Personal tools

FF:12125-128D1: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 62: Line 62:
|rna_weight_ug=2.29196
|rna_weight_ug=2.29196
|sample_age=9-10weeks
|sample_age=9-10weeks
|sample_category=primary cells
|sample_cell_catalog=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_line=

Revision as of 16:28, 26 December 2012


Name:common myeloid progenitor CMP, biol_rep2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/8J
tissuebone marrow
dev stageNA
sexmale
age9-10weeks
cell typecommon myeloid progenitor
cell lineNA
companyNA
collaborationKitamura/Nakahara
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberrep2
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

CNhs12203

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.175
10040
10050.163
1006-0.18
1007-0.472
10080
1009-0.0572
1010.234
10100
1011-0.133
10120
1013-0.0822
1014-0.0874
10150.0104
1016-0.46
10170
10180
10190
1020
10200
10210
1022-0.198
10230.914
10240.409
1025-0.0611
10260
1027-0.048
10280
1029-0.176
103-0.0887
10300
1031-0.889
1032-0.315
10330.204
10340
10350
10360.583
10370
1038-0.519
10390.0382
1040
1040-0.22
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: CNhs12203

Jaspar motifP-value
MA0002.22.6399e-7
MA0003.10.987
MA0004.10.079
MA0006.10.889
MA0007.10.566
MA0009.10.951
MA0014.10.884
MA0017.10.227
MA0018.23.5854e-7
MA0019.10.887
MA0024.12.35336e-4
MA0025.10.0221
MA0027.10.602
MA0028.18.39657e-9
MA0029.10.206
MA0030.10.692
MA0031.10.255
MA0035.20.913
MA0038.10.0678
MA0039.20.857
MA0040.10.0209
MA0041.10.654
MA0042.10.797
MA0043.11.14945e-6
MA0046.17.70224e-11
MA0047.20.579
MA0048.10.01
MA0050.11.72402e-4
MA0051.10.00183
MA0052.10.184
MA0055.15.59975e-4
MA0057.10.656
MA0058.10.0285
MA0059.10.00412
MA0060.10.404
MA0061.11.26877e-6
MA0062.22.77349e-19
MA0065.20.0473
MA0066.10.139
MA0067.10.00939
MA0068.10.927
MA0069.10.582
MA0070.10.134
MA0071.10.164
MA0072.10.833
MA0073.10.665
MA0074.10.259
MA0076.14.90704e-10
MA0077.10.954
MA0078.10.326
MA0079.20.092
MA0080.21.90147e-12
MA0081.13.26091e-5
MA0083.10.0356
MA0084.10.169
MA0087.10.457
MA0088.10.248
MA0090.10.0127
MA0091.10.531
MA0092.10.554
MA0093.10.0668
MA0099.23.67506e-15
MA0100.11.6226e-4
MA0101.12.30999e-11
MA0102.21.23121e-4
MA0103.10.338
MA0104.20.0281
MA0105.13.37495e-7
MA0106.10.214
MA0107.12.01382e-10
MA0108.20.55
MA0111.10.894
MA0112.20.0614
MA0113.10.34
MA0114.10.942
MA0115.10.706
MA0116.10.00194
MA0117.10.12
MA0119.10.475
MA0122.10.147
MA0124.10.489
MA0125.10.0696
MA0131.10.0986
MA0135.10.311
MA0136.12.51879e-29
MA0137.26.05948e-4
MA0138.20.00364
MA0139.10.591
MA0140.10.569
MA0141.10.28
MA0142.10.914
MA0143.10.501
MA0144.10.0645
MA0145.10.998
MA0146.10.161
MA0147.10.0185
MA0148.10.968
MA0149.10.0877
MA0150.19.31657e-6
MA0152.10.999
MA0153.10.00271
MA0154.10.251
MA0155.10.724
MA0156.12.11871e-21
MA0157.10.231
MA0159.10.0258
MA0160.10.0381
MA0162.10.348
MA0163.11.62159e-6
MA0164.10.798
MA0258.10.122
MA0259.10.254



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: CNhs12203

Novel motifP-value
10.276
100.0611
1000.886
1010.958
1020.811
1030.136
1040.569
1050.6
1060.15
1070.634
1080.702
1090.0519
110.161
1100.105
1110.278
1120.104
1130.623
1140.479
1150.479
1160.597
1173.4265e-4
1180.273
1190.981
120.656
1200.213
1210.63
1220.501
1230.528
1240.453
1250.447
1260.435
1270.647
1280.481
1290.42
130.00416
1300.965
1310.624
1320.326
1330.159
1340.518
1350.778
1360.231
1370.0115
1380.305
1390.4
140.585
1400.91
1410.978
1420.982
1430.0435
1440.872
1450.132
1460.906
1470.768
1480.404
1490.29
150.0289
1500.651
1510.858
1520.516
1530.619
1540.927
1550.802
1560.223
1570.642
1580.0224
1590.624
1600.751
1610.0617
1620.623
1630.0929
1640.0119
1650.129
1660.166
1670.274
1680.724
1690.0149
170.458
180.394
190.614
20.153
200.0181
210.377
220.68
230.367
240.0355
250.268
260.00775
270.429
280.723
290.0149
30.114
300.258
310.722
320.595
330.0784
340.929
350.35
360.0309
370.0642
380.378
390.655
40.727
400.0683
410.0152
420.378
430.567
440.387
450.795
460.337
470.756
480.265
490.469
50.563
500.679
510.874
520.427
530.689
540.824
550.57
560.692
570.436
580.178
590.447
60.637
600.389
610.148
620.175
630.9
640.51
650.716
660.263
670.376
680.592
690.562
70.221
700.0857
710.0111
720.0932
730.0342
740.331
750.0103
760.13
770.284
780.193
790.734
80.0593
800.443
810.939
820.425
830.00824
840.995
850.757
860.22
870.0276
880.529
890.63
90.913
900.0321
910.931
920.696
930.0537
940.449
950.00154
960.931
970.898
980.268
990.334



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: CNhs12203


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)
0002032 (hematopoietic oligopotent progenitor cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000049 (common myeloid progenitor)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000041 (common myeloid progenitor 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:12125-128D1&oldid=2567311"