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|is_obsolete=
|is_obsolete=
|library_id=CNhs11214
|library_id=CNhs11214
|library_ids=CNhs11214
|name=kidney, neonate N00
|name=kidney, neonate N00
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 17:28, 25 October 2013


Name:kidney, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11214
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuekidney
dev stage0 day 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  DRS008872
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11214 CAGE DRX009009 DRR009883
Accession ID Mm9

Library idBAMCTSS
CNhs11214 DRZ001308 DRZ002691
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

CNhs11214

00
10
100
1000
1000-0.00633
10010.0621
10020.435
1003-0.0236
10040
10050
1006-0.0619
10070.134
10080
10090.107
1010.0246
10100
10110
10120.0324
10130.129
10140.173
10150.065
10160.302
10170
10180
10190
1020
10200
10210.0294
10220.136
10230
10240.0829
10250.107
10260
10270.0294
10280.0294
10290.296
1030.113
10300
10310.288
10320.0498
1033-0.00949
10340.0873
10350.0294
1036-0.0676
10370
10380.194
10390.104
1040
10400.216
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: CNhs11214

Jaspar motifP-value
MA0002.20.00414
MA0003.10.646
MA0004.10.674
MA0006.10.275
MA0007.10.638
MA0009.10.734
MA0014.10.816
MA0017.10.00364
MA0018.20.00155
MA0019.10.534
MA0024.10.109
MA0025.10.105
MA0027.10.839
MA0028.10.156
MA0029.10.351
MA0030.10.0316
MA0031.10.0634
MA0035.21.63583e-4
MA0038.10.282
MA0039.20.715
MA0040.10.77
MA0041.10.451
MA0042.10.944
MA0043.10.0115
MA0046.18.40061e-100
MA0047.20.101
MA0048.10.154
MA0050.10.221
MA0051.10.216
MA0052.13.41175e-5
MA0055.10.101
MA0057.10.531
MA0058.10.526
MA0059.10.0322
MA0060.10.18
MA0061.10.0424
MA0062.25.64293e-4
MA0065.20.914
MA0066.10.137
MA0067.10.362
MA0068.10.73
MA0069.10.0711
MA0070.10.734
MA0071.10.491
MA0072.10.11
MA0073.10.613
MA0074.10.577
MA0076.10.126
MA0077.10.767
MA0078.10.0119
MA0079.20.227
MA0080.27.08709e-5
MA0081.10.0429
MA0083.10.619
MA0084.10.912
MA0087.10.684
MA0088.10.084
MA0090.10.054
MA0091.10.083
MA0092.10.8
MA0093.10.68
MA0099.20.0262
MA0100.10.0622
MA0101.10.449
MA0102.20.277
MA0103.10.718
MA0104.20.0114
MA0105.19.59455e-5
MA0106.10.523
MA0107.10.428
MA0108.20.0937
MA0111.10.622
MA0112.20.012
MA0113.10.227
MA0114.10.0141
MA0115.10.661
MA0116.15.42836e-5
MA0117.10.301
MA0119.10.0983
MA0122.10.504
MA0124.10.8
MA0125.10.575
MA0131.10.513
MA0135.10.974
MA0136.11.69119e-6
MA0137.20.317
MA0138.20.0624
MA0139.10.172
MA0140.10.00111
MA0141.10.744
MA0142.10.00993
MA0143.10.942
MA0144.10.71
MA0145.10.547
MA0146.10.694
MA0147.10.00399
MA0148.10.674
MA0149.10.242
MA0150.10.0875
MA0152.10.012
MA0153.13.14361e-47
MA0154.10.027
MA0155.10.559
MA0156.12.24819e-4
MA0157.10.26
MA0159.10.225
MA0160.10.652
MA0162.10.903
MA0163.14.18277e-4
MA0164.10.866
MA0258.10.0166
MA0259.10.261



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: CNhs11214

Novel motifP-value
10.0208
100.128
1000.83
1010.291
1020.356
1030.668
1040.971
1050.648
1060.754
1070.126
1080.228
1090.314
110.119
1100.186
1110.0162
1120.648
1130.997
1140.0389
1150.604
1160.164
1170.0117
1180.215
1190.581
120.651
1200.286
1210.908
1220.54
1230.0841
1240.533
1250.115
1260.691
1270.187
1280.847
1290.328
130.771
1300.282
1310.276
1320.914
1330.254
1340.643
1350.806
1360.174
1370.0756
1380.00533
1390.12
140.778
1400.943
1410.486
1420.311
1430.228
1440.46
1450.913
1460.682
1470.419
1480.83
1490.373
150.219
1500.297
1510.0902
1520.177
1530.39
1540.743
1550.947
1564.07844e-7
1570.889
1580.93
1590.118
1600.806
1610.834
1620.305
1630.232
1640.278
1650.401
1660.574
1670.717
1680.637
1690.774
170.654
180.0211
190.391
20.414
200.824
210.624
220.894
230.233
240.706
250.114
260.672
270.743
280.309
290.0522
30.35
300.426
310.615
320.0727
330.686
340.913
350.0709
360.0177
370.427
380.361
390.279
40.91
400.332
410.0849
420.272
430.22
440.206
450.771
460.213
470.0993
480.324
490.196
50.216
500.679
510.616
520.135
530.649
540.328
550.216
560.25
570.351
580.526
590.142
60.785
600.605
610.963
620.0672
630.274
640.196
650.128
660.546
670.0166
680.126
690.595
70.453
700.0374
710.0368
720.231
730.566
740.267
750.0259
760.738
770.955
780.824
790.282
80.0547
800.0487
810.113
820.0871
830.119
840.654
850.0868
860.291
870.00289
880.456
890.349
90.821
900.17
910.831
920.259
930.681
940.0673
950.256
960.228
970.561
980.513
990.962



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: CNhs11214


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)
0000304 (mouse neonate N0 sample)
0011396 (mouse kidney- neonate N00 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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