Personal tools

FF:1261-18D4

From FANTOM5_SSTAR

Revision as of 20:08, 29 June 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:eyeball, 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
tissueeyeball
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

CNhs11023

00
10.117
100
1000.162
10000
10010.102
10020.507
10030.0707
10040.358
1005-0.0579
10060.0936
10070.122
10080
10090.0572
1010.0531
10100
10110.0105
10120.162
1013-0.182
10140.635
10150.214
10160.24
10170
10180.205
10190
1020
10200
10210
1022-0.00943
10230
1024-0.0251
10250.00122
10260
10270.462
10280
10290.411
1030.435
10300
10310.265
1032-0.0145
10330.061
10340
10350.061
10360.107
10370
10380.00183
1039-0.0828
1040
10400.0755
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: CNhs11023

Jaspar motifP-value
MA0002.29.23806e-4
MA0003.10.2
MA0004.10.256
MA0006.10.198
MA0007.10.155
MA0009.10.266
MA0014.10.0887
MA0017.14.99677e-9
MA0018.20.341
MA0019.10.386
MA0024.10.00128
MA0025.10.00364
MA0027.10.913
MA0028.10.0314
MA0029.10.962
MA0030.10.403
MA0031.10.00526
MA0035.20.0391
MA0038.10.0234
MA0039.20.00364
MA0040.10.0255
MA0041.10.224
MA0042.10.68
MA0043.10.245
MA0046.11.95346e-8
MA0047.25.54701e-4
MA0048.10.753
MA0050.12.82702e-6
MA0051.11.38275e-6
MA0052.10.725
MA0055.10.693
MA0057.10.189
MA0058.10.205
MA0059.10.474
MA0060.15.47283e-6
MA0061.10.016
MA0062.21.79216e-7
MA0065.22.52591e-8
MA0066.10.609
MA0067.10.261
MA0068.10.938
MA0069.10.127
MA0070.10.989
MA0071.10.277
MA0072.10.815
MA0073.10.514
MA0074.10.126
MA0076.10.0753
MA0077.10.0371
MA0078.10.948
MA0079.20.589
MA0080.27.95856e-14
MA0081.10.0137
MA0083.10.849
MA0084.10.534
MA0087.10.663
MA0088.10.151
MA0090.10.827
MA0091.10.0854
MA0092.10.804
MA0093.10.277
MA0099.24.97896e-6
MA0100.10.248
MA0101.10.00263
MA0102.20.883
MA0103.17.00291e-4
MA0104.20.973
MA0105.10.135
MA0106.10.831
MA0107.10.00231
MA0108.23.21203e-8
MA0111.10.916
MA0112.25.86761e-4
MA0113.10.163
MA0114.19.73086e-8
MA0115.11.51037e-4
MA0116.10.115
MA0117.10.318
MA0119.10.0602
MA0122.10.448
MA0124.10.179
MA0125.10.00204
MA0131.10.647
MA0135.10.194
MA0136.14.02056e-19
MA0137.27.10417e-4
MA0138.20.716
MA0139.10.0423
MA0140.10.363
MA0141.14.22844e-6
MA0142.10.365
MA0143.10.0541
MA0144.10.00321
MA0145.10.0296
MA0146.10.0105
MA0147.10.845
MA0148.10.00353
MA0149.10.0145
MA0150.10.00995
MA0152.10.136
MA0153.13.75895e-9
MA0154.10.0132
MA0155.10.95
MA0156.12.93249e-13
MA0157.10.0164
MA0159.10.00506
MA0160.11.42316e-4
MA0162.10.606
MA0163.10.0214
MA0164.10.801
MA0258.10.00268
MA0259.10.858



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: CNhs11023

Novel motifP-value
10.192
100.236
1000.759
1010.971
1020.39
1030.0445
1040.51
1050.418
1060.0387
1070.503
1080.869
1090.0122
110.0293
1100.133
1110.00218
1120.00348
1130.924
1140.0289
1150.807
1160.342
1170.0166
1180.41
1190.178
120.517
1200.516
1210.126
1220.789
1230.965
1240.978
1250.0215
1260.166
1270.196
1280.352
1290.428
130.00295
1300.922
1310.559
1320.509
1330.877
1340.424
1350.43
1360.00452
1370.886
1380.407
1390.0524
140.868
1400.774
1410.132
1420.713
1430.48
1440.446
1450.112
1460.285
1470.502
1480.276
1490.156
150.0248
1500.238
1510.246
1520.0145
1530.926
1540.911
1550.24
1560.226
1570.899
1580.19
1590.628
1600.923
1610.173
1620.891
1630.101
1640.00563
1650.0213
1660.449
1670.61
1680.415
1690.00324
170.0551
180.761
190.422
20.449
200.363
210.433
220.248
230.53
240.0419
250.392
260.131
270.464
280.263
290.0347
30.112
300.85
310.769
320.681
330.0786
340.597
350.771
360.112
370.02
380.132
390.478
40.547
400.0395
410.106
420.451
430.196
440.198
450.275
460.32
470.146
480.0566
490.204
50.173
500.983
510.555
520.337
530.91
540.668
550.511
560.378
570.848
580.244
590.0375
60.739
600.0414
610.561
620.141
630.117
640.536
650.0882
660.973
670.428
680.099
690.886
70.16
700.012
710.0579
720.148
730.00331
740.955
750.0223
760.393
770.125
780.0943
790.345
80.101
800.162
810.418
820.0197
830.726
840.494
850.0608
860.154
873.97623e-4
880.79
890.15
90.452
900.345
910.73
920.209
930.25
940.703
950.0107
960.75
970.55
980.259
990.853



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: CNhs11023


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)
0000483 (epithelium)
0000033 (head)
0000479 (tissue)
0002346 (neurectoderm)
0000047 (simple eye)
0004121 (ectoderm-derived structure)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000480 (anatomical group)
0000923 (germ layer)
0002050 (embryonic structure)
0005423 (developing anatomical structure)
0001444 (subdivision of head)
0000481 (multi-tissue structure)
0000467 (anatomical system)
0001062 (anatomical entity)
0000119 (cell layer)
0005291 (embryonic tissue)
0000020 (sense organ)
0001032 (sensory system)
0005085 (ectodermal placode)
0001048 (primordium)
0006598 (presumptive structure)
0002532 (epiblast (generic))
0004088 (ocular region)
0000153 (anterior region of body)
0007811 (craniocervical region)
0000924 (ectoderm)
0002104 (visual system)
0004456 (entire sense organ system)
0001456 (face)
0003075 (neural plate)
0003056 (pre-chordal neural plate)
0003072 (optic cup)
0003071 (eye primordium)
0006601 (presumptive ectoderm)
0004128 (optic vesicle)
0007284 (presumptive neural plate)

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:1261-18D4&oldid=1844117"