Personal tools

FF:413-26A8

From FANTOM5_SSTAR

Revision as of 19:18, 16 October 2013 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:forelimb, embryo E14
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:developmental
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissueforelimb
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  DRS008829
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{library_id}}} {{{accession_numbers}}}
Accession ID Mm9

Library idBAMCTSS
{{{library_id}}}
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

CNhs10577

00
10
100
1000
10000
1001-0.0275
10020.1
10030.208
10040
10050
1006-0.0589
10070.0577
10080
1009-0.00941
1010.0717
10100
10110
10120
1013-0.126
10140.319
10150.3
10160.386
10170
10180.321
10190
1020
10200
10210.158
10220
10230
1024-0.0337
10250
10260.0566
10270.0374
10280
1029-0.0899
1030.321
10300
10310.357
1032-0.0243
10330.0109
10340
10350
10360.14
10370
1038-0.00817
1039-0.129
1040
10400.101
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: CNhs10577

Jaspar motifP-value
MA0002.20.00477
MA0003.10.727
MA0004.10.959
MA0006.10.684
MA0007.10.278
MA0009.10.265
MA0014.10.155
MA0017.11.88791e-8
MA0018.20.728
MA0019.10.663
MA0024.12.87209e-4
MA0025.10.264
MA0027.10.107
MA0028.10.968
MA0029.10.617
MA0030.10.0476
MA0031.10.0257
MA0035.24.46668e-5
MA0038.10.201
MA0039.20.248
MA0040.10.0898
MA0041.10.697
MA0042.10.269
MA0043.10.21
MA0046.12.90481e-21
MA0047.20.00189
MA0048.10.465
MA0050.12.87925e-5
MA0051.14.26837e-4
MA0052.17.17367e-4
MA0055.10.272
MA0057.10.271
MA0058.10.874
MA0059.10.586
MA0060.17.66799e-7
MA0061.10.267
MA0062.20.2
MA0065.28.18238e-5
MA0066.10.0908
MA0067.10.0944
MA0068.10.268
MA0069.10.933
MA0070.10.487
MA0071.10.0141
MA0072.10.00727
MA0073.10.954
MA0074.10.782
MA0076.10.849
MA0077.10.171
MA0078.10.708
MA0079.20.0965
MA0080.22.11135e-9
MA0081.10.282
MA0083.10.231
MA0084.10.329
MA0087.10.947
MA0088.10.389
MA0090.10.188
MA0091.10.823
MA0092.10.814
MA0093.10.865
MA0099.20.0127
MA0100.10.562
MA0101.10.451
MA0102.20.239
MA0103.10.00262
MA0104.20.967
MA0105.10.147
MA0106.10.426
MA0107.10.236
MA0108.29.94962e-4
MA0111.10.142
MA0112.21.92679e-5
MA0113.10.177
MA0114.11.10185e-6
MA0115.10.00474
MA0116.10.00402
MA0117.10.0914
MA0119.10.0787
MA0122.10.696
MA0124.10.448
MA0125.10.201
MA0131.10.433
MA0135.10.325
MA0136.11.01077e-6
MA0137.20.2
MA0138.21.94066e-4
MA0139.10.00184
MA0140.14.91067e-5
MA0141.11.33398e-4
MA0142.10.521
MA0143.10.109
MA0144.10.39
MA0145.10.243
MA0146.10.977
MA0147.10.99
MA0148.14.49569e-5
MA0149.10.00252
MA0150.11.81337e-4
MA0152.10.118
MA0153.14.6595e-18
MA0154.14.57562e-4
MA0155.10.319
MA0156.10.00182
MA0157.10.263
MA0159.10.00617
MA0160.10.00191
MA0162.10.992
MA0163.10.291
MA0164.10.688
MA0258.12.42242e-4
MA0259.10.888



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: CNhs10577

Novel motifP-value
10.0375
100.208
1000.834
1010.68
1020.584
1030.0189
1040.55
1050.765
1060.0311
1070.2
1080.77
1090.275
110.206
1100.282
1110.00935
1120.0157
1130.485
1140.00765
1150.722
1160.922
1170.284
1180.358
1190.0295
120.551
1200.759
1210.466
1220.863
1230.108
1240.232
1250.141
1260.232
1270.0639
1280.0674
1290.0899
130.796
1300.189
1310.919
1320.502
1330.71
1340.769
1350.736
1360.55
1370.766
1380.688
1390.00175
140.275
1400.105
1410.388
1420.81
1430.584
1440.531
1450.308
1460.426
1470.334
1480.16
1490.511
150.0534
1500.702
1510.0112
1520.48
1530.142
1540.647
1550.784
1564.74515e-4
1570.173
1580.16
1590.0592
1600.921
1610.288
1620.822
1630.0431
1640.25
1650.18
1660.157
1670.313
1680.728
1690.183
170.171
180.222
190.267
20.645
200.902
210.802
220.64
230.217
240.79
250.232
260.664
270.513
280.192
290.286
30.158
300.669
310.379
320.412
330.632
340.966
350.0313
360.165
370.189
380.345
390.796
40.49
400.321
410.507
420.398
430.114
440.0628
450.846
460.292
470.122
480.13
490.062
50.118
500.501
510.6
520.438
530.751
540.397
550.824
560.389
570.463
580.217
590.433
60.471
600.19
610.451
620.0588
630.354
640.408
650.229
660.491
670.731
680.00457
690.47
70.261
700.00304
710.251
720.465
730.554
740.413
750.0782
760.892
770.272
780.569
790.764
80.0966
800.0639
810.435
820.113
830.492
840.54
850.019
860.758
870.625
880.891
890.511
90.834
900.028
910.652
920.114
930.364
940.677
950.335
960.243
970.701
980.208
990.95



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: CNhs10577


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)
0002102 (forelimb)
0000479 (tissue)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)
0004708 (paired limb/fin)
0002101 (limb)
0004710 (pectoral appendage)
0010317 (germ layer / neural crest derived structure)
0010707 (appendage girdle complex)
0000153 (anterior region of body)
0010708 (pectoral complex)

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)
0011342 (mouse forelimb- 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:0006603 (presumptive mesoderm)
UBERON:0005417 (forelimb bud)
UBERON:0005733 (limb field)
UBERON:0005732 (limb/fin field)
UBERON:0005729 (forelimb/pectoral fin field)
UBERON:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

{{{1}}} Accession numbers
MethodSample accession id
{{{2}}} 
Library accession numbers

Library idMethodExp. accession idRun accession id
{{{4}}} {{{3}}}
Accession ID

Library idBAMCTSS
{{{4}}}
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:413-26A8&oldid=3076765"