Personal tools

FF:639-21E3: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 46: Line 46:
|library_id=CNhs11213
|library_id=CNhs11213
|library_id_phase_based=2:CNhs11213
|library_id_phase_based=2:CNhs11213
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520neonate%2520N00.CNhs11213.639-21E3.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.tissue.hCAGE/heart%252c%2520neonate%2520N00.CNhs11213.639-21E3.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/heart%252c%2520neonate%2520N00.CNhs11213.639-21E3.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/heart%252c%2520neonate%2520N00.CNhs11213.639-21E3.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.tissue.hCAGE/heart%252c%2520neonate%2520N00.CNhs11213.639-21E3.mm9.nobarcode.rdna.fa.gz
|name=heart, neonate N00
|name=heart, neonate N00
|namespace=FANTOM5
|namespace=FANTOM5

Revision as of 18:20, 17 May 2017


Name:heart, neonate N00
Species:Mouse (Mus musculus)
Library ID:CNhs11213
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueheart
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005147
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11213 CAGE DRX008979 DRR009853
Accession ID Mm9

Library idBAMCTSS
CNhs11213 DRZ001278 DRZ002661
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

CNhs11213

00
10
100.458
1000
10000.208
10010.435
10020.24
1003-0.0122
10040
1005-0.0575
10060.395
10070.0651
10080
10090.173
101-0.0248
10100
1011-0.0164
10120.0799
1013-0.2
10140.451
1015-0.0108
10160.159
10170
10180
10190
1020
10200
10210.0817
10220.756
10230
10240.259
10250
10260
10270
10280.048
10290.204
1030.13
10300
10310.185
10320.0948
1033-0.0273
10340
10350.618
1036-0.185
10370
10380.193
10390.386
1040
10400.164
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: CNhs11213

Jaspar motifP-value
MA0002.20.034
MA0003.10.733
MA0004.10.206
MA0006.10.414
MA0007.10.941
MA0009.10.757
MA0014.10.652
MA0017.10.0309
MA0018.20.173
MA0019.10.808
MA0024.10.164
MA0025.10.455
MA0027.10.643
MA0028.10.0757
MA0029.10.953
MA0030.10.633
MA0031.10.854
MA0035.20.237
MA0038.10.458
MA0039.20.0441
MA0040.10.227
MA0041.10.478
MA0042.10.623
MA0043.10.225
MA0046.12.29514e-15
MA0047.20.818
MA0048.10.0873
MA0050.10.0872
MA0051.10.145
MA0052.19.60146e-27
MA0055.10.00528
MA0057.10.793
MA0058.10.234
MA0059.10.18
MA0060.10.0012
MA0061.10.178
MA0062.22.41688e-5
MA0065.20.819
MA0066.10.781
MA0067.10.845
MA0068.10.247
MA0069.10.321
MA0070.10.995
MA0071.10.438
MA0072.10.587
MA0073.10.946
MA0074.10.446
MA0076.10.015
MA0077.10.976
MA0078.10.95
MA0079.20.397
MA0080.20.0117
MA0081.10.936
MA0083.14.14744e-13
MA0084.10.97
MA0087.10.388
MA0088.10.09
MA0090.12.97719e-4
MA0091.10.965
MA0092.10.372
MA0093.10.195
MA0099.22.95202e-4
MA0100.10.585
MA0101.10.349
MA0102.20.0205
MA0103.13.41365e-5
MA0104.20.0749
MA0105.10.241
MA0106.10.805
MA0107.10.453
MA0108.20.979
MA0111.10.582
MA0112.20.0204
MA0113.10.325
MA0114.10.00154
MA0115.10.601
MA0116.10.0556
MA0117.10.836
MA0119.10.12
MA0122.10.583
MA0124.10.705
MA0125.10.443
MA0131.10.809
MA0135.10.29
MA0136.10.00412
MA0137.20.129
MA0138.20.922
MA0139.10.136
MA0140.10.156
MA0141.19.63969e-8
MA0142.10.086
MA0143.10.595
MA0144.10.852
MA0145.10.6
MA0146.10.27
MA0147.10.071
MA0148.10.655
MA0149.10.299
MA0150.10.225
MA0152.10.108
MA0153.11.96848e-11
MA0154.10.553
MA0155.10.354
MA0156.13.94118e-4
MA0157.10.615
MA0159.10.0086
MA0160.10.00472
MA0162.10.268
MA0163.10.823
MA0164.10.401
MA0258.10.121
MA0259.10.363



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: CNhs11213

Novel motifP-value
10.434
100.644
1000.689
1010.367
1020.79
1030.722
1040.547
1050.481
1060.283
1070.198
1080.876
1090.662
110.895
1100.274
1110.323
1120.393
1130.391
1140.295
1150.957
1160.255
1170.729
1180.412
1190.489
120.944
1200.261
1210.59
1220.438
1230.251
1240.445
1250.919
1260.614
1270.138
1280.72
1290.637
135.41498e-4
1300.269
1310.413
1320.985
1330.473
1340.975
1350.808
1360.0563
1370.3
1380.133
1390.572
140.89
1400.548
1410.424
1420.857
1430.43
1440.131
1450.129
1460.665
1470.749
1480.992
1490.404
150.677
1500.188
1510.36
1520.248
1530.922
1540.582
1550.126
1565.13022e-36
1570.755
1580.105
1590.0158
1600.289
1610.354
1620.813
1630.552
1640.256
1650.04
1660.55
1670.769
1680.705
1690.00493
170.59
180.039
190.228
20.665
200.198
210.399
220.309
230.0448
240.497
250.613
260.0831
270.271
280.341
290.369
30.895
300.0869
310.816
320.412
330.235
340.472
350.263
360.0893
370.0745
380.105
390.993
40.478
400.00554
410.993
420.549
430.581
440.996
450.256
460.917
470.748
480.923
490.371
50.13
500.626
510.892
520.6
530.421
540.976
550.232
560.972
570.426
580.91
590.153
60.0459
600.437
610.721
620.531
630.435
640.521
650.0461
660.367
670.951
680.67
690.23
70.223
700.168
710.302
720.107
730.112
740.944
750.294
760.461
770.915
780.0875
790.497
80.889
800.0309
810.447
820.705
830.989
840.442
850.157
860.768
872.81429e-6
880.376
890.105
90.38
900.906
910.242
920.463
930.292
940.865
950.187
960.485
970.217
980.714
990.342



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: CNhs11213


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)
0000304 (mouse neonate N0 sample)
0011393 (mouse heart- neonate N00 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:639-21E3&oldid=4336229"