Personal tools

FF:1353-25F3

From FANTOM5_SSTAR

Revision as of 22:12, 10 August 2017 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:kidney, neonate N25
Species:Mouse (Mus musculus)
Library ID:CNhs11122
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuekidney
dev stage25 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  SAMD00005166
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11122 CAGE DRX009012 DRR009886
Accession ID Mm9

Library idBAMCTSS
CNhs11122 DRZ001311 DRZ002694
Accession ID Mm10

Library idBAMCTSS
CNhs11122 DRZ012661 DRZ014044
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

CNhs11122

00
10
100
1000
10000
10010.169
10020.572
1003-0.0841
10040
10050
10060
1007-0.0261
10080
10090.00611
101-0.0788
10100
10110
10120.0207
10130.392
1014-0.0218
1015-0.239
1016-0.153
10170
10180.118
10190
1020
10200
1021-0.0487
10220.422
10230
10240.341
10250
10260
10270
10280.0633
10290.239
1030
10300
1031-0.0365
10320.419
1033-0.00316
10340.478
10350.0633
1036-0.265
10370
10380.0955
10390.526
1040
10400.162
10410.119



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: CNhs11122

Jaspar motifP-value
MA0002.20.124
MA0003.10.254
MA0004.10.574
MA0006.10.0418
MA0007.10.448
MA0009.10.324
MA0014.10.115
MA0017.14.4864e-22
MA0018.22.6847e-6
MA0019.10.273
MA0024.15.06949e-5
MA0025.10.961
MA0027.10.539
MA0028.10.814
MA0029.10.493
MA0030.10.0303
MA0031.10.00176
MA0035.20.00151
MA0038.10.396
MA0039.20.0216
MA0040.10.523
MA0041.10.336
MA0042.10.591
MA0043.12.88617e-4
MA0046.15.9426e-131
MA0047.20.00229
MA0048.10.362
MA0050.10.0747
MA0051.10.102
MA0052.10.00455
MA0055.10.335
MA0057.10.434
MA0058.10.421
MA0059.10.904
MA0060.10.0134
MA0061.10.68
MA0062.20.0493
MA0065.21.69466e-12
MA0066.10.537
MA0067.10.442
MA0068.10.715
MA0069.10.472
MA0070.10.796
MA0071.10.00482
MA0072.10.366
MA0073.10.875
MA0074.10.4
MA0076.10.486
MA0077.10.0334
MA0078.10.00169
MA0079.20.756
MA0080.20.104
MA0081.10.442
MA0083.10.046
MA0084.10.669
MA0087.10.468
MA0088.10.195
MA0090.10.0012
MA0091.10.35
MA0092.10.0697
MA0093.10.566
MA0099.20.768
MA0100.10.0227
MA0101.10.437
MA0102.20.679
MA0103.10.00151
MA0104.20.0887
MA0105.10.707
MA0106.10.308
MA0107.10.507
MA0108.28.57584e-5
MA0111.10.817
MA0112.25.3993e-4
MA0113.10.415
MA0114.12.54851e-27
MA0115.16.09359e-4
MA0116.10.766
MA0117.10.823
MA0119.10.0176
MA0122.10.322
MA0124.10.619
MA0125.10.472
MA0131.10.338
MA0135.10.839
MA0136.10.00428
MA0137.20.981
MA0138.20.972
MA0139.10.136
MA0140.10.0179
MA0141.11.56514e-9
MA0142.10.00475
MA0143.10.911
MA0144.10.618
MA0145.14.9839e-4
MA0146.10.175
MA0147.10.0627
MA0148.10.00426
MA0149.10.0239
MA0150.10.0656
MA0152.10.05
MA0153.16.46744e-57
MA0154.10.0722
MA0155.10.379
MA0156.10.143
MA0157.10.0286
MA0159.10.0197
MA0160.14.03364e-5
MA0162.10.16
MA0163.10.59
MA0164.10.554
MA0258.10.00554
MA0259.10.137



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: CNhs11122

Novel motifP-value
10.42
100.711
1000.963
1010.933
1020.304
1030.0224
1040.609
1050.62
1060.122
1070.102
1080.0262
1090.0226
110.263
1100.21
1110.67
1120.0923
1130.691
1140.379
1150.887
1160.463
1170.775
1180.375
1190.0849
120.847
1200.268
1210.716
1220.299
1230.0464
1240.482
1250.546
1260.381
1270.305
1280.153
1290.929
136.66475e-6
1300.125
1310.683
1320.823
1330.157
1340.58
1350.419
1360.259
1370.119
1380.0364
1390.341
140.176
1400.234
1410.701
1420.831
1430.361
1440.148
1450.131
1460.492
1470.57
1480.481
1490.285
150.184
1500.178
1510.488
1520.0665
1530.652
1540.493
1550.882
1560.174
1570.199
1580.986
1590.129
1600.199
1610.647
1620.375
1630.545
1640.792
1650.0171
1660.804
1670.762
1680.926
1690.00483
170.0412
180.0981
190.00466
20.204
200.798
210.835
220.0275
230.336
240.303
250.769
260.205
270.521
280.545
290.948
30.247
300.337
310.618
320.285
330.838
340.655
350.796
360.92
370.0412
380.329
390.402
40.701
400.356
410.253
420.886
430.287
440.816
450.261
460.694
470.44
480.226
490.177
50.851
500.965
510.61
520.0651
530.981
540.96
550.886
560.999
570.913
580.221
590.93
60.914
600.0298
610.489
620.313
630.345
640.982
650.311
660.424
670.103
680.81
690.667
70.0652
700.19
710.363
720.871
730.111
740.348
750.554
760.536
770.0814
780.0772
790.402
80.896
800.367
810.557
820.385
830.599
840.325
850.0201
860.528
870.254
880.726
890.736
90.756
900.327
910.41
920.607
930.813
940.203
950.575
960.34
970.368
980.33
990.376



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: CNhs11122


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)
0000309 (mouse neonate N25 sample)
0011482 (mouse kidney- neonate N25 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)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:1353-25F3&oldid=4345312"