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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008871
|DRA_sample_Accession=CAGE@SAMD00005277
|accession_numbers=CAGE;DRX009008;DRR009882;DRZ001307;DRZ002690
|accession_numbers=CAGE;DRX009008;DRR009882;DRZ001307;DRZ002690
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002113,UBERON:0002100,UBERON:0000479,UBERON:0000062,UBERON:0000475,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0009569,UBERON:0000489,UBERON:0005177,UBERON:0005172,UBERON:0005173,UBERON:0011143,UBERON:0001008,UBERON:0002417,UBERON:0000916
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0002113,UBERON:0002100,UBERON:0000479,UBERON:0000062,UBERON:0000475,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0009569,UBERON:0000489,UBERON:0005177,UBERON:0005172,UBERON:0005173,UBERON:0011143,UBERON:0001008,UBERON:0002417,UBERON:0000916

Revision as of 21:29, 31 July 2014


Name:kidney, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs11001
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuekidney
dev stage18 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  SAMD00005277
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11001 CAGE DRX009008 DRR009882
Accession ID Mm9

Library idBAMCTSS
CNhs11001 DRZ001307 DRZ002690
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

CNhs11001

00
10
100
1000
10000
10010.051
10020.546
10030.00188
10040
1005-0.0389
1006-0.0464
10070.0846
10080
10090.0615
1010.0371
10100
10110.0324
10120
10130.143
10140.156
10150.142
10160.117
10170
10180
10190
1020
10200
1021-0.0487
10220.077
10230
10240.077
10250.142
10260
10270
10280.077
10290.351
1030.111
10300
10310.29
10320.0701
10330.133
10340
10350.077
10360.06
10370
10380.0307
10390.0744
1040
10400.173
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: CNhs11001

Jaspar motifP-value
MA0002.20.00202
MA0003.10.689
MA0004.10.687
MA0006.10.332
MA0007.10.683
MA0009.10.568
MA0014.10.803
MA0017.10.00452
MA0018.22.40895e-5
MA0019.10.328
MA0024.17.92733e-4
MA0025.10.00383
MA0027.10.998
MA0028.10.51
MA0029.10.207
MA0030.10.702
MA0031.10.689
MA0035.28.87645e-6
MA0038.10.388
MA0039.20.553
MA0040.10.545
MA0041.10.25
MA0042.10.638
MA0043.10.0023
MA0046.11.18331e-88
MA0047.20.623
MA0048.13.7845e-4
MA0050.10.124
MA0051.10.0596
MA0052.11.87829e-5
MA0055.14.29493e-4
MA0057.10.645
MA0058.10.566
MA0059.10.819
MA0060.10.00328
MA0061.10.101
MA0062.22.3339e-4
MA0065.20.991
MA0066.10.463
MA0067.10.116
MA0068.10.979
MA0069.10.0653
MA0070.10.739
MA0071.10.475
MA0072.10.0586
MA0073.10.682
MA0074.10.634
MA0076.10.154
MA0077.10.34
MA0078.10.0329
MA0079.20.208
MA0080.23.64623e-5
MA0081.10.0797
MA0083.10.501
MA0084.10.755
MA0087.10.928
MA0088.10.915
MA0090.10.0211
MA0091.10.575
MA0092.10.524
MA0093.10.655
MA0099.29.54234e-4
MA0100.10.0803
MA0101.10.379
MA0102.20.0779
MA0103.10.723
MA0104.20.184
MA0105.10.397
MA0106.10.677
MA0107.10.204
MA0108.20.0148
MA0111.10.774
MA0112.20.492
MA0113.10.566
MA0114.18.50727e-4
MA0115.10.923
MA0116.10.112
MA0117.10.0156
MA0119.10.501
MA0122.10.367
MA0124.10.896
MA0125.10.736
MA0131.10.65
MA0135.10.55
MA0136.11.13604e-7
MA0137.20.318
MA0138.20.00761
MA0139.10.928
MA0140.16.0058e-4
MA0141.10.596
MA0142.10.0932
MA0143.10.512
MA0144.10.429
MA0145.10.302
MA0146.10.415
MA0147.10.155
MA0148.10.56
MA0149.10.317
MA0150.10.0201
MA0152.10.0237
MA0153.11.31386e-38
MA0154.10.699
MA0155.10.286
MA0156.16.48259e-5
MA0157.10.796
MA0159.10.475
MA0160.10.416
MA0162.10.204
MA0163.10.575
MA0164.10.985
MA0258.10.0684
MA0259.10.651



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: CNhs11001

Novel motifP-value
10.0597
100.963
1000.493
1010.527
1020.494
1030.563
1040.524
1050.913
1060.709
1070.476
1080.281
1090.602
110.18
1100.852
1110.0688
1120.55
1130.719
1140.00717
1150.831
1160.311
1170.0774
1180.269
1190.963
120.583
1200.241
1210.505
1220.956
1230.0983
1240.506
1250.147
1260.394
1270.0801
1280.752
1290.583
130.0468
1300.256
1310.298
1320.636
1330.55
1340.63
1350.847
1360.266
1370.284
1380.0258
1390.226
140.492
1400.999
1410.998
1420.0917
1430.37
1440.196
1450.386
1460.553
1470.145
1480.711
1490.606
150.254
1500.229
1510.0163
1520.407
1530.475
1540.359
1550.639
1560.0244
1570.815
1580.517
1590.279
1600.157
1610.769
1620.672
1630.0881
1640.194
1650.21
1660.156
1670.746
1680.656
1690.252
170.622
180.0312
190.0578
20.461
200.712
210.926
220.599
230.264
240.635
250.198
260.656
270.915
280.276
290.478
30.821
300.666
310.414
320.0329
330.929
340.807
350.0861
360.131
370.994
380.608
390.325
40.965
400.412
410.0482
420.675
430.354
440.291
450.818
460.512
470.218
480.409
490.278
50.264
500.525
510.786
520.408
530.773
540.242
550.303
560.277
570.933
580.763
590.373
60.932
600.86
610.352
620.0969
630.347
640.571
650.244
660.479
670.0546
680.054
690.735
70.905
700.0449
710.73
720.441
730.487
740.927
750.231
760.921
770.888
780.821
790.481
80.224
800.0351
810.164
820.0607
830.293
840.59
850.185
860.563
877.63323e-4
880.502
890.296
90.768
900.426
910.753
920.242
930.75
940.39
950.179
960.65
970.735
980.384
990.515



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: CNhs11001


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)
0000302 (mouse embryonic day 18 sample)
0011512 (mouse kidney- embryo E18 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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