Personal tools

FF:1035-18D5: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 46: Line 46:
|library_id=CNhs11006
|library_id=CNhs11006
|library_id_phase_based=2:CNhs11006
|library_id_phase_based=2:CNhs11006
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;1035
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;1035
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520embryo%2520E17.CNhs11006.1035-18D5.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520embryo%2520E17.CNhs11006.1035-18D5.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520embryo%2520E17.CNhs11006.1035-18D5.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/stomach%252c%2520embryo%2520E17.CNhs11006.1035-18D5.mm10.nobarcode.ctss.bed.gz

Revision as of 19:26, 18 May 2017


Name:stomach, embryo E17
Species:Mouse (Mus musculus)
Library ID:CNhs11006
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuestomach
dev stage17 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  SAMD00005724
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11006 CAGE DRX009094 DRR009968
Accession ID Mm9

Library idBAMCTSS
CNhs11006 DRZ001393 DRZ002776
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

CNhs11006

00
10
100
1000
10000.152
10010.0365
10020.505
10030.0399
10040
10050.0825
1006-0.151
10070.0354
10080
10090.111
1010.0456
10100.0825
10110.0462
10120
10130.0425
10140.627
10150.074
10160.157
10171.09
10180.427
10190
1020
10200
10210
1022-0.0704
10230
10240.0561
10250.862
10260.053
10270.0908
10280
10290.391
1030.311
10300.0825
10310.365
10320.103
10330.00724
10340.0655
10350
10360.147
10370
10380.0245
1039-0.0782
1040
10400.0578
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: CNhs11006

Jaspar motifP-value
MA0002.20.0554
MA0003.10.56
MA0004.10.19
MA0006.10.101
MA0007.10.782
MA0009.10.0523
MA0014.10.977
MA0017.10.0363
MA0018.21.97629e-6
MA0019.10.181
MA0024.10.232
MA0025.18.61966e-5
MA0027.10.059
MA0028.11.62471e-4
MA0029.10.52
MA0030.10.764
MA0031.10.541
MA0035.20.205
MA0038.10.745
MA0039.20.0386
MA0040.10.628
MA0041.10.139
MA0042.10.307
MA0043.11.20495e-4
MA0046.10.00275
MA0047.20.00617
MA0048.10.0963
MA0050.10.00323
MA0051.11.77101e-5
MA0052.12.35314e-4
MA0055.10.883
MA0057.10.079
MA0058.10.0135
MA0059.10.262
MA0060.10.887
MA0061.10.856
MA0062.23.32671e-11
MA0065.20.0822
MA0066.10.984
MA0067.10.0308
MA0068.10.102
MA0069.10.146
MA0070.10.753
MA0071.10.00108
MA0072.10.0526
MA0073.10.652
MA0074.10.987
MA0076.19.85564e-6
MA0077.10.709
MA0078.10.197
MA0079.20.828
MA0080.29.52272e-5
MA0081.11.41243e-4
MA0083.12.70082e-7
MA0084.10.807
MA0087.10.334
MA0088.10.158
MA0090.10.234
MA0091.10.731
MA0092.10.123
MA0093.10.125
MA0099.21.71985e-4
MA0100.10.00402
MA0101.10.085
MA0102.20.55
MA0103.13.77306e-4
MA0104.20.114
MA0105.10.126
MA0106.10.0763
MA0107.10.101
MA0108.20.0025
MA0111.10.985
MA0112.20.0679
MA0113.10.695
MA0114.10.174
MA0115.10.0237
MA0116.10.0402
MA0117.10.024
MA0119.10.521
MA0122.10.243
MA0124.10.709
MA0125.10.429
MA0131.10.608
MA0135.10.637
MA0136.11.57956e-6
MA0137.20.127
MA0138.20.724
MA0139.10.466
MA0140.10.181
MA0141.11.68576e-4
MA0142.10.272
MA0143.10.238
MA0144.10.918
MA0145.10.0773
MA0146.10.792
MA0147.10.0918
MA0148.10.00644
MA0149.10.759
MA0150.10.0309
MA0152.10.0346
MA0153.13.61198e-4
MA0154.10.0266
MA0155.10.294
MA0156.15.31489e-5
MA0157.10.868
MA0159.10.389
MA0160.11.27055e-4
MA0162.10.193
MA0163.10.0239
MA0164.10.432
MA0258.10.819
MA0259.10.259



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: CNhs11006

Novel motifP-value
10.603
100.459
1000.532
1010.836
1020.903
1030.13
1040.755
1050.922
1060.00507
1070.0204
1080.712
1090.983
110.634
1100.532
1110.941
1120.69
1130.125
1140.244
1150.938
1160.204
1170.467
1180.172
1190.801
120.734
1200.401
1210.284
1220.502
1230.466
1240.502
1250.817
1260.167
1270.758
1280.0546
1290.546
130.0299
1300.342
1310.12
1320.501
1330.464
1340.318
1350.974
1360.386
1370.526
1380.0145
1390.652
140.817
1400.0488
1410.421
1420.521
1430.235
1440.291
1450.212
1460.486
1470.545
1480.75
1490.728
150.231
1500.48
1510.884
1520.164
1530.714
1540.907
1550.962
1563.31114e-6
1570.675
1580.681
1590.0288
1600.0373
1610.251
1620.541
1630.55
1640.804
1650.615
1660.199
1670.536
1680.162
1690.0553
170.0623
180.362
190.0262
20.609
200.358
210.107
220.315
230.537
240.516
250.0593
260.00251
270.827
280.78
290.752
30.789
300.105
310.746
320.132
330.907
340.875
350.409
360.552
370.223
380.739
390.17
40.173
400.805
410.275
420.572
430.368
440.373
450.372
460.405
470.804
480.597
490.688
50.451
500.283
510.592
520.0382
530.34
540.627
550.89
560.532
570.529
580.934
590.684
60.133
600.0862
610.603
620.435
630.669
640.743
650.903
660.427
670.838
680.146
690.219
70.385
700.414
710.0536
720.669
730.624
740.404
750.675
760.263
770.00157
780.629
790.884
80.873
800.164
810.761
820.85
830.995
840.414
850.742
860.672
870.00199
880.141
890.865
90.177
900.658
910.795
920.206
930.231
940.51
950.591
960.293
970.583
980.548
990.0756



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: CNhs11006


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)
0000945 (stomach)
0000479 (tissue)
0001007 (digestive system)
0004119 (endoderm-derived structure)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0004921 (subdivision of digestive tract)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010039 (food storage organ)
0010317 (germ layer / neural crest derived structure)
0001555 (digestive tract)
0005409 (gastrointestinal system)
0001041 (foregut)

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)
0000300 (mouse embryonic day 17 sample)
0011492 (mouse stomach- embryo E17 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:0006595 (presumptive endoderm)
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:1035-18D5&oldid=4337191"