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|library_id=CNhs11113
|library_id=CNhs11113
|library_id_phase_based=2:CNhs11113
|library_id_phase_based=2:CNhs11113
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;832
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;832
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N20.CNhs11113.832-19I1.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N20.CNhs11113.832-19I1.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N20.CNhs11113.832-19I1.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/kidney%252c%2520neonate%2520N20.CNhs11113.832-19I1.mm10.nobarcode.ctss.bed.gz

Revision as of 22:37, 18 May 2017


Name:kidney, neonate N20
Species:Mouse (Mus musculus)
Library ID:CNhs11113
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuekidney
dev stage20 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  SAMD00005493
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11113 CAGE DRX009011 DRR009885
Accession ID Mm9

Library idBAMCTSS
CNhs11113 DRZ001310 DRZ002693
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

CNhs11113

00
10
100
1000
10000
10010.1
10020.278
10030.0146
10040
10050
1006-0.143
1007-0.0152
10080
1009-0.0572
101-0.0497
10100
10110
10120
10130.376
10140
1015-0.251
1016-0.138
10170
10180.0598
10190
1020
10200
1021-0.00939
10220.504
10230
10240.353
10250
10260
10270
10280
10290.218
103-0.0424
10300
10310.00537
10320.235
1033-0.0154
10340.281
10350
1036-0.264
10370
10380.133
10390.471
1040
10400.209
10410.0598



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: CNhs11113

Jaspar motifP-value
MA0002.20.202
MA0003.10.227
MA0004.10.499
MA0006.10.0397
MA0007.10.325
MA0009.10.154
MA0014.10.137
MA0017.11.71076e-20
MA0018.26.36402e-6
MA0019.10.198
MA0024.16.12845e-6
MA0025.10.455
MA0027.10.436
MA0028.10.456
MA0029.10.291
MA0030.10.00357
MA0031.15.74045e-4
MA0035.20.00773
MA0038.10.439
MA0039.20.0145
MA0040.10.366
MA0041.10.488
MA0042.10.85
MA0043.10.00169
MA0046.13.1217e-134
MA0047.23.67272e-4
MA0048.10.4
MA0050.10.135
MA0051.10.277
MA0052.10.00275
MA0055.10.372
MA0057.10.5
MA0058.10.401
MA0059.10.594
MA0060.10.00303
MA0061.10.517
MA0062.20.00853
MA0065.22.36056e-12
MA0066.10.606
MA0067.10.25
MA0068.10.268
MA0069.10.719
MA0070.10.588
MA0071.10.00942
MA0072.10.809
MA0073.10.92
MA0074.10.377
MA0076.10.252
MA0077.10.0748
MA0078.10.00384
MA0079.20.796
MA0080.20.263
MA0081.10.57
MA0083.10.0363
MA0084.10.771
MA0087.10.184
MA0088.10.387
MA0090.10.00147
MA0091.10.291
MA0092.10.0388
MA0093.10.495
MA0099.20.787
MA0100.10.0113
MA0101.10.448
MA0102.20.526
MA0103.18.76532e-4
MA0104.20.0787
MA0105.10.345
MA0106.10.452
MA0107.10.607
MA0108.26.03859e-5
MA0111.10.784
MA0112.20.00699
MA0113.10.144
MA0114.11.31053e-28
MA0115.10.00741
MA0116.10.707
MA0117.10.869
MA0119.10.0478
MA0122.10.265
MA0124.10.444
MA0125.10.326
MA0131.10.269
MA0135.10.554
MA0136.10.0245
MA0137.20.677
MA0138.20.621
MA0139.10.197
MA0140.10.0274
MA0141.11.29342e-8
MA0142.10.0142
MA0143.10.734
MA0144.10.294
MA0145.14.40984e-4
MA0146.10.272
MA0147.10.0466
MA0148.17.65113e-4
MA0149.10.0339
MA0150.10.0906
MA0152.10.0491
MA0153.12.02245e-58
MA0154.10.0509
MA0155.10.399
MA0156.10.219
MA0157.10.0168
MA0159.10.0238
MA0160.18.41754e-5
MA0162.10.2
MA0163.10.888
MA0164.10.559
MA0258.10.0323
MA0259.10.126



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: CNhs11113

Novel motifP-value
10.888
100.748
1000.843
1010.851
1020.26
1030.0359
1040.502
1050.611
1060.0943
1070.0805
1080.0535
1090.0347
110.352
1100.215
1110.788
1120.0627
1130.822
1140.644
1150.771
1160.385
1170.363
1180.303
1190.0713
120.951
1200.356
1210.912
1220.281
1230.118
1240.342
1250.635
1260.274
1270.341
1280.115
1290.845
133.5072e-5
1300.168
1310.595
1320.91
1330.156
1340.386
1350.512
1360.105
1370.0535
1380.0322
1390.458
140.156
1400.223
1410.954
1420.552
1430.182
1440.0379
1450.106
1460.241
1470.476
1480.545
1490.285
150.21
1500.105
1510.813
1520.0373
1530.87
1540.632
1550.767
1560.236
1570.216
1580.82
1590.392
1600.236
1610.467
1620.404
1630.822
1640.692
1650.0377
1660.641
1670.812
1680.964
1690.00836
170.0639
180.0973
190.00483
20.0611
200.807
210.911
220.0313
230.289
240.251
250.788
260.36
270.364
280.493
290.692
30.397
300.185
310.523
320.158
330.75
340.621
350.678
360.637
370.0404
380.391
390.432
40.621
400.408
410.291
420.776
430.366
440.966
450.141
460.955
470.613
480.196
490.232
50.802
500.963
510.741
520.0418
530.842
540.89
550.901
560.818
570.931
580.269
590.709
60.647
600.0222
610.662
620.337
630.372
640.963
650.386
660.418
670.0496
680.955
690.863
70.134
700.173
710.769
720.752
730.0951
740.393
750.898
760.376
770.0624
780.108
790.427
80.673
800.463
810.482
820.398
830.293
840.319
850.0767
860.436
870.925
880.407
890.374
90.912
900.63
910.49
920.603
930.498
940.181
950.712
960.554
970.397
980.483
990.239



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: CNhs11113


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)
0000308 (mouse neonate N20 sample)
0011432 (mouse kidney- neonate N20 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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