Personal tools

FF:30-1C3

From FANTOM5_SSTAR

Revision as of 14:28, 27 January 2012 by Autoedit (talk | contribs) (Created page with "{{f5samples |id=FF:30-1C3 |name=skin, adult, biol_rep1 |sample_id=30 |rna_tube_id=30-1C3 |rna_box=30-1C3 |rna_position=30-1C3 |sample_cell_lot= |sample_cell_catalog= ...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search


Name:skin, adult, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueskin
dev stageadult
sexmale
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]





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

CNhs10492

00
10
100
1000
10000.473
10010.136
10020.0663
10030.218
10040
1005-0.0223
10060.238
10070.0784
10080
10090.297
1010.0114
10100
10110.175
10120
1013-0.0926
1014-0.0874
1015-0.173
1016-0.0295
10170
10180.681
10190
1020
10200
10210.0663
10220.321
10230
10240.23
10250
10260.0368
10270
10280
10290.114
1030.527
10300
1031-0.13
1032-0.09
10330
10340.124
10350.0663
1036-0.0797
10370
10380.0969
1039-0.121
1040
10400.15
10411.044



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 no result for this sample


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: CNhs10492

Jaspar motifP-value
MA0002.20.438
MA0003.10.369
MA0004.10.698
MA0006.10.0954
MA0007.10.833
MA0009.10.076
MA0014.10.477
MA0017.14.37132e-5
MA0018.20.128
MA0019.10.65
MA0024.10.00868
MA0025.10.14
MA0027.10.149
MA0028.14.22556e-4
MA0029.10.247
MA0030.10.0898
MA0031.10.0893
MA0035.20.0232
MA0038.10.0201
MA0039.20.0035
MA0040.10.0346
MA0041.10.738
MA0042.10.478
MA0043.10.912
MA0046.12.75812e-11
MA0047.20.79
MA0048.10.0113
MA0050.10.182
MA0051.10.0373
MA0052.11.71127e-17
MA0055.13.20498e-4
MA0057.10.151
MA0058.10.401
MA0059.10.0216
MA0060.10.292
MA0061.10.926
MA0062.21.03053e-4
MA0065.20.456
MA0066.10.396
MA0067.10.691
MA0068.10.679
MA0069.10.649
MA0070.10.675
MA0071.10.0846
MA0072.10.783
MA0073.10.987
MA0074.10.295
MA0076.18.14632e-4
MA0077.10.0246
MA0078.10.0373
MA0079.20.0248
MA0080.20.0998
MA0081.10.163
MA0083.10.00474
MA0084.10.221
MA0087.10.515
MA0088.10.503
MA0090.10.0241
MA0091.10.594
MA0092.10.737
MA0093.10.678
MA0099.24.11232e-17
MA0100.10.016
MA0101.10.821
MA0102.20.0775
MA0103.10.0732
MA0104.20.0445
MA0105.10.125
MA0106.10.0185
MA0107.10.32
MA0108.21.97277e-44
MA0111.10.773
MA0112.20.435
MA0113.10.198
MA0114.11.74484e-4
MA0115.10.00109
MA0116.10.332
MA0117.10.961
MA0119.10.906
MA0122.10.933
MA0124.10.274
MA0125.10.014
MA0131.10.25
MA0135.10.0355
MA0136.10.00569
MA0137.20.792
MA0138.20.339
MA0139.10.34
MA0140.10.0161
MA0141.10.00979
MA0142.10.367
MA0143.10.00939
MA0144.10.589
MA0145.10.0213
MA0146.10.32
MA0147.10.0253
MA0148.10.656
MA0149.10.323
MA0150.10.435
MA0152.10.0308
MA0153.11.99923e-8
MA0154.10.164
MA0155.10.673
MA0156.10.035
MA0157.10.0165
MA0159.10.129
MA0160.10.0493
MA0162.10.609
MA0163.10.112
MA0164.10.197
MA0258.10.9
MA0259.10.209



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: CNhs10492

Novel motifP-value
10.792
100.521
1000.84
1010.623
1020.685
1030.433
1040.187
1050.196
1060.0382
1070.0258
1080.625
1090.449
110.458
1100.738
1110.482
1120.307
1130.509
1140.743
1150.0458
1160.617
1170.276
1180.0452
1190.306
120.615
1200.219
1210.481
1220.438
1230.675
1240.681
1250.38
1260.957
1270.474
1280.146
1290.955
130.0417
1300.525
1310.404
1320.953
1330.629
1340.928
1350.298
1360.301
1370.997
1380.663
1390.702
140.267
1400.537
1410.386
1420.423
1430.266
1440.837
1450.966
1460.726
1470.155
1480.129
1490.948
150.434
1500.442
1510.34
1520.0215
1530.963
1540.442
1550.53
1562.62513e-13
1570.0234
1580.864
1590.889
1600.491
1610.155
1620.53
1630.344
1640.417
1650.605
1660.478
1670.00995
1680.887
1690.0369
170.0956
180.185
190.392
20.0543
200.154
210.498
220.298
230.188
240.741
250.564
260.0507
270.977
280.826
290.102
30.687
300.0489
310.501
320.537
330.333
340.659
350.0215
360.0221
370.515
380.776
390.16
40.253
400.483
410.656
420.783
430.945
440.352
450.188
460.569
470.94
480.962
490.337
50.853
500.624
510.812
520.0655
530.149
540.626
550.987
560.571
570.712
580.826
590.292
60.897
600.116
610.958
620.836
630.466
640.299
650.699
660.873
670.925
680.51
690.312
70.643
700.485
710.714
720.574
730.16
740.652
750.173
760.00151
770.0413
780.00586
790.0911
80.238
800.897
810.832
820.848
830.832
840.147
850.153
860.34
870.271
880.496
890.417
90.351
900.503
910.995
920.73
930.847
940.637
950.803
960.439
970.00445
980.291
990.316



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: CNhs10492


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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
0000014 (zone of skin)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0001003 (skin epidermis)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002097 (skin of body)
0002199 (integument)
0002416 (integumental system)
0002532 (epiblast (generic))
0003102 (surface structure)
0004121 (ectoderm-derived structure)
0005423 (developing anatomical structure)
0007023 (adult organism)
0007029 (surface)
0007376 (outer epithelium)
0007383 (enveloping layer of ectoderm)

FF: FANTOM5
NA

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
NA

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:30-1C3&oldid=7944"