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|profile_rnaseq=,,,
|profile_rnaseq=,,,
|profile_srnaseq=,,,
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|repeat_enrich_byfamily=-0.11779559634038,0,0,0,0,0,-0.346821001189179,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,-0.191893350882575,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.558422792324031,0,0,0,0,-0.0380569402921788,-0.209322725495826,-0.221348944226812,0.0958529111042259,-0.984211366477826,-0.269868638010351,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0.615459892883158,0.109040984486684,0,-0.00532372290983685,0,0,0,-0.117852935653321,0.0980421442728005,-0.158091042771083,-0.0770135788839859,0,0,-0.188533191709379,-0.179310411421406,0,0,-0.164906430868337,0.070018536168711,-0.59591488074057,0.171914090241992,0,0,0,0,0,0,-0.234576517650013,-0.723659654005111,-0.269803002231399,0,0,0,0,0
|rna_box=128
|rna_box=128
|rna_catalog_number=
|rna_catalog_number=

Revision as of 10:19, 24 September 2012


Name:MC1+Gr1+ myeloid-derived suppressor cells cancer, donor2 (0127 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

CNhs12198

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.175
10040
10051.157
1006-0.143
1007-0.277
10080
1009-0.2
101-0.243
10100
1011-0.132
10120
10130.0704
1014-0.0874
1015-0.18
1016-0.594
10170
10180
10190
1020
10200
1021-0.0487
1022-0.315
10230.572
1024-0.14
1025-0.0611
10260
10270
10280
1029-0.176
103-0.0887
10300
1031-0.911
1032-0.655
10330.184
10340
10350
10360.12
10370
1038-0.569
1039-0.531
1040
1040-0.593
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: CNhs12198

Jaspar motifP-value
MA0002.23.04236e-11
MA0003.10.988
MA0004.10.951
MA0006.10.231
MA0007.10.346
MA0009.10.495
MA0014.10.137
MA0017.10.211
MA0018.20.216
MA0019.10.963
MA0024.10.733
MA0025.10.022
MA0027.10.392
MA0028.11.32689e-5
MA0029.10.655
MA0030.10.77
MA0031.10.172
MA0035.20.726
MA0038.10.34
MA0039.20.037
MA0040.10.0527
MA0041.10.497
MA0042.10.907
MA0043.19.81432e-4
MA0046.12.3079e-9
MA0047.20.137
MA0048.10.139
MA0050.11.59624e-4
MA0051.10.00151
MA0052.10.00788
MA0055.10.0802
MA0057.10.972
MA0058.10.798
MA0059.10.758
MA0060.10.668
MA0061.10.0167
MA0062.25.66825e-19
MA0065.20.114
MA0066.10.225
MA0067.10.0203
MA0068.10.496
MA0069.10.546
MA0070.10.274
MA0071.10.276
MA0072.10.148
MA0073.10.618
MA0074.10.345
MA0076.11.90445e-6
MA0077.10.152
MA0078.10.742
MA0079.20.274
MA0080.21.77081e-15
MA0081.11.81931e-4
MA0083.10.521
MA0084.10.72
MA0087.10.73
MA0088.10.621
MA0090.10.0313
MA0091.10.758
MA0092.10.546
MA0093.10.93
MA0099.20.00219
MA0100.10.0242
MA0101.10.0169
MA0102.21.90909e-8
MA0103.10.953
MA0104.20.307
MA0105.11.26111e-4
MA0106.10.559
MA0107.10.0242
MA0108.20.202
MA0111.10.69
MA0112.20.00171
MA0113.10.364
MA0114.10.611
MA0115.10.486
MA0116.10.00107
MA0117.10.199
MA0119.10.655
MA0122.10.7
MA0124.10.834
MA0125.10.0116
MA0131.10.555
MA0135.10.877
MA0136.11.21268e-30
MA0137.20.00335
MA0138.20.235
MA0139.10.486
MA0140.10.864
MA0141.10.202
MA0142.10.337
MA0143.10.149
MA0144.10.0303
MA0145.10.27
MA0146.10.0573
MA0147.10.285
MA0148.10.216
MA0149.10.316
MA0150.11.48743e-5
MA0152.10.341
MA0153.10.00787
MA0154.10.0396
MA0155.10.935
MA0156.11.47119e-27
MA0157.10.31
MA0159.10.00626
MA0160.10.146
MA0162.10.342
MA0163.10.00784
MA0164.10.485
MA0258.10.0121
MA0259.10.624



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: CNhs12198

Novel motifP-value
10.155
100.0505
1000.717
1010.654
1020.401
1030.0924
1040.854
1050.476
1060.0794
1070.912
1080.838
1090.028
110.0602
1100.163
1110.416
1120.0208
1130.892
1140.209
1150.738
1160.843
1175.10109e-4
1180.369
1190.46
120.576
1200.08
1210.614
1220.634
1230.544
1240.989
1250.23
1260.435
1270.214
1280.219
1290.401
130.0525
1300.669
1310.625
1320.99
1330.0306
1340.751
1350.537
1360.41
1370.0455
1380.307
1390.109
140.433
1400.521
1410.636
1420.0501
1430.00173
1440.821
1450.102
1460.975
1470.439
1480.16
1490.98
150.0433
1500.315
1510.279
1520.231
1530.552
1540.869
1550.492
1560.746
1570.855
1580.0434
1590.593
1600.843
1610.0727
1620.73
1630.335
1640.0247
1650.144
1660.853
1670.712
1680.281
1690.00458
170.113
180.127
190.65
20.34
200.0531
210.491
220.379
230.485
240.0881
250.159
260.0912
270.661
280.181
290.00852
30.0561
300.475
310.718
320.809
330.118
340.831
350.512
360.0797
370.0655
380.253
390.908
40.584
400.147
410.0115
420.259
430.171
440.797
450.891
460.309
470.226
480.152
490.124
50.17
500.816
510.716
520.733
530.654
540.713
550.278
560.296
570.769
580.188
590.347
60.609
600.21
610.174
620.0944
630.592
640.474
650.218
660.567
670.19
680.785
690.619
70.0892
700.0822
710.0375
720.131
730.0395
740.107
750.00489
760.191
770.863
780.0898
790.471
80.205
800.0627
810.571
820.537
830.386
840.946
850.291
860.16
870.0975
880.455
890.662
90.455
900.125
910.533
920.397
930.352
940.0969
950.00888
960.817
970.841
980.362
990.351



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: CNhs12198


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)

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