Personal tools

FF:11777-124A4

From FANTOM5_SSTAR

Revision as of 14:05, 27 January 2012 by Autoedit (talk | contribs) (Created page with "{{f5samples |id=FF:11777-124A4 |name=CD41+ megakaryocyte control, donor2 |sample_id=11777 |rna_tube_id=124A4 |rna_box=124 |rna_position=A4 |sample_cell_lot= |sample_ce...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Name:CD41+ megakaryocyte control, donor2
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-2
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

CNhs13214

00
10
100
1000
1000-0.00757
1001-0.0631
1002-0.116
1003-0.175
10040
10050.0558
1006-0.143
1007-0.164
10080
1009-0.19
1010.157
10100
10110.0697
10120.00527
1013-0.161
1014-0.0874
1015-0.143
1016-0.594
10170
10180
10190
1020.15
10200.105
10210.192
1022-0.136
10230.0558
1024-0.14
1025-0.0611
10260
1027-0.048
10280
1029-0.121
103-0.0887
10300.504
1031-0.855
1032-0.599
10330.0455
10340
10350
10360.256
10370
1038-0.203
1039-0.0349
1040
1040-0.121
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: CNhs13214

Jaspar motifP-value
MA0002.28.7005e-6
MA0003.10.359
MA0004.10.123
MA0006.10.762
MA0007.10.854
MA0009.10.704
MA0014.10.784
MA0017.10.402
MA0018.20.896
MA0019.10.351
MA0024.10.992
MA0025.10.197
MA0027.10.683
MA0028.18.50536e-6
MA0029.10.217
MA0030.10.213
MA0031.10.738
MA0035.20.792
MA0038.10.492
MA0039.20.764
MA0040.10.627
MA0041.10.105
MA0042.10.676
MA0043.10.337
MA0046.18.27038e-10
MA0047.20.808
MA0048.10.417
MA0050.15.91297e-13
MA0051.11.34668e-7
MA0052.10.0095
MA0055.10.579
MA0057.10.945
MA0058.10.15
MA0059.10.0437
MA0060.10.0139
MA0061.18.62155e-7
MA0062.22.60718e-17
MA0065.20.332
MA0066.10.0299
MA0067.10.267
MA0068.10.0176
MA0069.10.428
MA0070.10.469
MA0071.10.595
MA0072.10.433
MA0073.10.629
MA0074.10.545
MA0076.11.27376e-6
MA0077.10.174
MA0078.10.78
MA0079.20.0637
MA0080.24.83288e-14
MA0081.19.56359e-4
MA0083.10.0254
MA0084.10.817
MA0087.10.85
MA0088.10.71
MA0090.10.00802
MA0091.10.341
MA0092.10.913
MA0093.10.15
MA0099.20.2
MA0100.10.345
MA0101.18.96315e-7
MA0102.20.742
MA0103.10.136
MA0104.20.194
MA0105.12.40151e-8
MA0106.10.92
MA0107.18.54509e-7
MA0108.26.07766e-6
MA0111.10.507
MA0112.20.0102
MA0113.10.336
MA0114.10.572
MA0115.10.874
MA0116.16.64422e-4
MA0117.10.704
MA0119.10.468
MA0122.10.954
MA0124.10.681
MA0125.10.0428
MA0131.10.427
MA0135.10.781
MA0136.13.73966e-19
MA0137.20.373
MA0138.20.0631
MA0139.10.148
MA0140.10.419
MA0141.10.771
MA0142.11.84672e-4
MA0143.10.15
MA0144.10.551
MA0145.10.485
MA0146.10.334
MA0147.10.135
MA0148.10.703
MA0149.10.138
MA0150.10.688
MA0152.10.341
MA0153.12.49962e-7
MA0154.10.00164
MA0155.10.671
MA0156.17.44747e-23
MA0157.10.348
MA0159.10.0181
MA0160.10.825
MA0162.10.581
MA0163.13.8006e-4
MA0164.10.579
MA0258.10.0176
MA0259.10.45



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: CNhs13214

Novel motifP-value
10.146
100.0276
1000.83
1010.932
1020.575
1030.09
1040.808
1050.802
1060.364
1070.796
1080.488
1090.159
110.194
1100.0695
1110.119
1120.0442
1130.215
1140.202
1150.629
1160.795
1176.18812e-4
1180.0876
1190.561
120.483
1200.523
1210.412
1220.866
1230.726
1240.981
1250.111
1260.247
1270.385
1280.19
1290.101
130.0749
1300.966
1310.637
1320.715
1330.844
1340.924
1350.899
1360.968
1370.134
1380.667
1390.292
140.987
1400.705
1410.129
1420.799
1430.019
1440.406
1450.143
1460.841
1470.852
1480.103
1490.564
150.098
1500.335
1510.165
1520.632
1530.226
1540.384
1550.246
1561.55351e-23
1570.912
1580.13
1590.665
1600.973
1610.0349
1620.357
1630.255
1640.0951
1650.378
1660.518
1670.124
1680.943
1690.113
170.54
180.302
190.932
20.121
200.0276
210.332
220.866
230.326
240.457
250.151
260.0243
270.708
280.21
290.019
30.0557
300.196
310.974
320.649
330.196
340.638
350.1
360.0535
370.0827
380.781
390.463
40.751
400.222
410.431
420.131
430.142
440.306
450.684
460.178
470.266
480.208
490.113
50.034
500.565
510.895
520.299
530.404
540.791
550.506
560.779
570.73
580.0976
590.398
60.629
600.736
610.0915
620.0481
630.801
640.689
650.828
660.927
670.786
680.0816
690.885
70.19
700.0207
710.0388
720.35
730.103
740.974
750.00388
760.0124
770.334
780.0694
790.789
80.0688
800.0175
810.548
820.197
830.129
840.519
850.608
860.172
870.572
880.495
890.645
90.946
900.022
910.598
920.264
930.252
940.201
950.136
960.307
970.799
980.175
990.338



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: CNhs13214


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:11777-124A4&oldid=6437"