
MA0057.10.857
MA0058.10.978
MA0059.10.404
MA0060.10.176
MA0061.10.00111
MA0062.24.31936e-20
MA0065.20.169
MA0066.10.218
MA0067.10.00127
MA0068.10.187
MA0069.10.554
MA0070.10.154
MA0071.10.244
MA0072.10.123
MA0073.10.539
MA0074.10.415
MA0076.11.70861e-5
MA0077.10.165
MA0078.10.91
MA0079.20.49
MA0080.21.21408e-15
MA0081.11.26927e-4
MA0083.10.313
MA0084.10.681
MA0087.10.348
MA0088.10.626
MA0090.10.0423
MA0091.10.956
MA0092.10.649
MA0093.10.729
MA0099.22.93304e-4
MA0100.10.0468
MA0101.10.0027
MA0102.29.30247e-10
MA0103.10.843
MA0104.20.0787
MA0105.18.64534e-6
MA0106.10.97
MA0107.18.55053e-4
MA0108.20.324
MA0111.10.675
MA0112.28.86788e-4
MA0113.10.865
MA0114.10.902
MA0115.10.524
MA0116.19.48156e-4
MA0117.10.0282
MA0119.10.696
MA0122.10.716
MA0124.10.764
MA0125.10.0231
MA0131.10.726
MA0135.10.729
MA0136.13.99908e-31
MA0137.20.184
MA0138.20.113
MA0139.10.705
MA0140.10.987
MA0141.10.361
MA0142.10.184
MA0143.10.144
MA0144.10.106
MA0145.10.206
MA0146.10.0827
MA0147.10.0504
MA0148.10.174
MA0149.10.514
MA0150.11.03704e-7
MA0152.10.421
MA0153.10.0223
MA0154.10.0488
MA0155.10.754
MA0156.11.62448e-28
MA0157.10.0996
MA0159.10.00871
MA0160.10.216
MA0162.10.582
MA0163.10.0379
MA0164.10.699
MA0258.10.0126
MA0259.10.409



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: CNhs12540

Novel motifP-value
10.211
100.054
1000.71
1010.676
1020.688
1030.293
1040.611
1050.386
1060.0272
1070.753
1080.984
1090.0969
110.116
1100.22
1110.599
1120.0554
1130.91
1140.114
1150.995
1160.666
1178.93524e-4
1180.474
1190.558
120.425
1200.0785
1210.444
1220.446
1230.218
1240.422
1250.184
1260.456
1270.323
1280.0578
1290.446
130.0692
1300.415
1310.84
1320.96
1330.0227
1340.863
1350.471
1360.365
1370.0315
1380.401
1390.0507
140.425
1400.316
1410.696
1420.00104
1430.00186
1440.651
1450.146
1460.967
1470.736
1480.14
1490.964
150.0576
1500.347
1510.143
1520.226
1530.252
1540.93
1550.717
1560.465
1570.734
1580.013
1590.526
1600.555
1610.194
1620.506
1630.164
1640.0627
1650.198
1660.636
1670.994
1680.156
1690.0049
170.271
180.184
190.492
20.287
200.0481
210.639
220.358
230.0997
240.204
250.29
260.13
270.534
280.0861
290.0487
30.099
300.392
310.755
320.917
330.226
340.782
350.621
360.127
370.0609
380.377
390.78
40.523
400.21
410.00824
420.282
430.136
440.914
450.867
460.387
470.401
480.283
490.117
50.139
500.702
510.836
520.949
530.663
540.655
550.598
560.253
570.93
580.196
590.62
60.819
600.226
610.443
620.106
630.735
640.669
650.29
660.539
670.3
680.935
690.49
70.186
700.0682
710.0394
720.307
730.0378
740.0571
750.00665
760.21
770.925
780.185
790.744
80.554
800.0834
810.47
820.362
830.187
840.976
850.219
860.08
870.207
880.525
890.954
90.514
900.0873
910.515
920.48
930.0874
940.136
950.0213
960.821
970.867
980.26
990.0871



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: CNhs12540


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)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
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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