Personal tools

FF:463-22H4: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:463-22H4
|id=FF:463-22H4
|name=intestine, embryo E16, biol_rep1
|name=intestine, embryo E16
|sample_id=463
|sample_id=463
|rna_tube_id=463-22H4
|rna_tube_id=22H4
|rna_box=463-22H4
|rna_box=22
|rna_position=463-22H4
|rna_position=H4
|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=CNhs10585,LSID653,,COMPLETED
|profile_hcage=CNhs10585,LSID653,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:39, 27 February 2012


Name:intestine, embryo E16
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueintestine
dev stage16 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
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

CNhs10585

00
10
100
1000
10000.107
10010.0627
10020.321
1003-0.038
10040
10050.038
1006-0.0706
10070.0044
10080
10090.0155
1010.059
10100.205
1011-0.0923
10120
10130.0177
10140.218
10150.0279
10160.0522
10170
10180.205
10190
1020
10200
10210
1022-0.0704
10230
1024-0.0101
10250.776
10260
10270.0318
10280
10290.27
1030.116
10300
10310.278
10320.134
10330
10340
10350.0282
1036-0.00386
10370
10380.0146
1039-0.0982
1040
10400
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 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: CNhs10585

Jaspar motifP-value
MA0002.20.492
MA0003.10.259
MA0004.10.0872
MA0006.10.108
MA0007.10.633
MA0009.10.865
MA0014.10.94
MA0017.11.70269e-25
MA0018.23.08014e-4
MA0019.10.151
MA0024.10.001
MA0025.10.0284
MA0027.10.372
MA0028.10.0638
MA0029.10.867
MA0030.10.662
MA0031.10.919
MA0035.29.37987e-7
MA0038.10.0738
MA0039.20.00542
MA0040.10.567
MA0041.10.571
MA0042.10.546
MA0043.10.0136
MA0046.11.89447e-90
MA0047.28.56919e-4
MA0048.10.229
MA0050.10.00952
MA0051.10.0353
MA0052.11.77495e-5
MA0055.10.313
MA0057.10.795
MA0058.10.0209
MA0059.10.692
MA0060.12.74001e-5
MA0061.10.945
MA0062.20.00631
MA0065.24.96742e-6
MA0066.10.802
MA0067.10.084
MA0068.10.37
MA0069.10.0915
MA0070.10.646
MA0071.10.528
MA0072.10.157
MA0073.10.895
MA0074.10.0412
MA0076.10.0229
MA0077.10.55
MA0078.10.685
MA0079.20.43
MA0080.20.339
MA0081.10.0228
MA0083.10.0201
MA0084.10.922
MA0087.10.605
MA0088.10.504
MA0090.10.205
MA0091.10.82
MA0092.10.504
MA0093.10.0431
MA0099.20.456
MA0100.10.00231
MA0101.10.288
MA0102.20.265
MA0103.11.28349e-4
MA0104.20.747
MA0105.10.709
MA0106.10.357
MA0107.10.218
MA0108.20.68
MA0111.10.403
MA0112.20.152
MA0113.10.563
MA0114.11.241e-38
MA0115.11.34759e-5
MA0116.10.54
MA0117.10.114
MA0119.10.702
MA0122.10.548
MA0124.10.455
MA0125.10.668
MA0131.10.556
MA0135.10.00953
MA0136.10.763
MA0137.20.921
MA0138.20.465
MA0139.10.0428
MA0140.10.0171
MA0141.10.0491
MA0142.10.285
MA0143.10.4
MA0144.10.314
MA0145.10.178
MA0146.10.289
MA0147.10.304
MA0148.16.14761e-5
MA0149.10.873
MA0150.10.0439
MA0152.10.652
MA0153.19.39258e-58
MA0154.10.0914
MA0155.10.00944
MA0156.10.32
MA0157.10.465
MA0159.10.164
MA0160.10.276
MA0162.10.236
MA0163.10.0867
MA0164.10.482
MA0258.10.986
MA0259.10.671



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: CNhs10585

Novel motifP-value
10.828
100.825
1000.462
1010.693
1020.25
1030.747
1040.959
1050.379
1060.0538
1070.0274
1080.94
1090.864
110.956
1100.558
1110.906
1120.388
1130.217
1140.283
1150.597
1160.964
1170.416
1180.587
1190.524
120.507
1200.726
1210.925
1220.824
1230.215
1240.512
1250.621
1260.0393
1270.795
1280.738
1290.886
131.74716e-4
1300.257
1310.914
1320.429
1330.119
1340.39
1350.419
1360.407
1370.45
1380.0199
1390.98
140.559
1400.0371
1410.418
1420.48
1430.0489
1440.29
1450.272
1460.0274
1470.302
1480.857
1490.363
150.744
1500.358
1510.703
1520.0763
1530.097
1540.365
1550.991
1560.319
1570.625
1580.374
1590.0311
1600.0186
1610.551
1620.967
1630.462
1640.692
1650.698
1660.49
1670.642
1680.189
1690.271
170.586
180.0429
190.0509
20.287
200.423
210.955
220.267
230.684
240.351
250.522
260.0885
270.632
280.222
290.966
30.801
300.19
310.636
320.77
330.0921
340.355
350.499
360.836
370.381
380.999
390.314
40.369
400.154
410.181
420.696
430.903
440.501
450.0798
460.785
470.983
480.94
490.226
50.555
500.391
510.752
520.0268
530.623
540.941
550.128
560.905
570.0926
580.956
590.673
60.869
600.145
610.265
620.118
630.889
640.949
650.908
660.79
670.0649
680.469
690.337
70.151
700.284
710.433
720.767
730.814
740.895
750.973
760.168
770.0373
780.401
790.287
80.466
800.148
810.367
820.787
830.391
840.399
850.919
860.484
870.858
880.579
890.664
90.792
900.431
910.148
920.977
930.386
940.0331
950.924
960.113
970.288
980.643
990.0661



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: CNhs10585


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
0000061 (anatomical structure)
0000160 (intestine)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004921 (subdivision of digestive tract)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0007026 (primitive gut)

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:463-22H4&oldid=416622"