Personal tools

FF:1063-29H9: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{
{{f5samples
|DRA_sample_Accession=CAGE@DRS008789
|accession_numbers=CAGE;DRX008926;DRR009800;DRZ001225;DRZ002608
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000029,UBERON:0000479,UBERON:0001097,UBERON:0000064,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003968,

Revision as of 12:03, 25 October 2013


Name:accessory axillary lymph node, adult
Species:Mouse (Mus musculus)
Library ID:CNhs10475
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueaccessory axillary lymph node
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

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008789
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10475 CAGE DRX008926 DRR009800
Accession ID Mm9

Library idBAMCTSS
CNhs10475 DRZ001225 DRZ002608
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


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

CNhs10475

00
10
100
1000
10000
10010.0725
1002-0.116
1003-0.123
10040
10050.228
1006-0.143
1007-0.0824
10080
10090.0497
1010.223
10100
10110.221
10120.1
10130.00147
1014-0.0874
1015-0.147
1016-0.272
10170
10180
10190
1020.1
10200
10210.0513
1022-0.124
10230.1
10240
10250
10260
10270
10280
10290.0304
103-0.0787
10300.733
1031-0.389
1032-0.184
10330.145
10340
10350
1036-0.00161
10370
1038-0.194
1039-0.153
1040
1040-0.0466
10410.361



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: CNhs10475

Jaspar motifP-value
MA0002.22.16405e-9
MA0003.10.64
MA0004.10.644
MA0006.10.188
MA0007.10.93
MA0009.10.804
MA0014.10.528
MA0017.10.879
MA0018.20.269
MA0019.10.143
MA0024.10.557
MA0025.10.924
MA0027.10.823
MA0028.17.00213e-5
MA0029.10.432
MA0030.10.369
MA0031.10.829
MA0035.20.732
MA0038.10.557
MA0039.20.455
MA0040.10.52
MA0041.10.67
MA0042.10.692
MA0043.10.832
MA0046.14.31292e-11
MA0047.20.969
MA0048.10.49
MA0050.19.44348e-24
MA0051.12.5034e-15
MA0052.10.0342
MA0055.10.343
MA0057.10.567
MA0058.10.795
MA0059.10.423
MA0060.10.0396
MA0061.14.50094e-14
MA0062.22.54414e-26
MA0065.20.897
MA0066.10.299
MA0067.10.368
MA0068.10.0175
MA0069.10.622
MA0070.10.468
MA0071.10.623
MA0072.10.221
MA0073.10.721
MA0074.10.872
MA0076.11.75874e-6
MA0077.10.0281
MA0078.10.58
MA0079.20.22
MA0080.24.7178e-16
MA0081.13.73571e-4
MA0083.10.27
MA0084.10.569
MA0087.10.391
MA0088.10.346
MA0090.10.00985
MA0091.10.627
MA0092.10.944
MA0093.10.631
MA0099.20.219
MA0100.10.805
MA0101.13.6079e-12
MA0102.20.0798
MA0103.10.631
MA0104.20.407
MA0105.13.73709e-8
MA0106.10.93
MA0107.11.06523e-15
MA0108.20.00308
MA0111.10.98
MA0112.20.0352
MA0113.10.377
MA0114.10.143
MA0115.10.78
MA0116.10.0192
MA0117.10.409
MA0119.10.378
MA0122.10.674
MA0124.10.379
MA0125.10.168
MA0131.10.662
MA0135.10.992
MA0136.15.77804e-26
MA0137.25.6304e-5
MA0138.20.0327
MA0139.10.202
MA0140.10.658
MA0141.10.0288
MA0142.18.18793e-6
MA0143.10.149
MA0144.10.0127
MA0145.10.733
MA0146.10.842
MA0147.10.297
MA0148.10.904
MA0149.10.974
MA0150.10.635
MA0152.10.876
MA0153.19.45679e-9
MA0154.12.4715e-4
MA0155.10.575
MA0156.13.96379e-39
MA0157.10.282
MA0159.10.191
MA0160.10.292
MA0162.10.368
MA0163.10.0158
MA0164.10.75
MA0258.10.336
MA0259.10.0531



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: CNhs10475

Novel motifP-value
10.742
100.196
1000.441
1010.786
1020.742
1030.242
1040.762
1050.695
1060.128
1070.326
1080.479
1090.479
110.779
1100.18
1110.564
1120.0263
1130.0185
1140.392
1150.982
1160.594
1170.00968
1180.278
1190.306
120.558
1200.985
1210.209
1220.659
1230.909
1240.488
1250.189
1260.902
1270.238
1280.131
1290.0518
130.254
1300.343
1310.699
1320.61
1330.898
1340.686
1350.388
1360.713
1370.13
1380.868
1390.838
140.408
1400.813
1410.0781
1420.582
1430.0142
1440.775
1450.349
1460.538
1470.618
1480.0915
1490.905
150.0577
1500.166
1510.0463
1520.565
1530.195
1540.709
1550.555
1560.612
1570.99
1580.222
1590.377
1600.888
1610.0715
1620.0977
1630.332
1640.213
1650.091
1660.68
1670.697
1680.977
1690.0571
170.664
180.633
190.424
20.904
200.272
210.857
220.567
230.967
240.104
250.196
260.133
270.15
280.0487
290.334
30.31
300.288
310.804
320.636
330.509
340.566
350.609
360.217
370.0312
380.077
390.335
40.398
400.6
410.865
420.18
430.174
440.546
450.227
460.285
470.319
480.355
490.333
50.244
500.912
510.986
520.634
530.789
540.409
550.808
560.699
570.457
580.0392
590.345
60.476
600.59
610.266
620.0792
630.695
640.694
650.332
660.662
670.504
680.469
690.345
70.196
700.225
710.197
720.146
730.0952
740.228
750.0447
760.299
770.297
780.0168
790.996
80.494
808.67614e-4
810.59
820.178
830.0399
840.876
850.746
860.385
870.919
880.396
890.659
90.341
900.216
910.868
920.692
930.168
940.28
950.483
960.988
970.941
980.138
990.336



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: CNhs10475


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)
0007023 (adult organism)
0000029 (lymph node)
0000479 (tissue)
0001097 (axillary lymph node)
0000064 (organ part)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003968 (peripheral lymph node)
0010707 (appendage girdle complex)
0002465 (lymphoid system)
0001467 (shoulder)
0010708 (pectoral complex)
0002193 (hemolymphoid system)
0002405 (immune system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue 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
NA

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:1063-29H9&oldid=3079301"