Personal tools

FF:431-16C8

From FANTOM5_SSTAR

Revision as of 15:47, 26 December 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:heart, embryo E15
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueheart
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
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

CNhs11017

00
10
100.201
1000
10000.253
10010.343
10020.406
1003-0.0271
10040
10050
10060.235
10070.0231
10080
10090.211
1010.00274
10100
1011-2.590399e-4
10120
1013-0.297
10140.523
10150.0902
10160.165
10170
10180
10190
1020
10200
10210
10220.552
10230
10240.165
10250
10260
10270
10280
10290.0762
1030.0539
10300
10310.358
10320.034
1033-0.0752
10340
10350.575
10360.0449
10370
10380.102
10390.0664
1040
10400.115
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: CNhs11017

Jaspar motifP-value
MA0002.20.0238
MA0003.10.55
MA0004.10.276
MA0006.10.886
MA0007.10.0901
MA0009.10.669
MA0014.10.527
MA0017.10.00966
MA0018.20.103
MA0019.10.558
MA0024.10.00262
MA0025.10.208
MA0027.10.098
MA0028.10.668
MA0029.10.505
MA0030.10.0656
MA0031.10.0971
MA0035.20.21
MA0038.10.883
MA0039.20.034
MA0040.10.044
MA0041.10.249
MA0042.10.396
MA0043.10.436
MA0046.18.0487e-16
MA0047.20.0222
MA0048.10.0214
MA0050.11.59763e-4
MA0051.10.0185
MA0052.13.60077e-28
MA0055.12.53487e-4
MA0057.10.818
MA0058.10.428
MA0059.10.901
MA0060.10.91
MA0061.10.28
MA0062.20.00705
MA0065.20.201
MA0066.10.72
MA0067.10.395
MA0068.10.195
MA0069.10.285
MA0070.10.534
MA0071.10.926
MA0072.10.143
MA0073.10.871
MA0074.10.696
MA0076.10.16
MA0077.10.839
MA0078.10.296
MA0079.20.72
MA0080.20.0313
MA0081.10.941
MA0083.11.32254e-14
MA0084.10.801
MA0087.10.751
MA0088.10.556
MA0090.10.00245
MA0091.10.774
MA0092.10.832
MA0093.10.31
MA0099.26.11104e-8
MA0100.10.792
MA0101.10.503
MA0102.20.00433
MA0103.11.3511e-6
MA0104.20.702
MA0105.10.578
MA0106.10.848
MA0107.10.498
MA0108.20.695
MA0111.10.548
MA0112.20.152
MA0113.10.568
MA0114.11.50481e-4
MA0115.10.833
MA0116.10.317
MA0117.10.236
MA0119.10.0372
MA0122.10.841
MA0124.10.408
MA0125.10.735
MA0131.10.963
MA0135.10.266
MA0136.10.0225
MA0137.20.0217
MA0138.20.24
MA0139.10.541
MA0140.10.148
MA0141.16.26454e-5
MA0142.10.237
MA0143.10.945
MA0144.10.186
MA0145.10.282
MA0146.10.945
MA0147.10.665
MA0148.10.0571
MA0149.10.116
MA0150.10.00334
MA0152.10.973
MA0153.14.81962e-11
MA0154.10.59
MA0155.10.24
MA0156.16.13926e-4
MA0157.10.237
MA0159.10.141
MA0160.10.0727
MA0162.10.0922
MA0163.10.198
MA0164.10.363
MA0258.10.717
MA0259.10.389



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: CNhs11017

Novel motifP-value
10.982
100.869
1000.725
1010.883
1020.667
1030.435
1040.927
1050.672
1060.373
1070.952
1080.978
1090.772
110.463
1100.175
1110.52
1120.267
1130.583
1140.652
1150.834
1160.344
1170.423
1180.249
1190.607
120.6
1200.144
1210.923
1220.28
1230.101
1240.756
1250.836
1260.947
1270.226
1280.0439
1290.864
130.00168
1300.375
1310.478
1320.687
1330.638
1340.737
1350.914
1360.0743
1370.502
1380.164
1390.605
140.923
1400.669
1410.365
1420.8
1430.512
1440.119
1450.0756
1460.332
1470.756
1480.871
1490.739
150.32
1500.329
1510.148
1520.754
1530.566
1540.704
1550.297
1560.0189
1570.596
1580.36
1590.0869
1600.31
1610.748
1620.915
1630.99
1640.734
1650.108
1660.586
1670.794
1680.574
1690.00506
170.288
180.104
190.246
20.343
200.247
210.739
220.447
230.284
240.614
250.473
260.0049
270.215
280.221
290.969
30.819
300.0391
310.461
320.505
330.111
340.528
350.25
360.138
370.272
380.585
390.455
40.513
400.00333
410.863
420.606
430.863
440.75
450.0453
460.951
470.843
480.954
490.569
50.973
500.525
510.953
520.695
530.741
540.654
550.183
560.766
570.323
580.886
590.324
60.0687
600.762
610.4
620.564
630.759
640.577
650.456
660.578
670.786
680.175
690.277
70.357
700.00975
710.0157
720.0814
730.547
740.891
750.33
760.544
770.617
780.393
790.373
80.712
800.0118
810.461
820.903
830.785
840.81
850.383
860.673
874.03396e-5
880.349
890.114
90.557
900.823
910.117
920.25
930.229
940.261
950.607
960.359
970.157
980.357
990.455



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: CNhs11017


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)
0007100 (primary circulatory organ)
0000948 (heart)
0000479 (tissue)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0010317 (germ layer / neural crest derived structure)
0004535 (cardiovascular system)
0001009 (circulatory 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)
0011347 (mouse heart- 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
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0004140 (primary heart field)
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:431-16C8&oldid=2566768"