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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0001134,UBERON:0002100,UBERON:0000483,UBERON:0000926,UBERON:0000479,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0000490,UBERON:0005291,UBERON:0002036,UBERON:0002385,UBERON:0000486,UBERON:0003104,UBERON:0000914,UBERON:0005256,UBERON:0006598,UBERON:0001015,UBERON:0002532,UBERON:0002329,UBERON:0002204,UBERON:0000383,UBERON:0003077,UBERON:0004290,UBERON:0009142,UBERON:0006603,UBERON:0003082,UBERON:0003059,UBERON:0007282,UBERON:0009618,UBERON:0007285
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001134,UBERON:0000479,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002036,UBERON:0002385,UBERON:0010317,UBERON:0001015,UBERON:0002204,UBERON:0000383
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000723,CL:0000048,CL:0000034,CL:0000012,CL:0002371,CL:0000355
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000723,CL:0000048,CL:0002371,CL:0000034,CL:0000355
|ancestors_in_disease_facet=DOID:4,DOID:0050686,DOID:162,DOID:14566,DOID:0060100,DOID:4045
|ancestors_in_disease_facet=DOID:4,DOID:0050686,DOID:162,DOID:14566,DOID:0060100,DOID:4045
|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000267,FF:0000268
|comment=Previously: MDSC (MC1-positiveGr1-positive) cancer, rep1 (10,11,12 3LL). TODO: full classification
|comment=Previously: MDSC (MC1-positiveGr1-positive) cancer, rep1 (10,11,12 3LL). TODO: full classification
|created_by=
|created_by=

Revision as of 22:39, 4 July 2012


Name:MC1+Gr1+ myeloid-derived suppressor cells cancer, donor1 (10,11,12 3LL)
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

CNhs12539

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.175
10040
10051.213
1006-0.143
1007-0.137
10080
1009-0.2
101-0.304
10100
1011-0.122
10120.101
1013-0.0649
1014-0.0851
1015-0.151
1016-0.594
10170
10180
10190
1020
10200
1021-0.0487
1022-0.315
10230.678
1024-0.14
1025-0.0611
10260
1027-0.048
10280
1029-0.0989
103-0.0887
10300
1031-0.911
1032-0.687
1033-0.0118
10340
10350
10360.137
10370
1038-0.48
1039-0.417
1040
1040-0.355
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: CNhs12539

Jaspar motifP-value
MA0002.27.61519e-12
MA0003.10.801
MA0004.10.569
MA0006.10.146
MA0007.10.579
MA0009.10.61
MA0014.10.217
MA0017.10.467
MA0018.20.146
MA0019.10.958
MA0024.10.48
MA0025.10.0167
MA0027.10.525
MA0028.14.43894e-6
MA0029.10.729
MA0030.10.901
MA0031.10.0438
MA0035.20.868
MA0038.10.164
MA0039.20.00971
MA0040.10.0752
MA0041.10.669
MA0042.10.939
MA0043.11.07844e-4
MA0046.12.65495e-10
MA0047.20.0479
MA0048.10.181
MA0050.17.60248e-6
MA0051.12.15609e-4
MA0052.10.00304
MA0055.10.167
MA0057.10.92
MA0058.10.772
MA0059.10.357
MA0060.10.461
MA0061.10.0161
MA0062.21.54276e-21
MA0065.20.267
MA0066.10.16
MA0067.10.0171
MA0068.10.383
MA0069.10.509
MA0070.10.397
MA0071.10.418
MA0072.10.214
MA0073.10.558
MA0074.10.517
MA0076.13.60152e-7
MA0077.10.136
MA0078.10.971
MA0079.20.652
MA0080.21.67736e-15
MA0081.12.07396e-4
MA0083.10.477
MA0084.10.894
MA0087.10.211
MA0088.10.902
MA0090.10.0225
MA0091.10.89
MA0092.10.716
MA0093.10.558
MA0099.20.00142
MA0100.10.0335
MA0101.10.0176
MA0102.22.93223e-9
MA0103.10.876
MA0104.20.071
MA0105.16.73137e-4
MA0106.10.883
MA0107.10.0152
MA0108.20.0274
MA0111.10.645
MA0112.20.00188
MA0113.10.487
MA0114.10.937
MA0115.10.473
MA0116.10.00198
MA0117.10.118
MA0119.10.562
MA0122.10.616
MA0124.10.613
MA0125.10.0252
MA0131.10.54
MA0135.10.763
MA0136.16.42253e-32
MA0137.20.0301
MA0138.20.184
MA0139.10.611
MA0140.10.579
MA0141.10.309
MA0142.10.351
MA0143.10.0498
MA0144.10.0503
MA0145.10.194
MA0146.10.0386
MA0147.10.0599
MA0148.10.165
MA0149.10.3
MA0150.16.60405e-6
MA0152.10.318
MA0153.10.0135
MA0154.10.0594
MA0155.10.754
MA0156.11.40605e-29
MA0157.10.17
MA0159.10.0148
MA0160.10.262
MA0162.10.619
MA0163.10.055
MA0164.10.565
MA0258.10.0115
MA0259.10.411



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: CNhs12539

Novel motifP-value
10.171
100.0553
1000.705
1010.729
1020.263
1030.193
1040.746
1050.496
1060.0565
1070.779
1080.846
1090.0485
110.0896
1100.271
1110.43
1120.0564
1130.926
1140.0977
1150.996
1160.894
1174.04043e-4
1180.42
1190.587
120.427
1200.0376
1210.67
1220.496
1230.314
1240.835
1250.26
1260.487
1270.21
1280.152
1290.45
130.09
1300.367
1310.601
1320.913
1330.0526
1340.766
1350.436
1360.286
1370.0549
1380.388
1390.0728
140.379
1400.63
1410.735
1420.0161
1430.00103
1440.928
1450.109
1460.976
1470.656
1480.163
1490.993
150.051
1500.42
1510.194
1520.167
1530.361
1540.697
1550.557
1560.812
1570.902
1580.0545
1590.631
1600.681
1610.097
1620.529
1630.381
1640.0332
1650.256
1660.696
1670.988
1680.194
1690.0162
170.234
180.108
190.635
20.298
200.036
210.426
220.394
230.276
240.144
250.216
260.13
270.676
280.0977
290.0172
30.0577
300.441
310.68
320.873
330.194
340.807
350.684
360.155
370.0675
380.348
390.827
40.63
400.214
410.0114
420.268
430.145
440.767
450.809
460.361
470.294
480.207
490.13
50.135
500.757
510.736
520.895
530.549
540.676
550.458
560.293
570.967
580.174
590.484
60.563
600.201
610.278
620.0898
630.693
640.676
650.323
660.544
670.212
680.954
690.495
70.155
700.08
710.0692
720.148
730.0267
740.19
750.00498
760.189
770.976
780.11
790.511
80.447
800.0399
810.523
820.498
830.492
840.958
850.209
860.0888
870.0951
880.476
890.996
90.526
900.17
910.558
920.681
930.406
940.142
950.00589
960.9
970.874
980.344
990.159



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: CNhs12539


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
NA

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