Personal tools

FF:762-6C4: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00004754
|DRA_sample_Accession=CAGE@SAMD00004754
|accession_numbers=CAGE;DRX009081;DRR009955;DRZ001380;DRZ002763
|accession_numbers=CAGE;DRX009081;DRR009955;DRZ001380;DRZ002763;DRZ012730;DRZ014113
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000014,UBERON:0001003,UBERON:0002097,UBERON:0002199,UBERON:0007029,UBERON:0000483,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0003102,UBERON:0007376,UBERON:0010371,UBERON:0010317,UBERON:0002416
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000014,UBERON:0001003,UBERON:0002097,UBERON:0002199,UBERON:0007029,UBERON:0000483,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0003102,UBERON:0007376,UBERON:0010371,UBERON:0010317,UBERON:0002416
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=

Revision as of 22:46, 10 August 2017


Name:skin, neonate N10
Species:Mouse (Mus musculus)
Library ID:CNhs11108
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueskin
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004754
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11108 CAGE DRX009081 DRR009955
Accession ID Mm9

Library idBAMCTSS
CNhs11108 DRZ001380 DRZ002763
Accession ID Mm10

Library idBAMCTSS
CNhs11108 DRZ012730 DRZ014113
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

CNhs11108

00
10
100
1000
10000.0262
1001-0.00258
10020.0544
10030.0635
10040
1005-0.0389
10060
10070.11
10080
10090.108
1010.0963
10100
10110.0383
10120
10130.0402
10140
1015-0.0319
1016-0.0547
10170
10180.818
10190
1020
10200
10210
10220.066
10230
10240.189
10250
10260
10270
10280
10290.121
1030.458
10300
1031-0.0483
1032-0.0097
1033-0.00922
10340
10350
1036-0.145
10370
1038-0.0116
1039-0.0661
1040
10400.0446
10410.422



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: CNhs11108

Jaspar motifP-value
MA0002.20.718
MA0003.10.445
MA0004.10.988
MA0006.10.0417
MA0007.10.503
MA0009.10.0296
MA0014.10.224
MA0017.12.59372e-5
MA0018.20.127
MA0019.10.437
MA0024.10.216
MA0025.10.767
MA0027.10.506
MA0028.10.00141
MA0029.10.288
MA0030.10.155
MA0031.10.304
MA0035.20.00927
MA0038.10.342
MA0039.20.00108
MA0040.10.0058
MA0041.10.261
MA0042.10.748
MA0043.10.595
MA0046.11.49317e-11
MA0047.20.436
MA0048.10.0425
MA0050.12.77308e-4
MA0051.10.0386
MA0052.10.00414
MA0055.18.19366e-5
MA0057.10.122
MA0058.10.694
MA0059.10.332
MA0060.10.873
MA0061.10.0908
MA0062.22.64447e-5
MA0065.20.13
MA0066.10.438
MA0067.10.97
MA0068.10.484
MA0069.10.872
MA0070.10.986
MA0071.10.0879
MA0072.10.607
MA0073.10.339
MA0074.10.28
MA0076.10.00208
MA0077.10.49
MA0078.10.131
MA0079.20.0271
MA0080.22.57479e-4
MA0081.10.00687
MA0083.10.216
MA0084.10.486
MA0087.10.76
MA0088.10.389
MA0090.10.00843
MA0091.10.623
MA0092.10.302
MA0093.10.903
MA0099.26.4689e-19
MA0100.10.105
MA0101.10.253
MA0102.20.36
MA0103.13.03949e-4
MA0104.20.111
MA0105.10.0496
MA0106.10.0123
MA0107.10.284
MA0108.23.84437e-65
MA0111.10.932
MA0112.20.99
MA0113.10.0111
MA0114.11.1671e-4
MA0115.10.00117
MA0116.10.243
MA0117.10.801
MA0119.10.828
MA0122.10.533
MA0124.10.655
MA0125.13.40407e-5
MA0131.10.311
MA0135.10.0347
MA0136.12.4286e-5
MA0137.20.208
MA0138.20.941
MA0139.10.32
MA0140.10.0176
MA0141.13.80858e-4
MA0142.10.88
MA0143.10.238
MA0144.10.808
MA0145.10.0926
MA0146.10.226
MA0147.10.067
MA0148.10.357
MA0149.10.41
MA0150.10.635
MA0152.10.479
MA0153.12.73757e-8
MA0154.10.814
MA0155.10.543
MA0156.11.06888e-4
MA0157.10.0555
MA0159.10.15
MA0160.10.0141
MA0162.10.383
MA0163.10.245
MA0164.10.219
MA0258.10.272
MA0259.10.327



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: CNhs11108

Novel motifP-value
10.873
100.874
1000.891
1010.465
1020.154
1030.562
1040.0674
1050.754
1060.0274
1070.0152
1080.355
1090.535
110.783
1100.732
1110.748
1120.746
1130.759
1140.585
1150.206
1160.773
1170.647
1180.111
1190.624
120.921
1200.837
1210.956
1220.966
1230.949
1240.399
1250.557
1260.559
1270.498
1280.159
1290.717
130.107
1300.877
1310.229
1320.868
1330.559
1340.764
1350.0834
1360.15
1370.34
1380.2
1390.394
140.469
1400.307
1410.569
1420.895
1430.346
1440.424
1450.469
1460.443
1470.0604
1480.153
1490.591
150.174
1500.12
1510.908
1520.00824
1530.735
1540.722
1550.944
1560.133
1570.12
1580.575
1590.249
1600.507
1610.375
1620.857
1630.942
1640.513
1650.216
1660.483
1670.0194
1680.601
1690.104
170.0597
180.338
190.655
20.0322
200.0942
210.346
220.613
230.0787
240.748
250.267
260.00809
270.824
280.868
290.297
30.717
300.0338
310.301
320.641
330.808
340.958
350.0233
360.0248
370.679
380.921
390.168
40.728
400.564
410.794
420.619
430.741
440.497
450.381
460.505
470.841
480.975
490.389
50.416
500.815
510.871
520.0806
530.228
540.527
550.401
560.743
570.642
580.982
590.717
60.798
600.0737
610.502
620.826
630.68
640.359
650.946
660.821
670.487
680.146
690.236
70.747
700.184
710.552
720.733
730.145
740.925
750.395
760.0063
770.0606
780.0108
790.421
80.541
800.344
810.257
820.653
830.273
840.393
850.0902
860.18
870.0672
880.715
890.37
90.477
900.99
910.758
920.982
930.746
940.556
950.744
960.984
970.0576
980.804
990.166



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: CNhs11108


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)
0000014 (zone of skin)
0001003 (skin epidermis)
0002097 (skin of body)
0002199 (integument)
0007029 (surface)
0000483 (epithelium)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0003102 (surface structure)
0007376 (outer epithelium)
0010371 (ecto-epithelium)
0010317 (germ layer / neural crest derived structure)
0002416 (integumental system)

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)
0011421 (mouse skin- 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:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:762-6C4&oldid=4345926"