Personal tools

FF:1262-18F5: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 46: Line 46:
|library_id=CNhs11026
|library_id=CNhs11026
|library_id_phase_based=2:CNhs11026
|library_id_phase_based=2:CNhs11026
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;1262
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;1262
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E18.CNhs11026.1262-18F5.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E18.CNhs11026.1262-18F5.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E18.CNhs11026.1262-18F5.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/adrenal%2520gland%252c%2520embryo%2520E18.CNhs11026.1262-18F5.mm10.nobarcode.ctss.bed.gz

Revision as of 21:59, 18 May 2017


Name:adrenal gland, embryo E18
Species:Mouse (Mus musculus)
Library ID:CNhs11026
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueadrenal gland
dev stage18 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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005611
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11026 CAGE DRX008931 DRR009805
Accession ID Mm9

Library idBAMCTSS
CNhs11026 DRZ001230 DRZ002613
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs11026

00
10.0595
100
1000
10000.0522
10010.0246
10020.221
1003-0.12
10040
10050
10060.132
10079.728956e-4
10080
10090.148
101-0.00691
10100
1011-0.0929
10120.0166
10130.0717
10140.313
1015-0.0481
1016-0.0358
10170
10180
10190
1020
10200
1021-0.00821
10220
10230
10240.061
10250
10260.0315
10270
10280
10290.0289
1030.162
10300
10310.134
1032-0.00893
10330
10340
10350
1036-0.0143
10370
1038-0.119
10390.196
1040
10400.00921
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



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: CNhs11026

Jaspar motifP-value
MA0002.20.022
MA0003.10.434
MA0004.10.00832
MA0006.10.833
MA0007.10.816
MA0009.10.0255
MA0014.10.218
MA0017.10.0285
MA0018.20.864
MA0019.10.562
MA0024.10.864
MA0025.10.446
MA0027.10.00498
MA0028.10.202
MA0029.10.00103
MA0030.10.481
MA0031.10.54
MA0035.20.807
MA0038.10.327
MA0039.20.657
MA0040.10.0413
MA0041.10.00973
MA0042.10.258
MA0043.10.277
MA0046.10.0477
MA0047.20.238
MA0048.10.0178
MA0050.10.887
MA0051.10.22
MA0052.10.0147
MA0055.10.339
MA0057.10.262
MA0058.10.136
MA0059.10.467
MA0060.10.994
MA0061.10.642
MA0062.20.411
MA0065.20.612
MA0066.10.929
MA0067.10.547
MA0068.10.143
MA0069.10.0837
MA0070.10.0131
MA0071.10.0259
MA0072.10.0358
MA0073.10.969
MA0074.10.418
MA0076.10.355
MA0077.10.796
MA0078.10.839
MA0079.20.721
MA0080.21.11528e-6
MA0081.10.121
MA0083.10.0972
MA0084.10.119
MA0087.10.0257
MA0088.10.0912
MA0090.10.244
MA0091.10.461
MA0092.10.947
MA0093.10.0299
MA0099.20.975
MA0100.10.0646
MA0101.10.172
MA0102.20.201
MA0103.11.25243e-9
MA0104.20.138
MA0105.10.364
MA0106.10.497
MA0107.10.0257
MA0108.20.247
MA0111.10.336
MA0112.20.0525
MA0113.10.56
MA0114.10.586
MA0115.10.171
MA0116.10.198
MA0117.10.592
MA0119.10.0141
MA0122.10.245
MA0124.10.765
MA0125.10.185
MA0131.10.467
MA0135.10.461
MA0136.11.22874e-4
MA0137.20.627
MA0138.20.221
MA0139.10.87
MA0140.10.028
MA0141.17.30535e-6
MA0142.10.847
MA0143.10.176
MA0144.10.963
MA0145.10.568
MA0146.10.798
MA0147.10.0786
MA0148.10.498
MA0149.10.216
MA0150.10.306
MA0152.10.78
MA0153.10.00169
MA0154.10.0446
MA0155.10.768
MA0156.10.00395
MA0157.10.283
MA0159.10.253
MA0160.10.0423
MA0162.10.254
MA0163.10.026
MA0164.10.997
MA0258.10.532
MA0259.10.371



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: CNhs11026

Novel motifP-value
10.157
100.798
1000.734
1010.885
1020.402
1030.35
1040.901
1050.175
1060.0905
1070.962
1080.12
1090.921
110.717
1100.0673
1110.209
1120.749
1130.567
1140.59
1150.809
1160.652
1170.521
1180.568
1190.889
120.874
1200.12
1210.354
1220.542
1230.122
1240.249
1250.585
1260.048
1270.655
1280.0261
1290.81
130.685
1300.427
1310.398
1320.571
1330.208
1340.163
1350.0745
1360.977
1370.59
1380.217
1390.926
140.775
1400.503
1410.726
1420.882
1430.439
1440.148
1450.684
1460.887
1470.473
1480.424
1490.152
150.82
1500.463
1510.733
1520.514
1530.536
1540.194
1550.671
1568.51262e-5
1570.42
1580.36
1590.831
1600.298
1610.977
1620.902
1630.262
1640.562
1650.809
1660.649
1670.629
1680.309
1690.101
170.891
180.181
190.112
20.432
200.395
210.645
220.141
230.59
240.294
250.41
260.27
270.982
280.33
290.763
30.492
300.766
310.974
320.728
330.411
340.76
350.307
360.958
370.257
380.864
390.623
40.392
400.847
416.07432e-5
420.932
430.805
440.205
450.178
460.417
470.688
480.782
490.527
50.621
500.516
510.835
520.178
530.395
540.862
550.00934
560.825
570.44
580.268
590.83
60.375
600.068
610.304
620.377
630.813
640.606
650.556
660.356
670.913
680.586
690.323
70.218
700.0101
710.768
720.703
730.294
740.925
750.489
760.979
770.229
780.442
790.901
80.536
800.36
810.644
820.0908
830.138
840.374
850.198
860.856
870.0171
880.964
890.29
90.512
900.72
910.205
920.535
930.403
940.787
950.118
960.481
970.962
980.619
990.41



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: CNhs11026


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)
0000922 (embryo)
0002369 (adrenal gland)
0002100 (trunk)
0000479 (tissue)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009569 (subdivision of trunk)
0002368 (endocrine gland)
0005177 (trunk region element)
0005172 (abdomen element)
0002530 (gland)
0006858 (adrenal/interrenal gland)
0010317 (germ layer / neural crest derived structure)
0005173 (abdominal segment element)
0002417 (abdominal segment of trunk)
0000949 (endocrine system)
0000916 (abdomen)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000302 (mouse embryonic day 18 sample)
0011518 (adrenal gland - embryo E18 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
UBERON:0002532 (epiblast (generic))
UBERON:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:1262-18F5&oldid=4338348"