Personal tools

FF:644-26D1: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:644-26D1
|id=FF:644-26D1
|name=intestine, neonate N00, biol_rep1
|name=intestine, neonate N00
|sample_id=644
|sample_id=644
|rna_tube_id=644-26D1
|rna_tube_id=26D1
|rna_box=644-26D1
|rna_box=26
|rna_position=644-26D1
|rna_position=D1
|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=CNhs11126,LSID735,,COMPLETED
|profile_hcage=CNhs11126,LSID735,release008,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:39, 27 February 2012


Name:intestine, 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
tissueintestine
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

CNhs11126

00
10
100
1000
10000.0961
10010.0453
10020.0516
1003-0.058
10040
10050.229
1006-0.0512
1007-0.0584
10081.878
10090.1
101-0.105
10100
1011-0.154
10120
10130.304
1014-0.0874
1015-0.342
1016-0.222
10170
10180.585
10190
1020
10200
10210
10220.0983
10230
10240
10250.584
10260
1027-0.0134
10280
10290.582
1030.169
10300
1031-0.172
10320.64
10330
10340
10350
1036-0.183
10370
10380.0862
1039-0.043
1040
1040-0.216
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: CNhs11126

Jaspar motifP-value
MA0002.20.0106
MA0003.10.15
MA0004.10.722
MA0006.10.0441
MA0007.10.578
MA0009.10.347
MA0014.10.359
MA0017.13.73907e-22
MA0018.20.00692
MA0019.10.384
MA0024.10.0286
MA0025.10.163
MA0027.10.875
MA0028.10.343
MA0029.10.96
MA0030.10.382
MA0031.10.576
MA0035.24.33673e-6
MA0038.10.387
MA0039.20.00661
MA0040.10.206
MA0041.10.21
MA0042.10.842
MA0043.10.0388
MA0046.16.40895e-33
MA0047.20.0504
MA0048.10.381
MA0050.11.5073e-6
MA0051.15.58828e-5
MA0052.19.27913e-5
MA0055.10.387
MA0057.10.135
MA0058.10.51
MA0059.10.97
MA0060.10.00217
MA0061.10.402
MA0062.20.236
MA0065.22.03617e-13
MA0066.10.127
MA0067.10.164
MA0068.10.0793
MA0069.10.218
MA0070.10.239
MA0071.10.472
MA0072.10.401
MA0073.10.693
MA0074.10.101
MA0076.10.129
MA0077.10.793
MA0078.10.583
MA0079.20.376
MA0080.20.00447
MA0081.10.311
MA0083.10.756
MA0084.10.883
MA0087.10.735
MA0088.10.866
MA0090.10.711
MA0091.10.846
MA0092.10.286
MA0093.10.659
MA0099.20.0211
MA0100.10.148
MA0101.10.995
MA0102.20.16
MA0103.11.28856e-5
MA0104.20.11
MA0105.10.198
MA0106.10.745
MA0107.10.869
MA0108.20.724
MA0111.10.951
MA0112.23.47894e-5
MA0113.10.677
MA0114.12.22337e-26
MA0115.11.9569e-10
MA0116.10.208
MA0117.10.973
MA0119.10.0637
MA0122.10.712
MA0124.10.358
MA0125.10.0949
MA0131.10.42
MA0135.10.267
MA0136.10.0248
MA0137.20.862
MA0138.20.581
MA0139.10.0551
MA0140.10.0347
MA0141.14.98095e-5
MA0142.10.42
MA0143.10.294
MA0144.10.0902
MA0145.10.00907
MA0146.10.335
MA0147.10.182
MA0148.10.00428
MA0149.10.0236
MA0150.10.88
MA0152.10.157
MA0153.16.91296e-29
MA0154.10.0183
MA0155.10.249
MA0156.10.175
MA0157.10.45
MA0159.10.00175
MA0160.10.00804
MA0162.10.127
MA0163.10.018
MA0164.10.987
MA0258.10.00945
MA0259.10.25



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: CNhs11126

Novel motifP-value
10.139
100.186
1000.969
1010.713
1020.767
1030.19
1040.925
1050.412
1060.00942
1070.0231
1080.854
1090.0786
110.141
1100.27
1110.0395
1120.0239
1130.435
1140.047
1150.561
1160.25
1170.224
1180.514
1190.0915
120.794
1200.696
1210.755
1220.733
1230.315
1240.903
1250.591
1260.097
1270.251
1280.0757
1290.408
130.00234
1300.585
1310.0339
1320.602
1330.684
1340.838
1350.473
1360.158
1370.454
1380.639
1390.048
140.676
1400.525
1410.298
1420.868
1430.692
1440.637
1450.121
1460.266
1470.312
1480.163
1490.552
150.206
1500.225
1510.504
1520.0324
1530.71
1540.346
1550.193
1560.738
1570.869
1580.731
1590.399
1600.237
1610.35
1620.919
1630.396
1640.141
1650.398
1660.614
1670.942
1680.801
1690.0122
170.0961
180.0823
190.0899
20.274
200.858
210.982
220.366
230.203
240.762
250.755
260.00595
270.491
280.662
290.227
30.179
300.419
310.584
320.00355
330.282
340.809
350.533
360.774
370.0401
380.399
390.165
40.457
400.31
410.404
420.462
430.216
440.296
450.4
460.232
470.284
480.259
490.154
50.68
500.526
510.565
520.0753
530.994
540.48
550.609
560.484
570.786
580.48
590.105
60.797
600.043
610.194
620.353
630.166
640.628
650.181
660.582
670.556
680.11
690.992
70.0827
700.0223
710.091
720.589
730.0976
740.969
750.144
760.897
770.106
780.0441
790.579
80.136
800.492
810.641
820.061
830.785
840.466
850.0358
860.159
870.31
880.74
890.306
90.653
900.209
910.112
920.241
930.585
940.363
950.146
960.723
970.334
980.995
990.0358



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: CNhs11126


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:644-26D1&oldid=416625"