Personal tools

FF:1556-45F2

From FANTOM5_SSTAR

Revision as of 20:06, 17 October 2013 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:pancreas, embryo E15
Species:Mouse (Mus musculus)
Library ID:CNhs11042
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainDBA/2
tissuepancreas
dev stage15 days embryo
sexmixture
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008919
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11042 CAGE DRX009056 DRR009930
Accession ID Mm9

Library idBAMCTSS
CNhs11042 DRZ001355 DRZ002738
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

CNhs11042

00
10
100
1000
10000.115
10010.0159
10020.195
1003-0.0969
10040
1005-0.0389
1006-0.143
10070.0212
10080
1009-0.0754
1010.0901
10101.064
1011-0.0439
10120
10130.171
10140.28
10150.285
1016-0.016
10170
10180
10190
1020
10200
10210.0247
10220
10230
1024-0.0899
10250.28
10260
1027-0.048
10280
1029-0.0138
1030.133
10300
10310.204
1032-0.0689
10330.0242
10340.115
10350
10360.217
10370
1038-0.0184
10390.0495
1040
10400.0282
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: CNhs11042

Jaspar motifP-value
MA0002.20.0122
MA0003.10.718
MA0004.10.0451
MA0006.10.52
MA0007.10.135
MA0009.10.725
MA0014.10.886
MA0017.10.816
MA0018.20.0362
MA0019.10.678
MA0024.12.95834e-8
MA0025.10.00257
MA0027.10.107
MA0028.16.46695e-5
MA0029.10.0921
MA0030.10.18
MA0031.10.138
MA0035.20.531
MA0038.10.722
MA0039.20.918
MA0040.10.0701
MA0041.10.278
MA0042.10.582
MA0043.10.135
MA0046.14.1104e-34
MA0047.20.163
MA0048.10.0149
MA0050.11.88758e-4
MA0051.11.83347e-5
MA0052.11.44208e-7
MA0055.13.87029e-5
MA0057.10.999
MA0058.10.0393
MA0059.19.62342e-6
MA0060.12.83914e-9
MA0061.10.936
MA0062.20.00113
MA0065.20.479
MA0066.10.786
MA0067.10.0257
MA0068.10.661
MA0069.10.705
MA0070.10.527
MA0071.10.797
MA0072.10.267
MA0073.10.921
MA0074.10.238
MA0076.16.46382e-4
MA0077.10.634
MA0078.10.735
MA0079.20.525
MA0080.27.87469e-5
MA0081.10.0554
MA0083.10.00512
MA0084.10.37
MA0087.10.315
MA0088.10.0698
MA0090.10.287
MA0091.10.00239
MA0092.10.55
MA0093.10.0539
MA0099.26.24194e-5
MA0100.10.213
MA0101.10.628
MA0102.20.00151
MA0103.16.12214e-4
MA0104.20.0102
MA0105.10.211
MA0106.10.689
MA0107.10.14
MA0108.20.462
MA0111.10.327
MA0112.20.346
MA0113.10.676
MA0114.10.927
MA0115.10.732
MA0116.10.258
MA0117.10.0484
MA0119.10.343
MA0122.10.713
MA0124.10.888
MA0125.10.672
MA0131.10.0448
MA0135.10.725
MA0136.10.0186
MA0137.20.753
MA0138.20.00819
MA0139.10.156
MA0140.10.0921
MA0141.10.427
MA0142.10.0499
MA0143.10.879
MA0144.10.893
MA0145.10.838
MA0146.10.446
MA0147.12.59441e-4
MA0148.10.41
MA0149.10.538
MA0150.16.7415e-4
MA0152.10.576
MA0153.11.2e-16
MA0154.10.32
MA0155.10.191
MA0156.10.929
MA0157.10.433
MA0159.10.558
MA0160.10.967
MA0162.10.314
MA0163.19.04564e-4
MA0164.10.727
MA0258.10.684
MA0259.10.0629



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: CNhs11042

Novel motifP-value
10.947
100.241
1000.251
1010.425
1020.577
1030.458
1040.506
1050.62
1060.581
1070.144
1080.66
1090.0603
110.684
1100.135
1110.887
1120.678
1130.0494
1140.236
1150.795
1160.481
1170.114
1180.413
1190.507
120.47
1200.381
1210.115
1220.837
1230.00955
1240.0638
1250.899
1260.127
1270.162
1280.509
1290.0325
133.07162e-5
1300.677
1310.775
1320.79
1330.654
1340.0469
1350.371
1360.0697
1370.869
1380.0643
1390.0417
140.312
1400.805
1410.515
1420.384
1430.164
1440.292
1450.19
1460.891
1470.198
1480.974
1490.655
150.202
1500.433
1510.209
1520.314
1530.543
1540.644
1550.857
1561.86543e-5
1570.485
1580.793
1590.131
1600.211
1610.062
1620.164
1630.209
1640.708
1650.71
1660.316
1670.687
1680.552
1690.411
170.585
180.317
190.299
20.163
200.135
210.761
220.982
230.0175
240.0505
250.526
260.0325
270.629
280.0431
290.188
30.544
300.594
310.68
320.895
330.193
340.958
350.762
360.139
370.365
380.695
390.12
40.362
400.067
410.0966
420.509
430.303
440.816
450.47
460.759
470.837
480.866
490.305
50.252
500.285
510.977
520.912
530.433
540.386
550.69
560.781
570.743
580.953
590.969
60.829
600.884
610.137
620.37
630.826
640.557
650.989
660.291
670.528
680.19
690.825
70.318
700.0732
710.057
720.51
730.138
740.39
750.332
760.201
770.941
780.691
790.294
80.15
800.0935
810.0874
820.848
830.577
840.0217
850.369
860.729
870.252
880.951
890.807
90.862
900.882
910.845
920.936
930.434
940.159
950.0461
960.92
970.61
980.619
990.289



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: CNhs11042


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

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0001264 (pancreas)
0002100 (trunk)
0000479 (tissue)
0000466 (immaterial anatomical entity)
0002075 (viscus)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002323 (body cavity)
0005177 (trunk region element)
0000464 (anatomical space)
0004458 (body cavity or lining)
0000949 (endocrine system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000298 (mouse embryonic day 15 sample)
0011257 (mouse pancreas- embryo E15 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
FF:0000294 (mouse embryonic day 11 sample)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:1556-45F2&oldid=3079067"