Personal tools

FF:464-22A5: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005783
|DRA_sample_Accession=CAGE@SAMD00005783
|accession_numbers=CAGE;DRX009006;DRR009880;DRZ001305;DRZ002688
|accession_numbers=CAGE;DRX009006;DRR009880;DRZ001305;DRZ002688;DRZ012655;DRZ014038
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002113,UBERON:0002100,UBERON:0000479,UBERON:0000062,UBERON:0000475,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0009569,UBERON:0000489,UBERON:0005177,UBERON:0005172,UBERON:0005173,UBERON:0011143,UBERON:0001008,UBERON:0002417,UBERON:0000916
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002113,UBERON:0002100,UBERON:0000479,UBERON:0000062,UBERON:0000475,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0009569,UBERON:0000489,UBERON:0005177,UBERON:0005172,UBERON:0005173,UBERON:0011143,UBERON:0001008,UBERON:0002417,UBERON:0000916
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=

Revision as of 22:36, 10 August 2017


Name:kidney, embryo E16
Species:Mouse (Mus musculus)
Library ID:CNhs10584
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuekidney
dev stage16 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  SAMD00005783
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10584 CAGE DRX009006 DRR009880
Accession ID Mm9

Library idBAMCTSS
CNhs10584 DRZ001305 DRZ002688
Accession ID Mm10

Library idBAMCTSS
CNhs10584 DRZ012655 DRZ014038
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

CNhs10584

00
10
100
1000
1000-0.0355
1001-0.0631
10020.0614
1003-0.123
10040
1005-0.201
1006-0.143
10070.137
10080
10090.0681
1010.0864
10100
1011-0.00937
10120
1013-0.0717
10140
10150.21
10160.111
10170
10180
10190
1020
10200
10210
1022-0.0704
10230
10240
10250
10260.0674
1027-0.048
10280
1029-0.148
1030
10300
10310.338
10320.086
1033-0.0665
10340
10350
10360.042
10370
1038-0.0289
1039-0.129
1040
10400.166
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: CNhs10584

Jaspar motifP-value
MA0002.20.0369
MA0003.10.6
MA0004.10.535
MA0006.10.793
MA0007.10.862
MA0009.10.344
MA0014.10.147
MA0017.10.851
MA0018.20.0736
MA0019.10.451
MA0024.16.63102e-7
MA0025.10.0386
MA0027.10.829
MA0028.10.935
MA0029.10.21
MA0030.10.599
MA0031.10.838
MA0035.27.80504e-4
MA0038.10.041
MA0039.20.908
MA0040.10.796
MA0041.10.204
MA0042.10.611
MA0043.10.204
MA0046.11.82509e-56
MA0047.20.412
MA0048.10.0837
MA0050.11.15639e-6
MA0051.16.03886e-4
MA0052.13.7009e-5
MA0055.10.0387
MA0057.10.494
MA0058.10.494
MA0059.10.358
MA0060.18.07892e-9
MA0061.10.687
MA0062.20.123
MA0065.20.0894
MA0066.10.136
MA0067.10.24
MA0068.10.946
MA0069.10.206
MA0070.10.779
MA0071.10.144
MA0072.10.145
MA0073.10.905
MA0074.10.979
MA0076.10.858
MA0077.10.301
MA0078.10.918
MA0079.20.967
MA0080.20.00189
MA0081.10.364
MA0083.10.98
MA0084.10.174
MA0087.10.847
MA0088.10.846
MA0090.10.328
MA0091.10.29
MA0092.10.734
MA0093.10.508
MA0099.20.0253
MA0100.10.515
MA0101.10.392
MA0102.20.0864
MA0103.10.302
MA0104.20.0656
MA0105.10.343
MA0106.10.139
MA0107.10.59
MA0108.20.0747
MA0111.10.646
MA0112.20.00959
MA0113.10.296
MA0114.10.81
MA0115.10.369
MA0116.10.00773
MA0117.10.0213
MA0119.10.0745
MA0122.10.734
MA0124.10.992
MA0125.10.842
MA0131.10.691
MA0135.10.361
MA0136.10.00333
MA0137.20.339
MA0138.20.00849
MA0139.10.279
MA0140.10.0357
MA0141.10.175
MA0142.10.219
MA0143.10.13
MA0144.10.717
MA0145.10.546
MA0146.10.34
MA0147.10.0869
MA0148.10.573
MA0149.10.0373
MA0150.10.0217
MA0152.10.0855
MA0153.17.76624e-34
MA0154.10.11
MA0155.10.12
MA0156.10.107
MA0157.10.513
MA0159.10.0413
MA0160.10.336
MA0162.10.359
MA0163.10.0753
MA0164.10.938
MA0258.10.00883
MA0259.10.606



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: CNhs10584

Novel motifP-value
10.00482
100.638
1000.714
1010.996
1020.545
1030.108
1040.62
1050.893
1060.4
1070.882
1080.936
1090.121
110.0993
1100.523
1110.00766
1120.483
1130.986
1140.00649
1150.0727
1160.32
1170.0546
1180.0496
1190.441
120.972
1200.201
1210.858
1220.629
1230.0175
1240.935
1250.236
1260.997
1270.288
1280.117
1290.531
130.84
1300.351
1310.234
1320.74
1330.649
1340.227
1350.862
1360.0897
1370.295
1380.186
1390.00677
140.684
1400.48
1410.889
1420.153
1430.536
1440.24
1450.912
1460.95
1470.774
1480.597
1490.484
150.0912
1500.185
1510.101
1520.973
1530.845
1540.611
1550.943
1560.107
1570.877
1580.997
1590.873
1600.532
1610.21
1620.756
1630.0793
1640.424
1650.808
1660.49
1670.133
1680.329
1690.988
170.531
180.108
190.571
20.659
200.942
210.554
220.792
230.0998
240.704
250.347
260.547
270.817
280.111
290.284
30.182
300.387
310.343
320.083
330.463
340.861
350.0199
360.19
370.157
380.727
390.567
40.752
400.707
410.233
420.432
430.145
440.0287
450.931
460.307
470.0455
480.171
490.0978
50.0959
500.418
510.659
520.687
530.899
540.192
550.54
560.341
570.143
580.25
590.187
60.978
600.976
610.916
620.063
630.279
640.665
650.268
660.579
670.409
680.0956
690.365
70.511
700.00287
710.377
720.531
730.198
740.954
750.071
760.351
770.696
780.779
790.757
80.0813
800.3
810.149
820.0559
830.344
840.318
850.13
860.674
870.113
880.765
890.502
90.688
900.0705
910.381
920.0325
930.565
940.321
950.124
960.326
970.436
980.401
990.779



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: CNhs10584


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)
0000299 (mouse embryonic day 16 sample)
0011363 (mouse kidney- embryo E16 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:464-22A5&oldid=4345865"