Personal tools

FF:411-4I9: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 48: Line 48:
|profile_rnaseq=,,,
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|repeat_enrich_byfamily=0.0177292598321035,0,0,0,0,0,-0.570764676537707,0,0,0,0,0.160845510961369,0,0,0,0,0,0,0.00373061764345689,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.418752783464148,0,0,0,0.24518475135791,0,-0.139487721065885,0,-0.202907513775371,-0.468865509863558,0.245477218603917,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0,0,0,-0.00192807751944503,-0.145748560213918,-0.115026688813355,-0.158091042771083,-0.0663821023609715,0,-0.0780086007519514,-0.0294170999679055,0,0,0,0,-0.230994980909835,-0.0110164454100559,-0.0788315948399074,0,0,0,0,0,0,-0.0567576797734015,-0.275053764368594,-0.0493986422894283,0,0,0,0,0
|rna_box=4
|rna_box=4
|rna_catalog_number=
|rna_catalog_number=

Revision as of 10:42, 24 September 2012


Name:kidney, embryo E14
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuekidney
dev stage14 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

CNhs10606

00
10
100
1000
1000-0.00177
1001-0.0749
10020.126
1003-0.0754
10040
1005-0.0575
1006-0.108
10070.141
10080
1009-0.0145
1010.0657
10100
10110
10120
1013-0.143
10140.14
10150.307
10160.226
10170
10180
10190
1020
10200.0754
10210.14
1022-0.109
10230
1024-0.0496
10250.0348
10260
10270
10280
1029-0.148
1030.0223
10300
10310.359
1032-0.0175
10330.00893
10340
10350
10360.081
10370
1038-0.166
1039-0.104
1040
10400.0558
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: CNhs10606

Jaspar motifP-value
MA0002.20.149
MA0003.10.379
MA0004.10.659
MA0006.10.901
MA0007.10.55
MA0009.10.312
MA0014.10.336
MA0017.10.031
MA0018.20.317
MA0019.10.32
MA0024.14.63847e-6
MA0025.10.477
MA0027.10.0733
MA0028.10.00113
MA0029.10.396
MA0030.10.585
MA0031.10.297
MA0035.20.0876
MA0038.10.0439
MA0039.20.672
MA0040.10.902
MA0041.10.198
MA0042.10.676
MA0043.10.0775
MA0046.15.15563e-8
MA0047.20.361
MA0048.10.0139
MA0050.17.65232e-8
MA0051.14.2583e-5
MA0052.10.0263
MA0055.16.61729e-4
MA0057.10.63
MA0058.10.332
MA0059.10.248
MA0060.11.38014e-17
MA0061.10.343
MA0062.20.00276
MA0065.20.21
MA0066.10.167
MA0067.10.118
MA0068.10.818
MA0069.10.143
MA0070.10.214
MA0071.10.445
MA0072.10.0424
MA0073.10.833
MA0074.10.193
MA0076.10.00356
MA0077.10.0345
MA0078.10.703
MA0079.20.691
MA0080.20.00316
MA0081.10.833
MA0083.10.0165
MA0084.10.531
MA0087.10.949
MA0088.10.698
MA0090.10.456
MA0091.10.628
MA0092.10.387
MA0093.10.612
MA0099.20.0653
MA0100.10.766
MA0101.10.734
MA0102.20.119
MA0103.10.0728
MA0104.20.126
MA0105.10.764
MA0106.10.137
MA0107.10.565
MA0108.20.0774
MA0111.10.55
MA0112.20.00817
MA0113.10.739
MA0114.10.0644
MA0115.10.434
MA0116.10.453
MA0117.10.0502
MA0119.10.0229
MA0122.10.964
MA0124.10.736
MA0125.10.422
MA0131.10.108
MA0135.10.0111
MA0136.10.713
MA0137.20.932
MA0138.20.011
MA0139.10.658
MA0140.10.05
MA0141.10.0939
MA0142.10.452
MA0143.10.126
MA0144.10.888
MA0145.10.731
MA0146.10.488
MA0147.10.0904
MA0148.10.027
MA0149.10.109
MA0150.10.00459
MA0152.10.96
MA0153.17.41388e-4
MA0154.10.0244
MA0155.10.0991
MA0156.10.626
MA0157.10.214
MA0159.10.234
MA0160.10.243
MA0162.10.41
MA0163.10.791
MA0164.10.779
MA0258.10.00438
MA0259.10.488



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: CNhs10606

Novel motifP-value
10.0143
100.344
1000.659
1010.664
1020.946
1030.0373
1040.963
1050.445
1060.031
1070.291
1080.731
1090.927
110.383
1100.834
1110.0118
1120.21
1130.382
1140.00704
1150.765
1160.62
1170.9
1180.243
1190.172
120.812
1200.766
1210.462
1220.697
1230.0751
1240.552
1250.271
1260.837
1270.0116
1280.121
1290.0746
130.793
1300.621
1310.78
1320.42
1330.815
1340.306
1350.572
1360.0568
1370.263
1380.28
1390.00147
140.202
1400.0295
1410.427
1420.0126
1430.656
1440.478
1450.957
1460.904
1470.361
1480.34
1490.299
150.109
1500.586
1510.0765
1520.316
1530.116
1540.42
1550.528
1560.132
1570.93
1580.389
1590.0614
1600.995
1610.431
1620.922
1630.058
1640.427
1650.916
1660.324
1670.132
1680.391
1690.867
170.217
180.426
190.775
20.759
200.508
210.575
220.821
230.0122
240.612
250.441
260.756
270.816
280.157
290.834
30.279
300.65
310.375
320.345
330.333
340.657
350.054
360.91
370.434
380.491
390.844
40.966
400.421
410.574
420.392
430.135
440.707
450.788
460.278
470.334
480.479
490.0601
50.0832
500.346
510.373
520.666
530.671
540.245
550.433
560.322
570.376
580.206
590.578
60.724
600.447
610.942
620.053
630.281
640.935
650.379
660.113
670.429
680.237
690.541
70.423
700.0164
710.691
720.787
730.637
740.672
750.551
760.719
770.714
780.779
790.556
80.621
800.111
810.295
820.105
830.193
840.424
850.0161
860.982
870.0541
880.981
890.288
90.456
900.00158
910.335
920.0306
930.533
940.136
950.947
960.174
970.673
980.287
990.778



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: CNhs10606


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)
0000296 (mouse embryonic day 14 sample)
0011341 (mouse kidney- embryo E14 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)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:411-4I9&oldid=2141530"