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|profile_rnaseq=,,,
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|repeat_enrich_byfamily=0.00439169576088696,0,0,0,0,0,0.35256598983742,0,0,0,0,-0.0843392403965415,0,0,0,0,0,0,0.0524812333199587,0,0,0,0,0,0,0,0,0,0,0,0,0.950542353544701,-0.558422792324031,0,0,0,0,0,-0.0871354333945594,0.0651281994657644,0.00394791388440252,0.882181219536773,-0.025494053807818,0,0,0,0,0,0,0,0,0,0,0,0,-0.0660055475634404,0,0,0,0,0,0,0.0288590436029832,0.244374584202533,0.514040340140897,0,-0.20244242069718,0.0891593514903143,0.905449262932074,-0.0185003911660262,0,0,0.0822100552120089,0.267133216643496,0,0,0.110277255510705,0.224073445917175,0.438317223312278,-0.0788315948399074,0.0270064156616068,0,0,0,0,0,0.308681000557866,0.0982137104990524,0.244237337909497,0,0,0.514040340140897,0.601903489292675,0
|rna_box=104
|rna_box=104
|rna_catalog_number=N/A
|rna_catalog_number=N/A

Revision as of 11:04, 24 September 2012


Name:visual cortex - wildtype, neonate N30, donor2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueVisual cortex
dev stagepostnatal day 30
sexmale
ageP30
cell typemixed
cell lineN/A
companyN/A
collaborationMichela Fagiolini/Alka Saxena/Piero Carninci
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberN/A
catalog numberN/A
sample typeVisual cortex tissue
extraction protocol (Details)Total RNA Trizol Qiagen minElute
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

CNhs13035

00
10.848
100
1000
10000
10010
1002-0.0941
10030.337
10040
1005-0.0389
10060.677
1007-0.228
10080
1009-0.19
101-0.111
10100
10111.06
10120.244
10130.127
1014-0.0851
1015-0.0585
1016-0.337
10170
10180
10190
1020
10200.604
10210
1022-0.0704
10230
1024-0.0899
10250
10260
10270.497
10280
10290.0615
103-0.0848
10300
1031-0.627
10320.0829
10330
10340
10350
1036-0.183
10370
1038-0.0337
10390.0616
1040
1040-0.216
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: CNhs13035

Jaspar motifP-value
MA0002.20.0133
MA0003.10.293
MA0004.10.564
MA0006.10.0941
MA0007.10.344
MA0009.10.667
MA0014.10.738
MA0017.14.56049e-7
MA0018.20.017
MA0019.10.172
MA0024.10.0163
MA0025.10.0797
MA0027.10.0707
MA0028.10.0415
MA0029.10.521
MA0030.10.501
MA0031.10.0256
MA0035.20.0181
MA0038.10.606
MA0039.20.00215
MA0040.10.073
MA0041.10.298
MA0042.10.437
MA0043.10.384
MA0046.12.79799e-10
MA0047.28.10748e-4
MA0048.10.0454
MA0050.19.27572e-6
MA0051.17.1989e-4
MA0052.10.856
MA0055.10.0106
MA0057.10.594
MA0058.10.388
MA0059.10.309
MA0060.10.0261
MA0061.10.0307
MA0062.21.4104e-4
MA0065.24.91823e-6
MA0066.10.15
MA0067.10.539
MA0068.10.199
MA0069.10.0462
MA0070.10.952
MA0071.10.0434
MA0072.10.243
MA0073.10.873
MA0074.10.132
MA0076.10.0774
MA0077.10.575
MA0078.10.926
MA0079.20.93
MA0080.21.27549e-10
MA0081.10.212
MA0083.13.4634e-4
MA0084.10.561
MA0087.10.54
MA0088.10.343
MA0090.10.131
MA0091.10.367
MA0092.10.254
MA0093.10.585
MA0099.20.00503
MA0100.10.338
MA0101.10.00712
MA0102.20.269
MA0103.10.388
MA0104.20.914
MA0105.10.0419
MA0106.10.0887
MA0107.10.0155
MA0108.21.21104e-5
MA0111.10.738
MA0112.20.00268
MA0113.10.255
MA0114.15.8289e-6
MA0115.17.7563e-4
MA0116.10.178
MA0117.10.788
MA0119.10.143
MA0122.10.765
MA0124.10.824
MA0125.10.27
MA0131.10.74
MA0135.10.318
MA0136.15.25452e-12
MA0137.20.169
MA0138.20.0015
MA0139.10.562
MA0140.18.18981e-4
MA0141.10.00325
MA0142.10.594
MA0143.10.493
MA0144.10.111
MA0145.10.0933
MA0146.10.0127
MA0147.10.966
MA0148.14.38299e-4
MA0149.10.376
MA0150.10.281
MA0152.10.898
MA0153.13.67898e-10
MA0154.10.0609
MA0155.10.309
MA0156.16.50832e-11
MA0157.10.0526
MA0159.10.0179
MA0160.10.00693
MA0162.10.199
MA0163.10.00724
MA0164.10.913
MA0258.10.0735
MA0259.10.735



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: CNhs13035

Novel motifP-value
10.403
100.084
1000.52
1010.442
1020.935
1030.278
1040.909
1050.536
1060.0409
1070.138
1080.361
1090.00211
110.0938
1100.0558
1110.485
1120.0169
1130.345
1140.74
1150.821
1160.388
1170.00508
1180.687
1190.191
120.864
1200.846
1210.0475
1220.967
1235.75021e-4
1240.026
1250.741
1260.0474
1270.661
1280.066
1290.442
136.10764e-9
1300.0296
1310.509
1320.735
1330.36
1340.0482
1350.529
1360.00813
1370.483
1380.682
1390.692
140.784
1400.323
1410.991
1420.959
1430.637
1440.487
1455.84465e-5
1460.174
1470.0992
1480.533
1490.342
150.33
1500.0353
1510.877
1520.062
1530.957
1540.992
1550.355
1563.04106e-9
1570.163
1580.322
1590.657
1600.319
1610.0708
1620.611
1630.738
1640.0779
1650.135
1660.696
1670.248
1680.568
1690.00411
170.0643
180.776
190.0684
20.846
200.0426
210.26
220.0761
230.675
240.00941
250.972
261.82929e-6
270.379
280.706
290.0277
30.0562
300.913
310.857
320.763
330.195
340.427
350.409
360.492
370.0175
380.353
390.203
40.178
400.126
410.517
420.197
430.148
440.966
450.557
460.232
470.574
480.319
490.349
50.446
500.152
510.786
520.172
530.57
540.973
550.992
560.466
570.978
580.399
590.135
60.87
600.0348
610.0437
620.285
630.135
640.696
650.304
660.494
670.957
680.396
690.218
70.0195
700.433
710.00775
720.404
730.0218
740.44
750.0543
760.744
770.417
780.00149
790.389
80.149
800.691
810.746
820.372
830.0317
840.792
850.268
860.212
870.0155
880.558
890.922
90.366
900.963
910.169
920.461
930.554
940.983
950.0169
960.594
970.829
980.476
990.53



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: CNhs13035


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)
0000955 (brain)
0002021 (occipital lobe)
0000411 (visual cortex)
0000956 (cerebral cortex)
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)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0001950 (neocortex)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000004 (tissue sample)
0000303 (neonate sample - mouse)
0000310 (mouse neonate N30 sample)
0011269 (mouse visual cortex from wildtype- neonate N30 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:0010316 (germ layer / neural crest)
FF:0000294 (mouse embryonic day 11 sample)

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