Personal tools

FF:1385-42H1

From FANTOM5_SSTAR

Revision as of 19:05, 4 June 2020 by Autoedit (talk | contribs)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Name:kidney, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11203
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissuekidney
dev stage30 days neonate
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  SAMD00005811
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11203 CAGE DRX009013 DRR009887
Accession ID Mm9

Library idBAMCTSS
CNhs11203 DRZ001312 DRZ002695
Accession ID Mm10

Library idBAMCTSS
CNhs11203 DRZ012662 DRZ014045
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

CNhs11203

00
10
100
1000
10000.0505
10010.0849
10020.276
1003-0.0712
10040
10050.0569
1006-0.0258
1007-0.0382
10080
10090.0796
101-0.101
10100
1011-0.0212
10120
10130.44
1014-0.0851
1015-0.279
1016-0.171
10170
10180.0505
10190
1020
10200
10210
10220.46
10230
10240.151
10250.0347
10260
10270
10280
10290.0266
103-0.0461
10300
1031-0.0667
10320.331
1033-0.016
10340.55
10350.0505
1036-0.181
10370
10380.0634
10390.563
1040
10400.0767
10410.0958



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: CNhs11203

Jaspar motifP-value
MA0002.20.44
MA0003.10.167
MA0004.10.368
MA0006.10.0259
MA0007.10.161
MA0009.10.2
MA0014.10.125
MA0017.12.75044e-24
MA0018.24.3287e-4
MA0019.10.237
MA0024.13.23945e-6
MA0025.10.108
MA0027.10.28
MA0028.10.766
MA0029.10.737
MA0030.10.00707
MA0031.13.96572e-5
MA0035.20.00833
MA0038.10.574
MA0039.20.00208
MA0040.10.183
MA0041.10.484
MA0042.10.491
MA0043.10.0109
MA0046.13.87088e-152
MA0047.22.44663e-4
MA0048.10.775
MA0050.10.341
MA0051.10.163
MA0052.10.0147
MA0055.10.232
MA0057.10.395
MA0058.10.18
MA0059.10.573
MA0060.10.166
MA0061.10.431
MA0062.20.321
MA0065.24.11967e-14
MA0066.10.885
MA0067.10.593
MA0068.10.258
MA0069.10.451
MA0070.10.949
MA0071.17.42148e-4
MA0072.10.0724
MA0073.10.787
MA0074.10.241
MA0076.10.89
MA0077.10.165
MA0078.10.00219
MA0079.20.245
MA0080.20.234
MA0081.10.591
MA0083.10.01
MA0084.10.643
MA0087.10.16
MA0088.10.337
MA0090.10.00279
MA0091.10.0717
MA0092.10.0915
MA0093.10.388
MA0099.20.79
MA0100.10.0189
MA0101.10.558
MA0102.20.805
MA0103.10.00205
MA0104.20.105
MA0105.10.27
MA0106.10.535
MA0107.10.521
MA0108.20.00314
MA0111.10.476
MA0112.20.0101
MA0113.10.11
MA0114.18.99282e-32
MA0115.14.80393e-4
MA0116.10.468
MA0117.10.564
MA0119.10.0679
MA0122.10.442
MA0124.10.43
MA0125.10.913
MA0131.10.583
MA0135.10.0878
MA0136.10.0813
MA0137.20.582
MA0138.20.504
MA0139.10.255
MA0140.10.0111
MA0141.11.70506e-10
MA0142.10.00237
MA0143.10.998
MA0144.10.17
MA0145.13.55991e-4
MA0146.10.0709
MA0147.10.0514
MA0148.15.01966e-4
MA0149.10.0246
MA0150.10.0184
MA0152.10.0949
MA0153.11.77109e-66
MA0154.10.129
MA0155.10.537
MA0156.10.359
MA0157.10.00104
MA0159.10.0108
MA0160.11.5805e-6
MA0162.10.242
MA0163.10.759
MA0164.10.417
MA0258.10.0203
MA0259.10.163



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: CNhs11203

Novel motifP-value
10.904
100.734
1000.882
1010.689
1020.221
1030.0975
1040.452
1050.66
1060.143
1070.17
1080.0508
1090.00748
110.238
1100.257
1110.963
1120.118
1130.728
1140.829
1150.937
1160.392
1170.596
1180.275
1190.0786
120.91
1200.406
1210.856
1220.0785
1230.041
1240.22
1250.159
1260.304
1270.237
1280.178
1290.736
133.39565e-5
1300.173
1310.687
1320.871
1330.193
1340.552
1350.43
1360.00412
1370.0954
1380.125
1390.729
140.179
1400.265
1410.81
1420.836
1430.362
1440.0742
1450.178
1460.257
1470.411
1480.883
1490.228
150.274
1500.198
1510.82
1520.0366
1530.652
1540.835
1550.899
1560.0153
1570.213
1580.596
1590.659
1600.57
1610.437
1620.344
1630.311
1640.997
1650.00852
1660.624
1670.818
1680.799
1690.0137
170.058
180.049
190.0244
20.109
200.933
210.817
220.0252
230.633
240.114
250.771
260.515
270.502
280.512
290.715
30.462
300.157
310.598
320.319
330.897
340.508
350.421
360.668
370.0264
380.444
390.386
40.673
400.215
410.36
420.611
430.506
440.669
450.11
460.826
470.381
480.184
490.433
50.513
500.728
510.798
520.0396
530.945
540.975
550.995
560.993
570.442
580.291
590.717
60.996
600.0376
610.92
620.381
630.262
640.951
650.349
660.713
670.0223
680.947
690.486
70.188
700.28
710.766
720.437
730.0356
740.232
750.58
760.375
770.0542
780.0987
790.37
80.755
800.465
810.366
820.297
830.424
840.0711
850.061
860.461
870.134
880.58
890.466
90.967
900.612
910.502
920.98
930.548
940.0652
950.252
960.538
970.384
980.338
990.248



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: CNhs11203


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)
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)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011483 (mouse kidney- neonate N30 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:1385-42H1&oldid=4578121"