Personal tools

FF:1283-20G3

From FANTOM5_SSTAR

Revision as of 17:55, 4 August 2017 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:heart, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs11030
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueheart
dev stage18 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  SAMD00004713
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11030 CAGE DRX008978 DRR009852
Accession ID Mm9

Library idBAMCTSS
CNhs11030 DRZ001277 DRZ002660
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11030

00
10
100.369
1000
10000.329
10010.38
10020.263
1003-0.123
10040
1005-0.148
10060.361
1007-0.00391
10080
10090.217
101-0.05
10100
1011-0.108
10120
1013-0.113
10140.229
1015-0.00234
10160.191
10170
10180
10190
1020
10200
1021-0.0487
10220.57
10230
10240.356
10250.0421
10260.103
10270.0422
10280
10290.14
1030.155
10300
10310.256
10320.0588
10330
10340
10350.566
1036-0.0697
10370
10380.118
10390.299
1040
10400.17
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: CNhs11030

Jaspar motifP-value
MA0002.20.00894
MA0003.10.648
MA0004.10.0712
MA0006.10.429
MA0007.10.69
MA0009.10.964
MA0014.10.407
MA0017.10.0588
MA0018.20.236
MA0019.10.88
MA0024.10.194
MA0025.10.332
MA0027.10.529
MA0028.10.111
MA0029.10.687
MA0030.10.105
MA0031.10.154
MA0035.20.127
MA0038.10.567
MA0039.20.707
MA0040.10.0956
MA0041.10.355
MA0042.10.501
MA0043.10.0961
MA0046.16.63961e-18
MA0047.20.225
MA0048.10.0453
MA0050.10.0031
MA0051.10.0197
MA0052.11.07261e-39
MA0055.12.72853e-5
MA0057.10.827
MA0058.10.153
MA0059.10.336
MA0060.10.326
MA0061.10.334
MA0062.23.76435e-7
MA0065.20.772
MA0066.10.539
MA0067.10.641
MA0068.10.412
MA0069.10.325
MA0070.10.853
MA0071.10.158
MA0072.10.223
MA0073.10.954
MA0074.10.467
MA0076.10.00242
MA0077.10.679
MA0078.10.629
MA0079.20.569
MA0080.29.12248e-4
MA0081.10.682
MA0083.12.98134e-21
MA0084.10.488
MA0087.10.307
MA0088.10.448
MA0090.15.04937e-6
MA0091.10.717
MA0092.10.472
MA0093.10.0851
MA0099.23.07508e-5
MA0100.10.48
MA0101.10.363
MA0102.20.00942
MA0103.11.65091e-5
MA0104.20.233
MA0105.10.881
MA0106.10.849
MA0107.10.521
MA0108.20.151
MA0111.10.527
MA0112.20.0137
MA0113.10.741
MA0114.10.00176
MA0115.10.446
MA0116.10.273
MA0117.10.645
MA0119.10.0241
MA0122.10.388
MA0124.10.839
MA0125.10.519
MA0131.10.988
MA0135.10.231
MA0136.11.29563e-4
MA0137.20.0697
MA0138.20.685
MA0139.10.399
MA0140.10.232
MA0141.13.16984e-10
MA0142.10.0291
MA0143.10.493
MA0144.10.905
MA0145.10.785
MA0146.10.211
MA0147.10.23
MA0148.10.304
MA0149.10.316
MA0150.10.0391
MA0152.10.641
MA0153.12.34209e-11
MA0154.10.131
MA0155.10.0635
MA0156.11.53933e-6
MA0157.10.56
MA0159.10.00245
MA0160.16.95184e-5
MA0162.10.0566
MA0163.10.98
MA0164.10.177
MA0258.10.198
MA0259.10.561



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: CNhs11030

Novel motifP-value
10.258
100.754
1000.744
1010.54
1020.923
1030.441
1040.698
1050.259
1060.889
1070.589
1080.641
1090.293
110.78
1100.184
1110.273
1120.167
1130.509
1140.727
1150.954
1160.343
1170.932
1180.561
1190.459
120.407
1200.0615
1210.79
1220.198
1230.455
1240.305
1250.83
1260.675
1270.225
1280.353
1290.422
136.45798e-5
1300.739
1310.766
1320.801
1330.433
1340.781
1350.953
1360.209
1370.209
1380.14
1390.988
140.445
1400.703
1410.552
1420.735
1430.425
1440.235
1450.124
1460.554
1470.937
1480.883
1490.099
150.926
1500.216
1510.269
1520.362
1530.621
1540.721
1550.0439
1560.355
1570.849
1580.259
1590.0524
1600.296
1610.696
1620.672
1630.894
1640.505
1650.0198
1660.415
1670.647
1680.37
1693.5324e-4
170.779
180.0195
190.0787
20.776
200.366
210.63
220.172
230.71
240.885
250.82
260.0108
270.263
280.221
290.835
30.946
300.0541
310.732
320.457
330.394
340.231
350.445
360.117
370.128
380.949
390.899
40.306
400.0193
410.863
420.588
430.482
440.835
450.24
460.886
470.98
480.702
490.382
50.775
500.315
510.801
520.732
530.847
540.896
550.224
560.919
570.383
580.909
590.0304
60.0498
600.681
610.872
620.557
630.207
640.752
650.775
660.354
670.959
680.458
690.15
70.104
700.0423
710.0118
720.118
730.15
740.299
750.435
760.961
770.42
780.314
790.434
80.912
800.0508
810.522
820.974
830.706
840.63
850.169
860.552
874.07694e-5
880.46
890.0465
90.168
900.909
910.132
920.485
930.273
940.637
950.169
960.414
970.23
980.609
990.881



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: CNhs11030


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)
0000302 (mouse embryonic day 18 sample)
0011515 (mouse heart- embryo E18 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:1283-20G3&oldid=4341596"