Personal tools

FF:1390-42D2: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 46: Line 46:
|library_id=CNhs11202
|library_id=CNhs11202
|library_id_phase_based=2:CNhs11202
|library_id_phase_based=2:CNhs11202
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;1390
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;1390
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520neonate%2520N30.CNhs11202.1390-42D2.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520neonate%2520N30.CNhs11202.1390-42D2.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520neonate%2520N30.CNhs11202.1390-42D2.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520neonate%2520N30.CNhs11202.1390-42D2.mm10.nobarcode.ctss.bed.gz

Revision as of 22:21, 18 May 2017


Name:heart, neonate N30
Species:Mouse (Mus musculus)
Library ID:CNhs11202
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueheart
dev stage30 days 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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004670
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11202 CAGE DRX008985 DRR009859
Accession ID Mm9

Library idBAMCTSS
CNhs11202 DRZ001284 DRZ002667
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

CNhs11202

00
10
100.848
1000
10000.733
10010.667
1002-0.039
10030.0655
10040
10050
10060.656
1007-0.0785
10080
10090.287
101-0.126
10100
1011-0.0604
10120.0547
1013-0.112
1014-0.0383
1015-0.164
1016-0.0438
10170
10180
10190
1020
10200
10210
10220.916
10230
10240.633
10250
10260.147
10270
10280
1029-0.029
1030
10300.0547
10310.0537
10320.145
1033-0.0118
10340
10350.317
1036-0.401
10370
10380.202
10390.791
1040
10400.21
10410.187



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: CNhs11202

Jaspar motifP-value
MA0002.20.327
MA0003.10.278
MA0004.10.0711
MA0006.10.121
MA0007.10.465
MA0009.10.786
MA0014.10.55
MA0017.10.907
MA0018.20.254
MA0019.10.206
MA0024.11.68837e-5
MA0025.10.0251
MA0027.10.952
MA0028.10.00944
MA0029.10.815
MA0030.10.571
MA0031.10.141
MA0035.29.76753e-8
MA0038.10.742
MA0039.20.172
MA0040.10.811
MA0041.10.96
MA0042.10.753
MA0043.10.571
MA0046.12.83545e-15
MA0047.20.26
MA0048.10.49
MA0050.10.169
MA0051.10.0257
MA0052.12.41372e-62
MA0055.10.469
MA0057.10.642
MA0058.10.0396
MA0059.10.0189
MA0060.11.95587e-7
MA0061.10.76
MA0062.22.40375e-6
MA0065.20.00686
MA0066.10.998
MA0067.10.75
MA0068.10.562
MA0069.10.295
MA0070.10.449
MA0071.13.15288e-4
MA0072.10.209
MA0073.10.563
MA0074.10.138
MA0076.18.11758e-4
MA0077.10.983
MA0078.10.284
MA0079.20.0471
MA0080.20.0427
MA0081.10.903
MA0083.16.5391e-10
MA0084.10.982
MA0087.10.281
MA0088.10.946
MA0090.11.30313e-5
MA0091.10.757
MA0092.10.255
MA0093.10.0504
MA0099.20.327
MA0100.10.0375
MA0101.10.677
MA0102.20.256
MA0103.10.00198
MA0104.20.00613
MA0105.10.597
MA0106.10.518
MA0107.10.869
MA0108.20.158
MA0111.10.928
MA0112.22.05695e-5
MA0113.10.0547
MA0114.10.733
MA0115.10.201
MA0116.10.243
MA0117.10.51
MA0119.10.0818
MA0122.10.0259
MA0124.10.398
MA0125.10.643
MA0131.10.24
MA0135.10.752
MA0136.10.00123
MA0137.20.373
MA0138.20.00613
MA0139.10.76
MA0140.15.0249e-4
MA0141.14.34077e-9
MA0142.10.0509
MA0143.10.163
MA0144.10.377
MA0145.10.0337
MA0146.10.0135
MA0147.10.00794
MA0148.10.395
MA0149.10.607
MA0150.10.00838
MA0152.10.333
MA0153.11.05449e-9
MA0154.10.0259
MA0155.10.368
MA0156.10.0226
MA0157.10.0338
MA0159.11.28034e-6
MA0160.13.38247e-6
MA0162.10.147
MA0163.10.842
MA0164.10.161
MA0258.10.0038
MA0259.10.099



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: CNhs11202

Novel motifP-value
10.213
100.626
1000.698
1010.571
1020.958
1030.661
1040.508
1050.098
1060.161
1070.173
1080.9
1090.23
110.432
1100.249
1110.258
1120.867
1130.853
1140.127
1150.933
1160.811
1170.778
1180.758
1190.122
120.769
1200.07
1210.0333
1220.972
1230.446
1240.484
1250.743
1260.679
1270.322
1280.608
1290.148
136.17536e-4
1300.77
1310.433
1320.702
1330.792
1340.617
1350.93
1360.888
1370.315
1380.249
1390.245
140.102
1400.742
1410.504
1420.852
1430.147
1440.42
1450.468
1460.443
1470.82
1480.313
1498.49759e-4
150.245
1500.604
1510.293
1520.03
1530.76
1540.95
1550.0386
1560.0451
1570.842
1580.0894
1590.328
1600.248
1610.762
1620.827
1630.123
1640.401
1650.00137
1660.219
1670.446
1680.294
1692.90633e-4
170.132
180.103
190.0317
20.339
200.766
210.262
220.023
230.429
240.752
250.789
260.192
270.922
280.827
290.514
30.427
300.7
310.496
320.634
330.454
340.155
350.73
360.463
370.00794
380.625
390.357
40.562
400.754
410.806
420.857
430.181
440.653
450.345
460.789
470.966
480.603
490.239
50.237
500.927
510.599
520.228
530.701
540.375
550.832
560.525
570.644
580.576
590.0482
60.087
600.127
610.93
620.609
630.104
640.822
650.427
660.216
670.487
680.802
690.0594
70.129
700.638
710.173
720.754
730.0239
740.273
750.968
760.653
770.272
780.026
790.762
80.929
800.859
810.623
820.167
830.272
840.0493
850.00281
860.617
870.459
880.891
890.0843
90.12
900.63
910.489
920.348
930.548
940.83
950.13
960.937
970.293
980.24
990.936



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: CNhs11202


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)
0007100 (primary circulatory organ)
0000948 (heart)
0000479 (tissue)
0010314 (structure with developmental contribution from neural crest)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0010317 (germ layer / neural crest derived structure)
0004535 (cardiovascular system)
0001009 (circulatory system)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011476 (mouse heart- neonate N30 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:0004872 (splanchnic layer of lateral plate mesoderm)
UBERON:0004140 (primary heart field)
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:1390-42D2&oldid=4339335"