Personal tools

FF:481-18A3

From FANTOM5_SSTAR

Revision as of 21:54, 31 July 2014 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:liver, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs10510
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueliver
dev stage17 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  SAMD00005008
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10510 CAGE DRX009020 DRR009894
Accession ID Mm9

Library idBAMCTSS
CNhs10510 DRZ001319 DRZ002702
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

CNhs10510

00
10
100
1000
10000
1001-0.0749
1002-0.0557
1003-0.123
10040
10050.333
1006-0.0329
1007-0.0786
10080
1009-0.19
1010.0346
10100
1011-0.108
10120
10130.104
10140.0842
1015-0.141
1016-0.276
10170
10180
10190
1020
10200
10210
1022-0.0704
10230
1024-0.041
10250.335
10260
1027-0.048
10280
1029-0.00408
103-0.038
10300
1031-0.0981
1032-0.177
10330
10340.482
10350
10360.138
10370
1038-0.2
10390.154
1040
1040-0.263
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: CNhs10510

Jaspar motifP-value
MA0002.20.00424
MA0003.10.156
MA0004.10.71
MA0006.10.281
MA0007.10.406
MA0009.10.322
MA0014.10.462
MA0017.18.5331e-13
MA0018.24.8606e-5
MA0019.10.387
MA0024.10.181
MA0025.10.736
MA0027.10.772
MA0028.10.67
MA0029.10.0533
MA0030.10.0439
MA0031.10.0367
MA0035.28.05326e-19
MA0038.10.387
MA0039.20.0212
MA0040.10.0763
MA0041.10.191
MA0042.10.661
MA0043.10.0456
MA0046.11.65324e-61
MA0047.27.49363e-8
MA0048.10.32
MA0050.10.486
MA0051.10.86
MA0052.10.00351
MA0055.10.365
MA0057.10.387
MA0058.10.598
MA0059.10.12
MA0060.10.116
MA0061.10.191
MA0062.20.528
MA0065.22.84427e-7
MA0066.10.0928
MA0067.10.182
MA0068.10.818
MA0069.10.102
MA0070.10.551
MA0071.10.0516
MA0072.10.0297
MA0073.10.72
MA0074.10.646
MA0076.10.895
MA0077.10.117
MA0078.10.475
MA0079.20.378
MA0080.26.13847e-5
MA0081.10.771
MA0083.10.694
MA0084.10.0999
MA0087.10.037
MA0088.10.128
MA0090.10.828
MA0091.10.592
MA0092.10.217
MA0093.10.738
MA0099.20.719
MA0100.10.604
MA0101.10.801
MA0102.20.00806
MA0103.10.383
MA0104.20.723
MA0105.10.00217
MA0106.10.613
MA0107.10.991
MA0108.20.842
MA0111.10.834
MA0112.28.50592e-4
MA0113.10.374
MA0114.11.09608e-10
MA0115.14.28077e-6
MA0116.10.00372
MA0117.10.836
MA0119.10.00787
MA0122.10.627
MA0124.10.666
MA0125.10.919
MA0131.10.938
MA0135.10.832
MA0136.10.00434
MA0137.20.5
MA0138.20.725
MA0139.10.154
MA0140.11.66283e-41
MA0141.10.00478
MA0142.10.163
MA0143.10.218
MA0144.10.535
MA0145.10.319
MA0146.10.0751
MA0147.10.608
MA0148.12.94482e-9
MA0149.10.0124
MA0150.10.004
MA0152.10.611
MA0153.15.13059e-48
MA0154.10.023
MA0155.10.745
MA0156.10.0699
MA0157.10.0503
MA0159.10.0181
MA0160.10.0146
MA0162.10.41
MA0163.11.69436e-4
MA0164.10.898
MA0258.10.0488
MA0259.10.979



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: CNhs10510

Novel motifP-value
10.0878
100.174
1000.535
1010.955
1020.304
1030.0113
1040.926
1050.711
1060.0714
1070.104
1080.65
1090.0222
110.0705
1100.105
1110.0506
1120.022
1130.93
1140.161
1150.812
1160.737
1170.0318
1180.126
1190.113
120.963
1200.581
1210.747
1220.593
1230.222
1240.285
1250.968
1260.157
1270.555
1280.0571
1290.573
136.01843e-4
1300.305
1310.0341
1320.528
1330.598
1340.387
1350.871
1360.299
1370.212
1380.71
1390.481
140.547
1400.231
1410.935
1420.0806
1430.385
1440.923
1450.0444
1460.353
1470.943
1480.776
1490.589
150.0725
1500.255
1510.317
1520.293
1530.648
1540.695
1550.558
1560.0616
1570.729
1580.749
1590.412
1600.115
1610.33
1620.585
1630.892
1640.0145
1650.347
1660.799
1670.482
1680.19
1690.0058
170.0968
180.658
190.0859
20.785
200.567
210.991
220.232
230.399
240.269
250.555
263.83887e-4
270.423
280.409
290.0509
30.0211
300.707
310.725
320.154
330.16
340.673
350.814
360.0385
370.107
380.486
390.614
40.649
400.0872
410.906
420.0817
430.0672
440.416
450.752
460.0958
470.154
480.133
490.0761
50.118
500.606
510.469
520.333
530.815
540.465
550.235
560.308
570.574
580.484
590.0957
60.85
600.121
610.32
620.0963
630.208
640.372
650.256
660.407
670.514
680.949
690.679
70.0621
700.201
710.0276
720.344
730.212
740.815
750.0482
760.918
770.467
780.0138
790.692
80.0136
800.0375
810.731
820.206
830.24
840.865
850.178
860.351
870.148
880.983
890.231
90.563
900.256
910.147
920.187
930.711
940.672
950.0879
960.117
970.762
980.229
990.291



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: CNhs10510


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)
0002107 (liver)
0002100 (trunk)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0002365 (exocrine gland)
0005172 (abdomen element)
0006925 (digestive gland)
0002530 (gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0002330 (exocrine system)
0000916 (abdomen)
0002423 (hepatobiliary 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)
0000300 (mouse embryonic day 17 sample)
0011369 (mouse liver- embryo E17 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
UBERON:0001041 (foregut)
UBERON:0002532 (epiblast (generic))
UBERON:0006595 (presumptive endoderm)
UBERON:0003104 (mesenchyme)
UBERON:0004161 (septum transversum)
UBERON:0009497 (epithelium of foregut-midgut junction)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:481-18A3&oldid=3271643"