Personal tools

FF:434-16F8

From FANTOM5_SSTAR

Revision as of 17:36, 16 October 2013 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:kidney, 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
tissuekidney
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  DRS008868
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{library_id}}} {{{accession_numbers}}}
Accession ID Mm9

Library idBAMCTSS
{{{library_id}}}
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

CNhs10997

00
10
100
1000.0367
1000-0.00761
1001-0.00676
10020.266
1003-0.087
10040
1005-0.0724
1006-0.0815
10070.13
10080
1009-0.0102
1010.134
10100.047
10110
10120
1013-0.188
10140.196
10150.214
10160.162
10170
10180
10190
1020
10200
10210.047
1022-0.0655
10230
10240.0736
10250.169
10260.0599
10270
10280.047
10290.219
1030.0982
10300
10310.335
1032-0.0645
10330
10340
10350.00898
10360.192
10370
10380.0282
1039-0.0467
1040
10400.0754
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: CNhs10997

Jaspar motifP-value
MA0002.23.78415e-4
MA0003.10.146
MA0004.10.72
MA0006.10.661
MA0007.10.511
MA0009.10.553
MA0014.10.546
MA0017.10.0787
MA0018.20.102
MA0019.10.937
MA0024.16.19678e-8
MA0025.11.66802e-4
MA0027.10.0515
MA0028.10.267
MA0029.10.98
MA0030.10.24
MA0031.10.00263
MA0035.20.0727
MA0038.10.0562
MA0039.20.0303
MA0040.10.322
MA0041.10.219
MA0042.10.451
MA0043.10.418
MA0046.14.54147e-22
MA0047.20.111
MA0048.10.0015
MA0050.12.32933e-4
MA0051.13.71033e-5
MA0052.12.67693e-5
MA0055.10.00533
MA0057.10.104
MA0058.10.699
MA0059.10.683
MA0060.11.33753e-9
MA0061.10.0785
MA0062.20.484
MA0065.20.00221
MA0066.10.0997
MA0067.10.232
MA0068.10.912
MA0069.10.23
MA0070.10.676
MA0071.10.057
MA0072.10.0148
MA0073.10.606
MA0074.10.567
MA0076.10.479
MA0077.10.751
MA0078.10.547
MA0079.20.0817
MA0080.22.58903e-10
MA0081.10.121
MA0083.10.805
MA0084.10.258
MA0087.10.168
MA0088.10.945
MA0090.10.703
MA0091.10.95
MA0092.10.501
MA0093.10.758
MA0099.21.32065e-5
MA0100.10.724
MA0101.10.457
MA0102.20.0477
MA0103.10.0112
MA0104.20.976
MA0105.10.149
MA0106.10.591
MA0107.10.145
MA0108.20.236
MA0111.10.588
MA0112.20.00116
MA0113.10.855
MA0114.10.0928
MA0115.10.355
MA0116.10.041
MA0117.10.0565
MA0119.10.0724
MA0122.10.969
MA0124.10.88
MA0125.10.794
MA0131.10.286
MA0135.10.35
MA0136.11.8694e-8
MA0137.20.0949
MA0138.20.00159
MA0139.10.197
MA0140.10.681
MA0141.10.0386
MA0142.10.575
MA0143.10.186
MA0144.10.133
MA0145.10.0406
MA0146.10.055
MA0147.10.975
MA0148.10.13
MA0149.10.0639
MA0150.10.00163
MA0152.10.0465
MA0153.12.16367e-9
MA0154.10.0117
MA0155.10.993
MA0156.10.00159
MA0157.10.0111
MA0159.10.0317
MA0160.10.0164
MA0162.10.981
MA0163.10.231
MA0164.10.517
MA0258.10.00125
MA0259.10.83



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: CNhs10997

Novel motifP-value
10.11
100.643
1000.731
1010.497
1020.785
1030.262
1040.723
1050.422
1060.0593
1070.654
1080.597
1090.228
110.129
1100.762
1110.0132
1120.178
1130.538
1140.00132
1150.572
1160.666
1170.33
1180.265
1190.178
120.681
1200.23
1210.325
1220.791
1230.0953
1240.578
1250.218
1260.871
1270.0372
1280.0909
1290.26
130.903
1300.269
1310.408
1320.25
1330.404
1340.448
1350.977
1360.676
1370.898
1380.0569
1390.00977
140.267
1400.68
1410.487
1420.648
1430.462
1440.655
1450.898
1460.382
1470.437
1480.593
1490.0589
150.076
1500.894
1510.0371
1520.188
1530.952
1540.406
1550.817
1560.314
1570.611
1580.65
1590.71
1600.727
1610.331
1620.882
1630.0207
1640.504
1650.473
1660.226
1670.996
1680.664
1690.0886
170.152
180.229
190.944
20.715
200.633
210.959
220.429
230.0467
240.445
250.241
260.68
270.473
280.225
290.705
30.39
300.745
310.343
320.0428
330.839
340.612
350.237
360.272
370.225
380.38
390.723
40.488
400.305
410.0466
420.534
430.172
440.0891
450.257
460.303
470.165
480.248
490.135
50.194
500.866
510.527
520.666
530.621
540.33
550.314
560.237
570.874
580.23
590.0671
60.682
600.255
610.925
620.0399
630.126
640.54
650.122
660.819
670.254
680.0696
690.552
70.403
701.68741e-4
710.519
720.161
730.0871
740.964
750.0719
760.768
770.265
780.33
790.342
80.4
800.0762
810.147
820.0296
830.427
840.206
850.0127
860.373
870.0162
880.935
890.0779
90.599
900.291
910.822
920.143
930.773
940.976
950.0848
960.372
970.795
980.157
990.989



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: CNhs10997


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)
0002113 (kidney)
0002100 (trunk)
0000479 (tissue)
0000062 (organ)
0000475 (organism subdivision)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0009569 (subdivision of trunk)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0005172 (abdomen element)
0005173 (abdominal segment element)
0011143 (upper urinary tract)
0001008 (renal system)
0002417 (abdominal segment of trunk)
0000916 (abdomen)

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)
0011350 (mouse kidney- 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:0003104 (mesenchyme)
UBERON:0003918 (kidney mesenchyme)
UBERON:0007687 (kidney field)
FF:0000294 (mouse embryonic day 11 sample)

{{{1}}} Accession numbers
MethodSample accession id
{{{2}}} 
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{4}}} {{{3}}}
Accession ID

Library idBAMCTSS
{{{4}}}
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:434-16F8&oldid=3076447"