Personal tools

FF:399-16E2

From FANTOM5_SSTAR

Revision as of 18:24, 17 October 2013 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:eyeball, embryo E14
Species:Mouse (Mus musculus)
Library ID:CNhs10521
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueeyeball
dev stage14 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  DRS008819
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10521 CAGE DRX008956 DRR009830
Accession ID Mm9

Library idBAMCTSS
CNhs10521 DRZ001255 DRZ002638
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

CNhs10521

00
10.0536
100
1000.0899
1000-0.0355
1001-0.0749
10020.208
1003-0.121
10040.503
1005-0.169
10060.0161
10070.0466
10080
1009-0.0572
1010.0814
10100
1011-0.0358
10120
1013-0.147
10140.283
10150.322
10160.207
10170
10180
10190
1020
10200
10210.116
1022-0.0842
10230
10240
1025-0.0611
10260
10270.486
10280
1029-0.129
1030.0605
10300
10310.209
1032-0.0175
10330.0466
10340
10350
10360.1
10370
1038-0.122
1039-0.121
1040
1040-0.0678
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: CNhs10521

Jaspar motifP-value
MA0002.29.20287e-4
MA0003.10.452
MA0004.10.857
MA0006.10.313
MA0007.10.319
MA0009.10.254
MA0014.10.463
MA0017.13.6258e-6
MA0018.20.0197
MA0019.10.981
MA0024.18.99982e-4
MA0025.10.622
MA0027.10.132
MA0028.10.305
MA0029.10.99
MA0030.10.178
MA0031.10.0546
MA0035.20.0726
MA0038.10.00411
MA0039.20.465
MA0040.10.201
MA0041.10.135
MA0042.10.756
MA0043.10.00611
MA0046.11.10616e-18
MA0047.20.00133
MA0048.10.934
MA0050.11.34247e-6
MA0051.12.05267e-4
MA0052.10.315
MA0055.10.241
MA0057.10.107
MA0058.10.934
MA0059.10.983
MA0060.11.6461e-20
MA0061.10.0366
MA0062.20.629
MA0065.25.52949e-6
MA0066.10.168
MA0067.10.901
MA0068.10.102
MA0069.10.0587
MA0070.10.137
MA0071.10.623
MA0072.10.583
MA0073.10.952
MA0074.10.433
MA0076.10.094
MA0077.14.98087e-4
MA0078.10.105
MA0079.20.629
MA0080.23.64073e-11
MA0081.10.198
MA0083.10.493
MA0084.10.107
MA0087.10.124
MA0088.10.659
MA0090.10.91
MA0091.10.421
MA0092.10.383
MA0093.10.898
MA0099.26.51738e-4
MA0100.10.861
MA0101.10.21
MA0102.20.156
MA0103.10.00287
MA0104.20.487
MA0105.10.00242
MA0106.10.267
MA0107.10.0679
MA0108.28.71863e-6
MA0111.10.408
MA0112.23.02324e-6
MA0113.10.332
MA0114.13.53403e-5
MA0115.10.0104
MA0116.10.0107
MA0117.10.598
MA0119.10.00217
MA0122.10.855
MA0124.10.747
MA0125.10.0294
MA0131.10.546
MA0135.10.0276
MA0136.15.09481e-6
MA0137.20.177
MA0138.20.113
MA0139.10.0835
MA0140.10.00979
MA0141.10.00589
MA0142.10.139
MA0143.10.00335
MA0144.10.0962
MA0145.10.0288
MA0146.10.177
MA0147.10.712
MA0148.13.08044e-5
MA0149.10.0553
MA0150.10.14
MA0152.10.961
MA0153.18.69294e-16
MA0154.18.84398e-4
MA0155.10.664
MA0156.10.0132
MA0157.10.0776
MA0159.10.0261
MA0160.10.0498
MA0162.10.684
MA0163.17.86216e-4
MA0164.10.831
MA0258.10.00166
MA0259.10.687



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: CNhs10521

Novel motifP-value
10.0588
100.107
1000.817
1010.59
1020.583
1030.0532
1040.983
1050.358
1060.00725
1070.0499
1080.844
1090.14
110.106
1100.081
1116.61576e-4
1120.0147
1130.705
1140.0188
1150.887
1160.51
1170.131
1180.495
1190.0451
120.541
1200.41
1210.797
1220.945
1230.754
1240.455
1250.115
1260.329
1270.0711
1280.0378
1290.169
130.0202
1300.756
1310.903
1320.296
1330.0723
1340.921
1350.0532
1360.728
1370.411
1380.4
1390.00759
140.547
1400.00977
1410.0636
1420.418
1430.59
1440.986
1450.0996
1460.577
1470.395
1480.109
1490.214
150.0829
1500.472
1510.221
1520.0741
1530.461
1540.362
1550.478
1564.20124e-4
1570.811
1580.209
1590.00926
1600.311
1610.475
1620.695
1630.51
1640.0272
1650.108
1660.751
1670.249
1680.652
1690.00106
170.0232
180.689
190.12
20.482
200.957
210.831
220.224
230.069
240.563
250.673
260.0487
270.457
280.298
290.22
30.101
300.766
310.568
320.12
330.656
340.938
350.417
360.313
370.046
380.36
390.355
40.485
400.618
410.981
420.325
430.112
440.157
450.482
460.122
470.139
480.129
490.12
50.0846
500.889
510.564
520.201
530.69
540.56
550.806
560.315
570.429
580.283
590.0833
60.563
600.0305
610.574
620.0794
630.107
640.589
650.138
660.226
670.729
680.039
690.562
70.135
700.0178
710.062
720.547
730.0959
740.346
750.0386
760.69
770.165
780.15
790.155
80.122
800.2
810.416
820.00982
830.895
840.702
850.00811
860.187
870.252
880.826
890.164
90.341
900.077
910.428
920.0591
930.0958
940.375
950.2
960.32
970.735
980.363
990.693



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: CNhs10521


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)
0000970 (eye)
0000019 (camera-type eye)
0000033 (head)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0000047 (simple eye)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0001032 (sensory system)
0010317 (germ layer / neural crest derived structure)
0004088 (ocular region)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002104 (visual system)
0004456 (entire sense organ system)
0001456 (face)

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)
0000296 (mouse embryonic day 14 sample)
0011335 (mouse eyeball- embryo E14 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:0006601 (presumptive ectoderm)
UBERON:0003056 (pre-chordal neural plate)
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:399-16E2&oldid=3078684"