Personal tools

FF:1349-25I2: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 62: Line 62:
|rna_weight_ug=
|rna_weight_ug=
|sample_age=
|sample_age=
|sample_category=developmental
|sample_cell_catalog=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_line=

Revision as of 15:57, 26 December 2012


Name:heart, neonate N03
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueheart
dev stage3 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
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

CNhs11221

00
10
100.519
1000
10000.477
10010.485
10020.202
10030.0694
10040
1005-0.0389
10060.486
10070.0286
10080
10090.204
101-0.0146
10100
1011-0.0214
10120.0662
1013-0.0931
10140.168
1015-0.0417
10160.167
10170
10180
10190
1020
10200
10210.0544
10220.732
10230
10240.272
10250
10260
10270
10280
10290.0266
1030.174
10300
10310.206
10320.132
10330
10340
10350.633
1036-0.194
10370
10380.194
10390.303
1040
10400.122
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: CNhs11221

Jaspar motifP-value
MA0002.20.0067
MA0003.10.651
MA0004.10.0282
MA0006.10.259
MA0007.10.33
MA0009.10.721
MA0014.10.552
MA0017.10.119
MA0018.20.375
MA0019.10.755
MA0024.10.142
MA0025.10.922
MA0027.10.422
MA0028.10.0621
MA0029.10.576
MA0030.10.211
MA0031.10.114
MA0035.20.0987
MA0038.10.624
MA0039.20.0466
MA0040.10.0934
MA0041.10.446
MA0042.10.542
MA0043.10.708
MA0046.15.26522e-16
MA0047.20.183
MA0048.10.0551
MA0050.10.00155
MA0051.10.0384
MA0052.18.16666e-44
MA0055.13.86953e-4
MA0057.10.955
MA0058.10.0464
MA0059.10.104
MA0060.10.0015
MA0061.10.148
MA0062.25.24898e-7
MA0065.20.944
MA0066.10.716
MA0067.10.542
MA0068.10.145
MA0069.10.237
MA0070.11
MA0071.10.0467
MA0072.10.863
MA0073.10.951
MA0074.10.128
MA0076.10.00465
MA0077.10.458
MA0078.10.554
MA0079.20.575
MA0080.21.99029e-4
MA0081.10.621
MA0083.11.38686e-17
MA0084.10.847
MA0087.10.377
MA0088.10.268
MA0090.13.129e-5
MA0091.10.919
MA0092.10.497
MA0093.10.0322
MA0099.27.48963e-5
MA0100.10.0877
MA0101.10.186
MA0102.20.00745
MA0103.13.78641e-6
MA0104.20.0681
MA0105.10.0887
MA0106.10.796
MA0107.10.333
MA0108.20.645
MA0111.10.593
MA0112.20.0453
MA0113.10.884
MA0114.10.0127
MA0115.10.597
MA0116.10.0451
MA0117.10.989
MA0119.10.249
MA0122.10.314
MA0124.10.564
MA0125.10.418
MA0131.10.687
MA0135.10.176
MA0136.11.33612e-5
MA0137.20.0512
MA0138.20.997
MA0139.10.216
MA0140.10.251
MA0141.14.60659e-11
MA0142.10.0487
MA0143.10.85
MA0144.10.986
MA0145.10.615
MA0146.10.173
MA0147.10.0511
MA0148.10.234
MA0149.10.332
MA0150.10.161
MA0152.10.971
MA0153.14.26692e-11
MA0154.10.659
MA0155.10.214
MA0156.14.66318e-7
MA0157.10.195
MA0159.19.40527e-4
MA0160.11.79819e-5
MA0162.10.139
MA0163.10.165
MA0164.10.146
MA0258.10.204
MA0259.10.936



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: CNhs11221

Novel motifP-value
10.269
100.737
1000.933
1010.558
1020.689
1030.349
1040.619
1050.371
1060.979
1070.541
1080.876
1090.546
110.685
1100.306
1110.28
1120.335
1130.65
1140.921
1150.993
1160.383
1170.917
1180.614
1190.828
120.843
1200.175
1210.692
1220.178
1230.16
1240.391
1250.61
1260.423
1270.227
1280.257
1290.613
135.58485e-4
1300.278
1310.537
1320.627
1330.396
1340.599
1350.928
1360.213
1370.251
1380.0669
1390.547
140.405
1400.495
1410.355
1420.776
1430.247
1440.248
1450.469
1460.624
1470.693
1480.798
1490.201
150.799
1500.133
1510.535
1520.253
1530.859
1540.863
1550.0892
1560.349
1570.764
1580.1
1590.0196
1600.513
1610.817
1620.453
1630.423
1640.723
1650.0475
1660.374
1670.91
1680.297
1699.35689e-4
170.844
180.0517
190.0993
20.625
200.397
210.498
220.187
230.473
240.684
250.662
260.0407
270.27
280.33
290.412
30.902
300.0488
310.829
320.875
330.162
340.295
350.379
360.0634
370.0981
380.956
390.849
40.211
400.0144
410.813
420.408
430.471
440.882
450.424
460.683
470.866
480.847
490.306
50.828
500.769
510.919
520.482
530.527
540.964
550.112
560.719
570.388
580.989
590.112
60.0527
600.555
610.652
620.649
630.36
640.703
650.564
660.363
670.834
680.351
690.123
70.142
700.0663
710.211
720.136
730.131
740.752
750.176
760.832
770.788
780.148
790.878
80.876
800.0118
810.663
820.656
830.801
840.48
850.232
860.548
872.72525e-5
880.415
890.157
90.279
900.811
910.255
920.842
930.401
940.674
950.283
960.447
970.281
980.787
990.811



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: CNhs11221


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)
0000311 (mouse neonate N3 sample)
0011474 (mouse heart- neonate N03 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:1349-25I2&oldid=2566883"