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|sample_category=developmental
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Revision as of 15:53, 26 December 2012


Name:kidney, neonate N10
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuekidney
dev stage10 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
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

CNhs11206

00
10
100
1000
1000-0.00962
10010.104
10020.691
1003-0.00321
10040
10050
1006-0.0988
10070.112
10080
10090.0897
101-0.0384
10100
1011-0.0201
10120.0266
10130.277
10140.0263
1015-0.0369
10160.181
10170
10180.0517
10190
1020
10200
10210
10220.288
10230
10240.14
10250
10260
10270
10280
10290.231
1030.0615
10300.0266
10310.241
10320.193
1033-0.0235
10340.0979
10350.0517
1036-0.0855
10370
10380.21
10390.167
1040
10400.305
10410.0266



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: CNhs11206

Jaspar motifP-value
MA0002.20.016
MA0003.10.256
MA0004.10.435
MA0006.10.0471
MA0007.10.636
MA0009.10.562
MA0014.10.425
MA0017.12.67397e-9
MA0018.23.08214e-5
MA0019.10.215
MA0024.10.619
MA0025.10.694
MA0027.10.488
MA0028.10.376
MA0029.10.352
MA0030.10.00476
MA0031.10.011
MA0035.27.73336e-4
MA0038.10.575
MA0039.20.0428
MA0040.10.964
MA0041.10.543
MA0042.10.918
MA0043.10.012
MA0046.17.35536e-132
MA0047.20.0135
MA0048.10.368
MA0050.10.84
MA0051.10.683
MA0052.10.00296
MA0055.10.135
MA0057.10.873
MA0058.10.428
MA0059.10.00874
MA0060.10.359
MA0061.10.119
MA0062.20.00931
MA0065.20.0725
MA0066.10.188
MA0067.10.285
MA0068.10.361
MA0069.10.172
MA0070.10.855
MA0071.10.588
MA0072.10.594
MA0073.10.542
MA0074.10.822
MA0076.10.289
MA0077.10.301
MA0078.10.00128
MA0079.20.122
MA0080.20.0754
MA0081.10.361
MA0083.10.203
MA0084.10.869
MA0087.10.383
MA0088.10.648
MA0090.17.35474e-4
MA0091.10.0915
MA0092.10.0859
MA0093.10.459
MA0099.20.0616
MA0100.10.0505
MA0101.10.582
MA0102.20.43
MA0103.10.363
MA0104.20.00135
MA0105.10.00256
MA0106.10.886
MA0107.10.836
MA0108.20.0156
MA0111.10.225
MA0112.20.31
MA0113.10.363
MA0114.12.80232e-10
MA0115.10.238
MA0116.11.95966e-4
MA0117.10.432
MA0119.10.707
MA0122.10.42
MA0124.10.655
MA0125.10.329
MA0131.10.686
MA0135.10.767
MA0136.10.00531
MA0137.20.914
MA0138.20.251
MA0139.10.909
MA0140.10.00624
MA0141.10.0642
MA0142.10.0154
MA0143.10.713
MA0144.10.522
MA0145.11.75271e-4
MA0146.10.518
MA0147.11.02071e-4
MA0148.10.0915
MA0149.10.842
MA0150.10.456
MA0152.10.0209
MA0153.12.04009e-58
MA0154.10.971
MA0155.10.328
MA0156.10.107
MA0157.10.112
MA0159.10.538
MA0160.10.471
MA0162.10.499
MA0163.10.00978
MA0164.10.582
MA0258.10.308
MA0259.10.0503



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: CNhs11206

Novel motifP-value
10.0782
100.0666
1000.811
1010.614
1020.176
1030.918
1040.642
1050.69
1060.706
1070.11
1080.0294
1090.97
110.261
1100.721
1110.0726
1120.472
1130.889
1140.0261
1150.511
1160.144
1170.012
1180.0342
1190.771
120.631
1200.178
1210.813
1220.335
1230.0495
1240.26
1250.101
1260.587
1270.105
1280.637
1290.782
130.0466
1300.0761
1310.524
1320.755
1330.276
1340.585
1350.94
1360.0847
1370.0356
1380.00705
1390.333
140.384
1400.971
1410.642
1420.201
1430.237
1440.0854
1450.556
1460.535
1470.522
1480.525
1490.898
150.676
1500.15
1510.219
1520.0574
1530.685
1540.863
1550.42
1560.347
1570.516
1580.498
1590.288
1600.647
1610.995
1620.282
1630.955
1640.263
1650.151
1660.669
1670.352
1680.932
1690.128
170.997
180.00397
190.0506
20.154
200.711
210.42
220.244
230.98
240.62
250.465
260.845
270.807
280.844
290.0729
30.569
300.224
310.658
320.0158
330.622
340.447
350.0188
360.0876
370.918
380.829
390.455
40.926
400.924
410.109
420.361
430.315
440.28
450.339
460.245
470.193
480.665
490.207
50.173
500.737
510.88
520.0683
530.837
540.477
550.664
560.318
570.438
580.978
590.58
60.781
600.229
610.886
620.253
630.657
640.291
650.585
660.701
670.0446
680.204
690.583
70.894
700.171
710.0432
720.288
730.876
740.222
750.115
760.246
770.506
780.961
790.218
80.0291
800.113
810.207
820.139
830.174
840.607
850.713
860.924
870.256
880.308
890.603
90.972
900.297
910.99
920.243
930.722
940.0816
950.421
960.462
970.321
980.9
990.736



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: CNhs11206


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)
0000305 (mouse neonate N10 sample)
0011419 (mouse kidney- neonate N10 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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