Personal tools

FF:443-27C5

From FANTOM5_SSTAR

Revision as of 18:41, 4 August 2017 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:testis, embryo E15
Species:Mouse (Mus musculus)
Library ID:CNhs11034
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuetestis
dev stage15 days embryo
sexmale
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  SAMD00005707
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11034 CAGE DRX009103 DRR009977
Accession ID Mm9

Library idBAMCTSS
CNhs11034 DRZ001402 DRZ002785
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

CNhs11034

00
10
100
1000
1000-0.0355
1001-0.0749
10020.363
1003-0.0745
10040
1005-0.132
1006-0.0582
10070.0483
10080
10090.00927
1010.0999
10100
10110
10120
1013-0.163
10140
10150.298
10160.377
10170
10180.0665
10190
1020
10200
10210
10220
10230
10240
10250
10260
10270.00553
10280
1029-0.0518
1030.0557
10300
10310.242
1032-0.0163
10330
10340
10350.0665
1036-0.0236
10370
1038-0.0566
10390.0195
1040
1040-0.0544
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: CNhs11034

Jaspar motifP-value
MA0002.20.0331
MA0003.10.631
MA0004.10.264
MA0006.10.189
MA0007.10.656
MA0009.10.878
MA0014.10.609
MA0017.10.0182
MA0018.20.604
MA0019.10.326
MA0024.11.18078e-7
MA0025.10.547
MA0027.10.144
MA0028.18.87583e-4
MA0029.10.678
MA0030.10.0311
MA0031.10.0905
MA0035.20.264
MA0038.10.0335
MA0039.20.0423
MA0040.10.332
MA0041.10.379
MA0042.10.414
MA0043.10.661
MA0046.13.63769e-24
MA0047.20.08
MA0048.10.0185
MA0050.12.09459e-4
MA0051.14.80874e-4
MA0052.10.00452
MA0055.14.75198e-4
MA0057.10.387
MA0058.10.0706
MA0059.10.0605
MA0060.15.51409e-15
MA0061.10.109
MA0062.20.00603
MA0065.20.0483
MA0066.10.0911
MA0067.10.646
MA0068.10.0348
MA0069.10.827
MA0070.10.439
MA0071.10.586
MA0072.10.427
MA0073.10.845
MA0074.10.655
MA0076.16.1391e-4
MA0077.10.548
MA0078.10.593
MA0079.20.488
MA0080.21.53644e-5
MA0081.10.887
MA0083.10.0815
MA0084.10.925
MA0087.10.546
MA0088.10.521
MA0090.10.79
MA0091.10.659
MA0092.10.485
MA0093.10.207
MA0099.21.37722e-4
MA0100.10.399
MA0101.10.626
MA0102.20.091
MA0103.10.00101
MA0104.20.0128
MA0105.10.0257
MA0106.10.608
MA0107.10.168
MA0108.20.0671
MA0111.10.176
MA0112.20.00514
MA0113.10.869
MA0114.10.0122
MA0115.10.363
MA0116.10.382
MA0117.10.0952
MA0119.10.432
MA0122.10.86
MA0124.10.315
MA0125.10.944
MA0131.10.278
MA0135.10.902
MA0136.10.122
MA0137.20.405
MA0138.20.00233
MA0139.10.729
MA0140.10.244
MA0141.10.0342
MA0142.10.415
MA0143.10.253
MA0144.10.311
MA0145.10.028
MA0146.10.22
MA0147.10.00945
MA0148.10.00703
MA0149.10.633
MA0150.10.00234
MA0152.10.701
MA0153.17.91459e-16
MA0154.10.0591
MA0155.10.819
MA0156.10.63
MA0157.10.106
MA0159.19.5101e-4
MA0160.10.317
MA0162.10.317
MA0163.10.711
MA0164.10.381
MA0258.10.00306
MA0259.10.0478



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: CNhs11034

Novel motifP-value
10.181
100.589
1000.506
1010.639
1020.549
1030.44
1040.988
1050.172
1066.43075e-4
1070.0172
1080.964
1090.802
110.586
1100.703
1110.516
1120.399
1130.306
1140.177
1150.577
1160.688
1170.46
1180.703
1190.261
120.655
1200.656
1210.534
1220.913
1230.193
1240.0665
1250.0943
1260.989
1270.239
1288.21339e-4
1290.031
130.668
1300.236
1310.813
1320.183
1330.864
1340.249
1350.981
1360.0724
1370.662
1380.693
1390.116
140.129
1400.457
1410.0484
1420.886
1430.116
1440.088
1450.973
1460.363
1470.377
1480.0612
1490.371
150.184
1500.953
1510.0427
1520.648
1530.244
1540.93
1550.666
1566.94651e-5
1570.591
1580.227
1590.0504
1600.884
1610.75
1620.636
1630.073
1640.615
1650.168
1660.918
1670.794
1680.181
1690.78
170.141
180.235
190.866
20.396
200.374
210.477
220.874
230.0399
240.652
250.4
260.939
270.224
280.252
290.521
30.407
300.714
310.163
320.192
330.404
340.989
350.0664
360.698
370.405
380.831
390.836
40.711
400.765
410.245
420.701
430.221
440.392
450.354
460.192
470.549
480.512
490.128
50.072
500.832
510.805
520.139
530.634
540.373
550.744
560.253
570.9
580.299
590.394
60.833
600.0336
610.593
620.166
630.215
640.885
650.255
660.312
670.345
685.76279e-4
690.707
70.444
700.0167
710.367
720.896
730.855
740.452
750.957
760.364
770.443
780.328
790.861
80.507
800.158
810.256
820.48
830.642
840.146
850.00771
860.316
870.213
880.675
890.0352
90.643
900.26
910.285
920.0629
930.645
940.176
950.361
960.395
970.891
980.0724
990.653



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: CNhs11034


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)
0000473 (testis)
0000991 (gonad)
0000479 (tissue)
0005156 (reproductive structure)
0000466 (immaterial anatomical entity)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0002553 (anatomical cavity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003135 (male reproductive organ)
0003133 (reproductive organ)
0002323 (body cavity)
0000464 (anatomical space)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0003101 (male organism)
0000079 (male reproductive 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)
0011352 (mouse testis- 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:0009117 (indifferent gonad)
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0005564 (gonad primordium)
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:443-27C5&oldid=4342800"