Personal tools

FF:15-8B2

From FANTOM5_SSTAR

Revision as of 00:34, 5 July 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Name:cerebellum, adult
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuecerebellum
dev stageadult
sexmale
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

CNhs10494

00
10.625
100
1000
10000
10010.0841
1002-0.116
10030.421
10040
10050.0956
10060.633
10070.0358
10080
1009-0.0786
101-0.0672
10100
10110.538
10120.274
10130.146
1014-0.0851
1015-0.116
1016-0.195
10170
10180
10190
1020
10200
10210
10220.0411
10230
10240
10250
10260
10270.331
10280
10290.443
103-0.0848
10300
1031-0.455
10320.179
10330
10340
10350.112
1036-0.165
10370
10380.128
10390.078
1040
1040-0.121
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: CNhs10494

Jaspar motifP-value
MA0002.20.0056
MA0003.10.168
MA0004.10.453
MA0006.10.112
MA0007.10.282
MA0009.10.365
MA0014.10.593
MA0017.14.62134e-6
MA0018.20.00425
MA0019.10.396
MA0024.10.0762
MA0025.10.00281
MA0027.10.026
MA0028.10.0841
MA0029.10.419
MA0030.10.451
MA0031.10.364
MA0035.20.00814
MA0038.10.916
MA0039.20.0166
MA0040.10.204
MA0041.10.885
MA0042.10.126
MA0043.10.0512
MA0046.11.22011e-11
MA0047.26.49894e-4
MA0048.10.128
MA0050.12.29806e-4
MA0051.15.39509e-4
MA0052.10.915
MA0055.10.106
MA0057.10.388
MA0058.10.366
MA0059.10.151
MA0060.10.6
MA0061.10.013
MA0062.27.91389e-4
MA0065.28.69887e-7
MA0066.10.278
MA0067.10.41
MA0068.10.26
MA0069.10.0921
MA0070.10.469
MA0071.10.86
MA0072.10.138
MA0073.10.8
MA0074.10.133
MA0076.10.185
MA0077.10.581
MA0078.10.832
MA0079.20.572
MA0080.23.58083e-10
MA0081.10.157
MA0083.17.36482e-4
MA0084.10.761
MA0087.10.322
MA0088.10.238
MA0090.10.0911
MA0091.10.291
MA0092.10.369
MA0093.10.499
MA0099.23.19839e-4
MA0100.10.267
MA0101.10.0189
MA0102.20.218
MA0103.10.336
MA0104.20.958
MA0105.10.00236
MA0106.10.0878
MA0107.10.0248
MA0108.24.92601e-8
MA0111.10.967
MA0112.20.00313
MA0113.10.735
MA0114.12.59382e-6
MA0115.10.00137
MA0116.10.0467
MA0117.10.946
MA0119.10.24
MA0122.10.941
MA0124.10.912
MA0125.10.0976
MA0131.10.859
MA0135.10.678
MA0136.11.28944e-14
MA0137.20.816
MA0138.21.74636e-4
MA0139.10.449
MA0140.11.69506e-4
MA0141.10.0204
MA0142.10.763
MA0143.10.911
MA0144.10.172
MA0145.10.118
MA0146.10.027
MA0147.10.777
MA0148.10.00125
MA0149.10.253
MA0150.10.208
MA0152.10.976
MA0153.15.11991e-14
MA0154.10.0591
MA0155.10.336
MA0156.11.30176e-10
MA0157.10.148
MA0159.10.0114
MA0160.10.0268
MA0162.10.196
MA0163.14.69073e-4
MA0164.10.849
MA0258.10.0969
MA0259.10.963



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: CNhs10494

Novel motifP-value
10.388
100.0799
1000.604
1010.918
1020.77
1030.0225
1040.723
1050.432
1060.0161
1070.155
1080.753
1090.00497
110.143
1100.101
1110.185
1120.00927
1130.348
1140.84
1150.996
1160.131
1170.00841
1180.296
1190.266
120.518
1200.737
1210.624
1220.836
1230.00752
1240.36
1250.341
1260.0296
1270.264
1280.0406
1290.419
131.98187e-7
1300.0444
1310.46
1320.856
1330.339
1340.348
1350.896
1360.0489
1370.374
1380.889
1390.274
140.924
1400.419
1410.851
1420.928
1430.387
1440.526
1451.35507e-4
1460.388
1470.206
1480.98
1490.719
150.243
1500.0637
1510.937
1520.0445
1530.589
1540.921
1550.392
1560.94
1570.478
1580.708
1590.169
1600.252
1610.814
1620.636
1630.684
1640.0387
1650.0497
1660.15
1670.733
1680.338
1690.00703
170.0654
180.929
190.195
20.968
200.055
210.144
220.176
230.542
240.0314
250.42
261.85435e-7
270.433
280.936
290.031
30.0711
300.888
310.848
320.644
330.193
340.677
350.479
360.141
370.0272
380.464
390.336
40.237
400.0361
410.333
420.251
430.151
440.113
450.643
460.0842
470.32
480.276
490.276
50.322
500.267
510.645
520.19
530.679
540.951
550.702
560.434
570.688
580.228
590.0813
60.677
600.0221
610.136
620.14
630.223
640.91
650.359
660.704
670.681
680.426
690.262
70.00675
700.169
710.0022
720.337
730.0333
740.728
750.0582
760.645
770.228
786.73397e-4
790.611
80.0537
800.832
810.916
820.417
830.354
840.583
850.35
860.156
870.0461
880.849
890.539
90.436
900.113
910.317
920.152
930.459
940.601
950.02
960.613
970.93
980.673
990.478



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: CNhs10494


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)
0007023 (adult organism)
0000955 (brain)
0002037 (cerebellum)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002680 (regional part of metencephalon)
0002616 (regional part of brain)
0004733 (segmental subdivision of hindbrain)
0004732 (segmental subdivision of nervous system)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001895 (metencephalon)
0002028 (hindbrain)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011276 (mouse cerebellum - adult 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
NA

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:15-8B2&oldid=1847222"