Personal tools

FF:12128-128D4: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 44: Line 44:
|is_obsolete=
|is_obsolete=
|library_id=CNhs12551
|library_id=CNhs12551
|library_ids=CNhs12551
|name=common myeloid progenitor CMP, biol_rep3
|name=common myeloid progenitor CMP, biol_rep3
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 17:29, 25 October 2013


Name:common myeloid progenitor CMP, biol_rep3
Species:Mouse (Mus musculus)
Library ID:CNhs12551
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 numberrep3
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008671
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12551 CAGE DRX008781 DRR009653
Accession ID Mm9

Library idBAMCTSS
CNhs12551 DRZ001078 DRZ002463
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

CNhs12551

00
10
100
1000
10000
1001-0.0749
1002-0.116
1003-0.0786
10040
10050.0413
1006-0.2
1007-0.288
10080
1009-0.161
1010.259
10100
10110
10120
1013-0.16
1014-0.0874
1015-0.0554
1016-0.496
10170
10180
10190
1020.052
10200.0983
10210
1022-0.221
10230.634
10240.457
1025-0.0611
10260
1027-0.048
10280
1029-0.131
103-0.0887
10300
1031-0.911
1032-0.436
10330.103
10340
10350
10360.544
10370
1038-0.283
10390.0315
1040
1040-0.23
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: CNhs12551

Jaspar motifP-value
MA0002.21.01348e-5
MA0003.10.606
MA0004.10.0749
MA0006.10.93
MA0007.10.54
MA0009.10.519
MA0014.10.845
MA0017.10.411
MA0018.25.50289e-6
MA0019.10.842
MA0024.17.82816e-5
MA0025.10.109
MA0027.10.329
MA0028.13.98595e-8
MA0029.10.188
MA0030.10.187
MA0031.10.62
MA0035.20.821
MA0038.10.059
MA0039.20.884
MA0040.10.071
MA0041.10.143
MA0042.10.373
MA0043.12.77667e-6
MA0046.11.43527e-15
MA0047.20.832
MA0048.10.00771
MA0050.15.0758e-8
MA0051.17.93014e-5
MA0052.10.453
MA0055.10.00272
MA0057.10.722
MA0058.10.0271
MA0059.10.00155
MA0060.10.519
MA0061.14.96743e-6
MA0062.21.23665e-17
MA0065.20.27
MA0066.10.176
MA0067.10.00454
MA0068.10.00676
MA0069.10.424
MA0070.10.141
MA0071.10.323
MA0072.10.892
MA0073.10.713
MA0074.10.344
MA0076.12.69709e-9
MA0077.10.275
MA0078.10.734
MA0079.20.0814
MA0080.21.5801e-12
MA0081.15.36974e-5
MA0083.10.00622
MA0084.10.625
MA0087.10.923
MA0088.10.209
MA0090.10.00592
MA0091.10.961
MA0092.10.585
MA0093.10.0636
MA0099.25.22816e-14
MA0100.13.48636e-4
MA0101.11.80075e-9
MA0102.29.73841e-5
MA0103.10.177
MA0104.20.0283
MA0105.11.61349e-6
MA0106.10.156
MA0107.11.76886e-8
MA0108.20.207
MA0111.10.838
MA0112.20.0669
MA0113.10.57
MA0114.10.56
MA0115.10.914
MA0116.10.00121
MA0117.10.267
MA0119.10.373
MA0122.10.162
MA0124.10.816
MA0125.10.0343
MA0131.10.114
MA0135.10.0285
MA0136.11.95447e-28
MA0137.20.00159
MA0138.24.2564e-4
MA0139.10.388
MA0140.10.541
MA0141.10.594
MA0142.10.791
MA0143.10.202
MA0144.10.103
MA0145.10.655
MA0146.10.191
MA0147.10.0165
MA0148.10.592
MA0149.10.111
MA0150.12.7925e-5
MA0152.10.837
MA0153.11.52204e-4
MA0154.10.261
MA0155.10.71
MA0156.14.52944e-22
MA0157.10.348
MA0159.10.0473
MA0160.10.264
MA0162.10.431
MA0163.12.561e-5
MA0164.10.603
MA0258.10.0828
MA0259.10.187



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: CNhs12551

Novel motifP-value
10.392
100.0457
1000.637
1010.905
1020.674
1030.27
1040.81
1050.544
1060.17
1070.912
1080.499
1090.0889
110.236
1100.148
1110.257
1120.144
1130.544
1140.493
1150.571
1160.777
1172.68768e-4
1180.215
1191
120.685
1200.306
1210.431
1220.435
1230.162
1240.412
1250.423
1260.512
1270.611
1280.244
1290.302
130.00129
1300.529
1310.338
1320.405
1330.353
1340.683
1350.713
1360.233
1370.00671
1380.793
1390.521
140.492
1400.481
1410.519
1420.861
1430.194
1440.89
1450.0553
1460.684
1470.576
1480.24
1490.151
150.034
1500.573
1510.811
1520.802
1530.411
1540.663
1550.947
1560.372
1570.937
1580.0595
1590.465
1600.567
1610.152
1620.396
1630.261
1640.0109
1650.158
1660.382
1670.224
1680.673
1690.0396
170.683
180.374
190.623
20.0711
200.0123
210.389
220.83
230.201
240.037
250.294
260.0043
270.354
280.694
290.0103
30.144
300.173
310.708
320.313
330.0919
340.613
350.525
360.0486
370.0477
380.518
390.641
40.594
400.156
410.0767
420.366
430.519
440.7
450.693
460.317
470.674
480.333
490.462
50.561
500.682
510.978
520.531
530.606
540.743
550.593
560.788
570.413
580.265
590.929
60.785
600.527
610.212
620.189
630.93
640.81
650.885
660.32
670.339
680.685
690.704
70.265
700.168
710.0155
720.117
730.0509
740.655
750.00647
760.049
770.132
780.143
790.691
80.0949
800.711
810.938
820.345
830.0703
840.38
850.52
860.213
870.0452
880.508
890.994
90.882
900.0306
910.843
920.991
930.167
940.458
950.003
960.998
970.938
980.523
990.231



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: CNhs12551


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:12128-128D4&oldid=3080248"