Personal tools

FF:11775-124A2

From FANTOM5_SSTAR

Revision as of 15:16, 15 February 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:CD41+ megakaryocyte control, donor1
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-1
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]





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

CNhs13212

00
10
100
1000
1000-0.00367
1001-0.00378
1002-0.116
1003-0.166
10040
10050.212
1006-0.143
1007-0.198
10080
1009-0.19
1010.158
10100
10110.105
10120
1013-0.126
1014-0.0874
1015-0.0904
1016-0.594
10170
10180
10190
1020.212
10200.0953
10210.212
1022-0.227
10230.0294
1024-0.14
1025-0.0611
10260
1027-0.048
10280
1029-0.119
103-0.0887
10300.619
1031-0.848
1032-0.536
10330.0526
10340
10350
10360.22
10370
1038-0.258
1039-0.0403
1040
1040-0.172
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: CNhs13212

Jaspar motifP-value
MA0002.22.70599e-6
MA0003.10.451
MA0004.10.112
MA0006.10.804
MA0007.10.776
MA0009.10.704
MA0014.10.747
MA0017.10.341
MA0018.20.738
MA0019.10.417
MA0024.10.979
MA0025.10.294
MA0027.10.838
MA0028.11.87225e-5
MA0029.10.214
MA0030.10.191
MA0031.10.76
MA0035.20.7
MA0038.10.437
MA0039.20.787
MA0040.10.694
MA0041.10.123
MA0042.10.717
MA0043.10.487
MA0046.16.81692e-10
MA0047.20.9
MA0048.10.421
MA0050.14.13943e-13
MA0051.12.93988e-8
MA0052.10.0123
MA0055.10.53
MA0057.10.986
MA0058.10.129
MA0059.10.0381
MA0060.10.0125
MA0061.11.21889e-6
MA0062.21.22846e-16
MA0065.20.26
MA0066.10.0418
MA0067.10.277
MA0068.10.0399
MA0069.10.499
MA0070.10.591
MA0071.10.495
MA0072.10.537
MA0073.10.705
MA0074.10.561
MA0076.12.53513e-6
MA0077.10.16
MA0078.10.756
MA0079.20.0694
MA0080.22.63883e-14
MA0081.10.001
MA0083.10.0432
MA0084.10.693
MA0087.10.825
MA0088.10.649
MA0090.10.00826
MA0091.10.304
MA0092.10.804
MA0093.10.128
MA0099.20.309
MA0100.10.358
MA0101.12.13392e-6
MA0102.20.805
MA0103.10.127
MA0104.20.14
MA0105.11.01321e-8
MA0106.10.836
MA0107.19.22729e-7
MA0108.25.49013e-5
MA0111.10.436
MA0112.20.00486
MA0113.10.238
MA0114.10.71
MA0115.10.785
MA0116.16.71082e-4
MA0117.10.769
MA0119.10.684
MA0122.10.979
MA0124.10.618
MA0125.10.0315
MA0131.10.457
MA0135.10.9
MA0136.11.60766e-19
MA0137.20.245
MA0138.20.0701
MA0139.10.12
MA0140.10.542
MA0141.10.685
MA0142.11.87284e-4
MA0143.10.217
MA0144.10.423
MA0145.10.647
MA0146.10.351
MA0147.10.0986
MA0148.10.885
MA0149.10.177
MA0150.10.638
MA0152.10.327
MA0153.14.76015e-7
MA0154.10.00128
MA0155.10.774
MA0156.14.03382e-23
MA0157.10.383
MA0159.10.0201
MA0160.10.736
MA0162.10.434
MA0163.11.47283e-4
MA0164.10.5
MA0258.10.0136
MA0259.10.458



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: CNhs13212

Novel motifP-value
10.13
100.0316
1000.829
1010.989
1020.59
1030.0689
1040.714
1050.749
1060.297
1070.852
1080.558
1090.124
110.167
1100.0575
1110.0665
1120.0435
1130.291
1140.154
1150.652
1160.922
1176.26559e-4
1180.113
1190.639
120.467
1200.432
1210.415
1220.847
1230.8
1240.878
1250.161
1260.239
1270.453
1280.145
1290.128
130.079
1300.904
1310.841
1320.696
1330.989
1340.949
1350.974
1360.888
1370.132
1380.789
1390.274
140.968
1400.843
1410.159
1420.661
1430.0123
1440.535
1450.119
1460.845
1470.805
1480.0892
1490.579
150.0869
1500.328
1510.16
1520.696
1530.188
1540.422
1550.249
1561.17834e-25
1570.839
1580.128
1590.745
1600.996
1610.0521
1620.322
1630.269
1640.0905
1650.316
1660.506
1670.136
1680.92
1690.0635
170.425
180.273
190.892
20.161
200.0328
210.329
220.826
230.348
240.464
250.189
260.0281
270.708
280.221
290.0192
30.051
300.233
310.931
320.802
330.217
340.717
350.0888
360.045
370.0684
380.716
390.533
40.768
400.204
410.361
420.121
430.139
440.276
450.753
460.165
470.215
480.163
490.108
50.0424
500.642
510.884
520.334
530.447
540.829
550.482
560.702
570.7
580.128
590.287
60.613
600.662
610.106
620.0526
630.715
640.614
650.711
660.981
670.711
680.0743
690.785
70.186
700.0121
710.0429
720.227
730.107
740.869
750.0033
760.0168
770.432
780.0933
790.723
80.0566
800.0148
810.531
820.202
830.148
840.513
850.509
860.157
870.515
880.518
890.561
90.873
900.0211
910.659
920.207
930.306
940.174
950.16
960.313
970.804
980.137
990.342



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: CNhs13212


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000050 (megakaryocyte-erythroid progenitor cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000553 (megakaryocyte progenitor cell)
0000556 (megakaryocyte)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000763 (myeloid cell)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

FF: FANTOM5
NA

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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:11775-124A2&oldid=413638"