Personal tools

FF:650-25G4: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:650-25G4
|id=FF:650-25G4
|name=skin, neonate N00, biol_rep1
|name=skin, neonate N00
|sample_id=650
|sample_id=650
|rna_tube_id=650-25G4
|rna_tube_id=25G4
|rna_box=650-25G4
|rna_box=25
|rna_position=650-25G4
|rna_position=G4
|sample_cell_lot=
|sample_cell_lot=
|sample_cell_catalog=
|sample_cell_catalog=
Line 32: Line 32:
|rna_concentration=
|rna_concentration=
|sample_note=
|sample_note=
|profile_hcage=CNhs11124,LSID734,,COMPLETED
|profile_hcage=CNhs11124,LSID734,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:52, 27 February 2012


Name:skin, neonate N00
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 stage0 day 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]





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

CNhs11124

00
10
100
1000
10000.065
10010.0975
1002-0.012
10030.152
10040
10050
10060.172
10070.0614
10080
10090.104
1010.0718
10100
10110.0307
10120.0145
10130.0224
10140.267
1015-0.0724
10160.092
10170
10180.554
10190
1020
10200
10210
10220.198
10230
10240.222
10250
10260.0356
10270.065
10280
10290.0568
1030.554
10300
10310.412
1032-0.131
1033-0.0752
10340.065
10350.065
10360.0742
10370
10380.0251
1039-0.11
1040
10400.288
10410.328



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: CNhs11124

Jaspar motifP-value
MA0002.20.00618
MA0003.10.553
MA0004.10.284
MA0006.10.0849
MA0007.10.845
MA0009.10.155
MA0014.10.682
MA0017.11.53909e-10
MA0018.20.00602
MA0019.10.258
MA0024.10.131
MA0025.10.936
MA0027.10.905
MA0028.14.41834e-8
MA0029.10.657
MA0030.10.145
MA0031.10.0468
MA0035.29.42179e-4
MA0038.10.457
MA0039.20.0526
MA0040.10.891
MA0041.10.248
MA0042.10.524
MA0043.10.245
MA0046.14.30148e-26
MA0047.20.277
MA0048.10.113
MA0050.10.198
MA0051.10.0625
MA0052.19.97678e-11
MA0055.10.0052
MA0057.10.391
MA0058.10.0774
MA0059.10.00405
MA0060.10.00132
MA0061.10.197
MA0062.22.30598e-10
MA0065.20.00441
MA0066.10.333
MA0067.10.532
MA0068.10.0851
MA0069.10.725
MA0070.10.553
MA0071.10.00463
MA0072.10.179
MA0073.10.902
MA0074.10.327
MA0076.11.38178e-7
MA0077.10.392
MA0078.10.0144
MA0079.20.0296
MA0080.22.46915e-5
MA0081.10.00391
MA0083.10.0056
MA0084.10.801
MA0087.10.112
MA0088.10.193
MA0090.10.0187
MA0091.10.818
MA0092.10.201
MA0093.10.208
MA0099.21.16458e-10
MA0100.10.014
MA0101.10.3
MA0102.20.423
MA0103.10.962
MA0104.20.0159
MA0105.10.0665
MA0106.10.137
MA0107.10.669
MA0108.21.81878e-14
MA0111.10.998
MA0112.20.701
MA0113.10.431
MA0114.12.5707e-10
MA0115.11.35561e-4
MA0116.10.0961
MA0117.10.529
MA0119.10.531
MA0122.10.543
MA0124.10.149
MA0125.10.0979
MA0131.10.797
MA0135.10.459
MA0136.17.30687e-10
MA0137.20.0924
MA0138.20.957
MA0139.10.0321
MA0140.10.00197
MA0141.11.33052e-7
MA0142.10.173
MA0143.10.0906
MA0144.10.564
MA0145.10.339
MA0146.10.657
MA0147.10.00632
MA0148.10.217
MA0149.10.14
MA0150.10.266
MA0152.10.014
MA0153.11.73122e-15
MA0154.10.599
MA0155.10.58
MA0156.11.07147e-6
MA0157.10.00272
MA0159.10.0242
MA0160.15.00719e-6
MA0162.10.508
MA0163.10.203
MA0164.10.283
MA0258.10.463
MA0259.10.156



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: CNhs11124

Novel motifP-value
10.24
100.434
1000.7
1010.771
1020.633
1030.142
1040.805
1050.349
1060.0258
1070.00342
1080.925
1090.135
110.226
1100.612
1110.0859
1120.412
1130.677
1140.736
1150.455
1160.408
1170.111
1180.0638
1190.481
120.242
1200.286
1210.286
1220.417
1230.794
1240.238
1250.504
1260.732
1270.716
1280.125
1290.245
130.139
1300.726
1310.344
1320.987
1330.141
1340.96
1350.446
1360.6
1370.451
1380.506
1390.372
140.461
1400.203
1410.619
1420.589
1430.152
1440.232
1450.405
1460.381
1470.162
1480.2
1490.907
150.0246
1500.404
1510.838
1520.0194
1530.898
1540.249
1550.533
1560.0215
1570.00245
1580.114
1590.348
1600.347
1610.125
1620.664
1630.751
1640.461
1650.518
1660.213
1670.0107
1680.82
1690.144
170.233
180.21
190.451
20.101
200.214
210.94
220.524
230.255
240.959
250.125
260.0676
270.701
280.889
290.0289
30.171
300.1
310.536
320.807
330.644
340.636
350.00408
360.0151
370.707
380.353
390.157
40.981
400.0442
410.285
420.678
430.906
440.0232
450.249
460.737
470.275
480.307
490.42
50.511
500.303
510.973
520.0633
530.269
540.655
550.82
560.687
570.617
580.855
590.782
60.766
600.082
610.875
620.479
630.544
640.19
650.416
660.0949
670.778
680.058
690.258
70.763
700.217
710.654
720.395
730.47
740.97
750.0755
760.0249
770.444
780.0505
790.533
80.137
800.114
810.587
820.766
830.303
840.377
850.399
860.107
870.607
880.882
890.266
90.396
900.398
910.873
920.783
930.515
940.442
950.445
960.714
970.194
980.46
990.224



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: CNhs11124


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)
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:650-25G4&oldid=417663"