Personal tools

FF:11779-124A6

From FANTOM5_SSTAR

Revision as of 10:16, 24 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:CD41+ megakaryocyte control, donor3
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 typemegakaryocyte
cell lineNA
companyNA
collaborationHozumi Motohashi (Tohoku University Graduate School of Medicine)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberPBS-4
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
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

CNhs13201

00
10
100
1000
1000-0.0355
1001-0.0631
1002-0.116
1003-0.175
10040
10050.0428
1006-0.143
1007-0.255
10080
1009-0.19
1010.0965
10100
10110.154
10120
1013-0.278
1014-0.0874
1015-0.036
1016-0.594
10170
10180
10190
1020.154
10200.237
10210.267
1022-0.187
10230
1024-0.14
1025-0.0611
10260
1027-0.048
10280
1029-0.0989
103-0.0887
10300.357
1031-0.879
1032-0.572
10330
10340.154
10350
10360.255
10370
1038-0.283
10390.00654
1040
1040-0.216
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: CNhs13201

Jaspar motifP-value
MA0002.21.73444e-5
MA0003.10.47
MA0004.10.154
MA0006.10.774
MA0007.10.742
MA0009.10.918
MA0014.10.648
MA0017.10.235
MA0018.20.41
MA0019.10.307
MA0024.10.656
MA0025.10.417
MA0027.10.672
MA0028.16.58487e-5
MA0029.10.217
MA0030.10.224
MA0031.10.763
MA0035.20.719
MA0038.10.55
MA0039.20.997
MA0040.10.602
MA0041.10.165
MA0042.10.793
MA0043.10.645
MA0046.18.9154e-10
MA0047.20.982
MA0048.10.423
MA0050.11.54385e-11
MA0051.17.16199e-7
MA0052.10.0132
MA0055.10.302
MA0057.10.994
MA0058.10.163
MA0059.10.0454
MA0060.10.0912
MA0061.12.56501e-6
MA0062.21.91382e-14
MA0065.20.222
MA0066.10.0643
MA0067.10.328
MA0068.10.00972
MA0069.10.827
MA0070.10.487
MA0071.10.595
MA0072.10.684
MA0073.10.714
MA0074.10.582
MA0076.13.91176e-5
MA0077.10.177
MA0078.10.935
MA0079.20.0778
MA0080.27.36393e-14
MA0081.10.00109
MA0083.10.0297
MA0084.10.697
MA0087.10.711
MA0088.10.51
MA0090.10.018
MA0091.10.24
MA0092.10.883
MA0093.10.173
MA0099.20.372
MA0100.10.251
MA0101.13.92649e-6
MA0102.20.834
MA0103.10.208
MA0104.20.182
MA0105.12.6298e-8
MA0106.10.76
MA0107.14.50546e-6
MA0108.26.30819e-4
MA0111.10.537
MA0112.20.0122
MA0113.10.17
MA0114.11
MA0115.10.843
MA0116.10.00136
MA0117.10.74
MA0119.10.764
MA0122.10.862
MA0124.10.788
MA0125.10.0422
MA0131.10.428
MA0135.10.949
MA0136.11.31335e-17
MA0137.20.475
MA0138.20.0704
MA0139.10.137
MA0140.10.00736
MA0141.10.549
MA0142.11.74909e-4
MA0143.10.277
MA0144.10.632
MA0145.10.466
MA0146.10.378
MA0147.10.134
MA0148.10.841
MA0149.10.0691
MA0150.10.344
MA0152.10.263
MA0153.15.90707e-6
MA0154.10.0021
MA0155.10.645
MA0156.18.01576e-20
MA0157.10.526
MA0159.10.0121
MA0160.10.802
MA0162.10.549
MA0163.12.08077e-4
MA0164.10.466
MA0258.10.0334
MA0259.10.454



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: CNhs13201

Novel motifP-value
10.12
100.021
1000.804
1010.999
1020.769
1030.0867
1040.777
1050.72
1060.304
1070.981
1080.527
1090.115
110.142
1100.0414
1110.194
1120.0431
1130.312
1140.378
1150.802
1160.881
1175.73887e-4
1180.0997
1190.512
120.588
1200.647
1210.432
1220.962
1230.715
1240.805
1250.117
1260.202
1270.488
1280.168
1290.213
130.0473
1300.83
1310.568
1320.531
1330.887
1340.664
1350.847
1360.9
1370.163
1380.636
1390.196
140.996
1400.833
1410.285
1420.407
1430.0261
1440.494
1450.0945
1460.893
1470.938
1480.0965
1490.486
150.0781
1500.323
1510.187
1520.692
1530.288
1540.405
1550.234
1562.95064e-31
1570.796
1580.075
1590.459
1600.92
1610.0621
1620.283
1630.358
1640.123
1650.293
1660.481
1670.196
1680.907
1690.099
170.437
180.214
190.796
20.103
200.0298
210.278
220.844
230.375
240.451
250.118
260.0163
270.742
280.28
290.00977
30.0509
300.248
310.99
320.992
330.145
340.715
350.104
360.0362
370.112
380.928
390.461
40.648
400.147
410.421
420.114
430.143
440.345
450.601
460.171
470.274
480.195
490.1
50.0388
500.7
510.908
520.391
530.549
540.875
550.46
560.643
570.561
580.146
590.327
60.713
600.637
610.0934
620.0553
630.689
640.579
650.869
660.978
670.739
680.0417
690.845
70.154
700.0151
710.0347
720.287
730.0932
740.959
750.00609
760.0231
770.348
780.0739
790.833
80.0661
800.0167
810.479
820.227
830.104
840.62
850.45
860.156
870.563
880.501
890.877
90.942
900.0149
910.509
920.263
930.248
940.161
950.181
960.33
970.832
980.223
990.339



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: CNhs13201


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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000556 (megakaryocyte)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002371 (bone marrow)
0001474 (bone element)
0000479 (tissue)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0004765 (skeletal element)
0010317 (germ layer / neural crest derived structure)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0002390 (hematopoietic system)
0002193 (hemolymphoid system)
0002405 (immune system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000343 (control treatment sample)
0011468 (mouse CD41-positive megakaryocyte control 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:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11779-124A6&oldid=2141357"