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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;483
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;483
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;483
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;483
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E17.CNhs11028.483-18I2.mm10.nobarcode.bam  
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E17.CNhs11028.483-18I2.mm10.nobarcode.bam  
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E17.CNhs11028.483-18I2.mm10.nobarcode.ctss.bed.gz  
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520embryo%2520E17.CNhs11028.483-18I2.mm10.nobarcode.ctss.bed.gz  

Revision as of 18:45, 4 August 2017


Name:kidney, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs11028
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuekidney
dev stage17 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  SAMD00005742
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11028 CAGE DRX009007 DRR009881
Accession ID Mm9

Library idBAMCTSS
CNhs11028 DRZ001306 DRZ002689
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

CNhs11028

00
10
100
1000
10000
10010.0395
10020.504
10030.00599
10040
1005-0.0382
10060.0366
10070.111
10080
10090.0171
1010.0824
10100
10110
10120
1013-0.0296
10140.305
10150.143
10160.206
10170
10180
10190
1020
10200
10210
10220.0216
10230
10240.0805
10250.12
10260
10270
10280
10290.321
1030.0907
10300
10310.353
10320.0135
10330.014
10340
10350.0805
10360.164
10370
10380.053
10390.0305
1040
10400.195
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: CNhs11028

Jaspar motifP-value
MA0002.20.00344
MA0003.10.848
MA0004.10.481
MA0006.10.464
MA0007.10.492
MA0009.10.563
MA0014.10.788
MA0017.10.182
MA0018.25.0839e-6
MA0019.10.812
MA0024.19.40417e-6
MA0025.11.31749e-4
MA0027.10.548
MA0028.10.674
MA0029.10.199
MA0030.10.722
MA0031.10.31
MA0035.22.59498e-5
MA0038.10.484
MA0039.20.172
MA0040.10.409
MA0041.10.177
MA0042.10.437
MA0043.10.00157
MA0046.12.35814e-69
MA0047.20.942
MA0048.11.68431e-4
MA0050.12.98739e-4
MA0051.13.30283e-5
MA0052.10.0028
MA0055.10.00282
MA0057.10.531
MA0058.10.35
MA0059.10.864
MA0060.10.0067
MA0061.10.088
MA0062.22.00038e-4
MA0065.20.639
MA0066.10.968
MA0067.10.0594
MA0068.10.737
MA0069.10.0947
MA0070.10.64
MA0071.10.237
MA0072.10.00466
MA0073.10.789
MA0074.10.737
MA0076.10.187
MA0077.10.436
MA0078.10.0878
MA0079.20.165
MA0080.22.23609e-8
MA0081.10.0789
MA0083.10.215
MA0084.10.883
MA0087.10.847
MA0088.10.987
MA0090.10.0753
MA0091.10.651
MA0092.10.654
MA0093.10.507
MA0099.27.54449e-5
MA0100.10.158
MA0101.10.251
MA0102.20.0138
MA0103.10.359
MA0104.20.273
MA0105.10.771
MA0106.10.89
MA0107.10.124
MA0108.20.36
MA0111.10.369
MA0112.20.394
MA0113.10.744
MA0114.10.0642
MA0115.10.893
MA0116.10.215
MA0117.10.0089
MA0119.10.404
MA0122.10.317
MA0124.10.825
MA0125.10.662
MA0131.10.555
MA0135.10.633
MA0136.11.53564e-11
MA0137.20.0313
MA0138.20.06
MA0139.10.984
MA0140.10.0238
MA0141.10.902
MA0142.10.131
MA0143.10.834
MA0144.10.181
MA0145.10.864
MA0146.10.453
MA0147.10.276
MA0148.10.479
MA0149.10.0924
MA0150.10.00667
MA0152.10.0373
MA0153.16.47626e-31
MA0154.10.291
MA0155.10.0756
MA0156.15.4675e-8
MA0157.10.337
MA0159.10.43
MA0160.10.272
MA0162.10.261
MA0163.10.433
MA0164.10.895
MA0258.10.048
MA0259.10.601



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: CNhs11028

Novel motifP-value
10.0808
100.765
1000.656
1010.827
1020.612
1030.89
1040.643
1050.944
1060.523
1070.254
1080.503
1090.691
110.175
1100.999
1110.0553
1120.865
1130.541
1140.00503
1150.787
1160.583
1170.0949
1180.141
1190.319
120.644
1200.265
1210.379
1220.976
1230.0546
1240.984
1250.204
1260.768
1270.0541
1280.467
1290.281
130.051
1300.228
1310.113
1320.183
1330.388
1340.624
1350.621
1360.503
1370.287
1380.0159
1390.105
140.377
1400.54
1410.836
1420.317
1430.481
1440.335
1450.251
1460.376
1470.189
1480.55
1490.273
150.103
1500.31
1510.0262
1520.819
1530.337
1540.154
1550.794
1560.39
1570.899
1580.783
1590.173
1600.186
1610.579
1620.388
1630.099
1640.396
1650.659
1660.205
1670.739
1680.897
1690.44
170.458
180.0445
190.211
20.539
200.805
210.985
220.629
230.334
240.779
250.307
260.593
270.759
280.164
290.594
30.921
300.97
310.41
320.138
330.966
340.988
350.0768
360.0543
370.717
380.557
390.455
40.969
400.0925
410.0544
420.67
430.257
440.399
450.565
460.576
470.291
480.408
490.193
50.253
500.443
510.647
520.62
530.641
540.303
550.192
560.238
570.934
580.597
590.304
60.93
600.996
610.534
620.0998
630.258
640.6
650.276
660.713
670.0807
680.0618
690.759
70.997
700.00536
710.749
720.159
730.202
740.913
750.135
760.935
770.935
780.374
790.464
80.349
800.038
810.277
820.164
830.449
840.86
850.165
860.49
878.82079e-5
880.848
890.397
90.843
900.505
910.872
920.28
930.761
940.555
950.0937
960.637
970.918
980.2
990.748



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: CNhs11028


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)
0000300 (mouse embryonic day 17 sample)
0011371 (mouse kidney- embryo E17 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)

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