Personal tools

FF:479-18E5

From FANTOM5_SSTAR

Revision as of 18:55, 14 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:heart, embryo E17
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueheart
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
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

CNhs11025

00
10
100.379
1000
10000.315
10010.388
10020.373
1003-0.0436
10040
1005-0.0591
10060.295
10070.00559
10080
10090.116
101-0.00755
10100
1011-0.0122
10120
1013-0.217
10140.6
10150.0579
10160.0775
10170
10180
10190
1020
10200
10210.0216
10220.628
10230
10240.244
10250
10260
10270
10280
10290.374
1030.165
10300
10310.113
10320.0259
1033-0.0153
10340
10350.652
1036-0.0454
10370
10380.0935
10390.313
1040
10400.113
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 no result for this sample


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: CNhs11025

Jaspar motifP-value
MA0002.20.0554
MA0003.10.414
MA0004.10.334
MA0006.10.919
MA0007.10.604
MA0009.10.954
MA0014.10.463
MA0017.10.0755
MA0018.20.0257
MA0019.10.688
MA0024.10.249
MA0025.10.0552
MA0027.10.35
MA0028.10.388
MA0029.10.654
MA0030.10.0722
MA0031.10.0939
MA0035.20.334
MA0038.10.907
MA0039.20.0184
MA0040.10.0616
MA0041.10.184
MA0042.10.39
MA0043.10.045
MA0046.16.19788e-16
MA0047.20.0853
MA0048.10.00477
MA0050.16.88672e-4
MA0051.10.00829
MA0052.11.95786e-22
MA0055.10.00118
MA0057.10.93
MA0058.10.313
MA0059.10.804
MA0060.10.00567
MA0061.10.427
MA0062.22.19507e-5
MA0065.20.849
MA0066.10.612
MA0067.10.336
MA0068.10.276
MA0069.10.352
MA0070.10.528
MA0071.10.324
MA0072.10.23
MA0073.10.909
MA0074.10.317
MA0076.10.0146
MA0077.10.941
MA0078.10.373
MA0079.20.142
MA0080.20.0031
MA0081.10.664
MA0083.19.52521e-12
MA0084.10.621
MA0087.10.706
MA0088.10.731
MA0090.10.00201
MA0091.10.64
MA0092.10.447
MA0093.10.291
MA0099.27.22051e-6
MA0100.10.441
MA0101.10.0842
MA0102.20.00736
MA0103.11.19286e-4
MA0104.20.935
MA0105.10.128
MA0106.10.4
MA0107.10.0946
MA0108.20.589
MA0111.10.797
MA0112.20.00152
MA0113.10.501
MA0114.10.0213
MA0115.10.909
MA0116.10.352
MA0117.10.854
MA0119.10.0264
MA0122.10.674
MA0124.10.737
MA0125.10.581
MA0131.10.895
MA0135.10.0416
MA0136.13.34275e-4
MA0137.20.0219
MA0138.20.67
MA0139.10.407
MA0140.10.232
MA0141.12.43975e-9
MA0142.10.171
MA0143.10.753
MA0144.10.492
MA0145.10.512
MA0146.10.576
MA0147.10.846
MA0148.10.182
MA0149.10.261
MA0150.10.0224
MA0152.10.317
MA0153.18.1181e-11
MA0154.10.131
MA0155.10.199
MA0156.17.43122e-7
MA0157.10.34
MA0159.10.00523
MA0160.10.005
MA0162.10.14
MA0163.10.0859
MA0164.10.416
MA0258.10.0669
MA0259.10.141



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: CNhs11025

Novel motifP-value
10.184
100.399
1000.798
1010.61
1020.847
1030.595
1040.818
1050.56
1060.995
1070.407
1080.923
1090.307
110.877
1100.0645
1110.318
1120.489
1130.383
1140.56
1150.99
1160.515
1170.182
1180.233
1190.808
120.905
1200.274
1210.604
1220.183
1230.184
1240.725
1250.674
1260.643
1270.203
1280.255
1290.626
132.12805e-4
1300.21
1310.206
1320.962
1330.455
1340.61
1350.996
1360.0203
1370.585
1380.104
1390.716
140.979
1400.244
1410.495
1420.751
1430.665
1440.0975
1450.0814
1460.374
1470.738
1480.722
1490.329
150.806
1500.131
1510.521
1520.776
1530.905
1540.688
1550.316
1568.8592e-7
1570.717
1580.214
1590.0199
1600.237
1610.782
1620.564
1630.906
1640.381
1650.0983
1660.594
1670.832
1680.494
1691.28258e-4
170.726
180.234
190.173
20.449
200.133
210.904
220.235
230.427
240.587
250.972
260.00478
270.319
280.407
290.353
30.431
300.0103
310.826
320.914
330.126
340.883
350.894
360.154
370.0503
380.449
390.855
40.369
400.00891
410.955
420.918
430.354
440.422
450.115
460.465
470.788
480.524
490.219
50.287
500.453
510.984
520.727
530.503
540.706
550.109
560.953
570.103
580.989
590.165
60.163
600.81
610.721
620.967
630.36
640.938
650.52
660.364
670.459
680.477
690.441
70.069
700.275
710.00745
720.178
730.309
740.178
750.964
760.335
770.619
780.117
790.596
80.357
800.00839
810.631
820.604
830.951
840.591
850.132
860.679
873.08935e-6
880.339
890.121
90.529
900.4
910.0941
920.889
930.312
940.221
950.431
960.281
970.171
980.705
990.638



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: CNhs11025


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
0000025 (tube)
0000061 (anatomical structure)
0000062 (organ)
0000119 (cell layer)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0000948 (heart)
0001009 (circulatory system)
0001048 (primordium)
0001062 (anatomical entity)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003084 (heart primordium)
0003914 (epithelial tube)
0004120 (mesoderm-derived structure)
0004140 (primary heart field)
0004141 (heart tube)
0004291 (heart rudiment)
0004535 (cardiovascular system)
0004872 (splanchnic layer of lateral plate mesoderm)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005498 (primitive heart tube)
0007005 (cardiac mesoderm)
0007100 (primary circulatory organ)

FF: FANTOM5
NA

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
NA

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:479-18E5&oldid=1697060"