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|sample_cell_line=
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Revision as of 16:16, 26 December 2012


Name:Mouse Neurons - substantia nigra, donor4
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesubstantia nigra
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companySciencell/3H
collaborationNA
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNASUB3
catalog numbercustom
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

CNhs12612

00
10.695
100
1000
10000
10010.0169
1002-0.0474
10030.0735
10040
10050.0412
10060.66
1007-0.19
10080
1009-0.067
101-0.216
10100
10110.281
10120
10130.111
10140
1015-0.0301
10160.00142
10170
10180
10190
1020
10200.546
10210.12
10220.148
10230
10240
10250
10260
10270.42
10280
1029-0.148
103-0.0736
10300
1031-0.378
10320.531
10330.0626
10340
10350
1036-0.0759
10370
1038-0.0327
10390.18
1040
1040-0.369
10410



CNhs12821



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: CNhs12612

Jaspar motifP-value
MA0002.20.0127
MA0003.10.488
MA0004.10.445
MA0006.10.193
MA0007.10.312
MA0009.10.933
MA0014.10.824
MA0017.13.12378e-6
MA0018.20.00288
MA0019.10.793
MA0024.10.0233
MA0025.15.68038e-4
MA0027.10.0694
MA0028.10.129
MA0029.10.851
MA0030.10.872
MA0031.10.342
MA0035.20.0721
MA0038.10.916
MA0039.20.0514
MA0040.10.627
MA0041.10.144
MA0042.10.309
MA0043.10.034
MA0046.13.72067e-6
MA0047.29.84777e-4
MA0048.10.0262
MA0050.13.33456e-6
MA0051.11.16883e-4
MA0052.10.98
MA0055.10.0187
MA0057.10.396
MA0058.10.51
MA0059.10.206
MA0060.10.797
MA0061.10.0143
MA0062.20.00355
MA0065.22.71854e-5
MA0066.10.1
MA0067.10.243
MA0068.10.983
MA0069.10.13
MA0070.10.21
MA0071.10.402
MA0072.10.933
MA0073.10.865
MA0074.10.242
MA0076.10.365
MA0077.10.13
MA0078.10.94
MA0079.20.162
MA0080.26.18274e-10
MA0081.10.169
MA0083.10.00205
MA0084.10.423
MA0087.10.18
MA0088.10.368
MA0090.10.0511
MA0091.10.226
MA0092.10.206
MA0093.10.499
MA0099.20.0238
MA0100.10.0826
MA0101.10.00917
MA0102.20.458
MA0103.10.397
MA0104.20.925
MA0105.10.00246
MA0106.10.0531
MA0107.10.0143
MA0108.20.00713
MA0111.10.971
MA0112.20.00161
MA0113.10.389
MA0114.14.03739e-6
MA0115.17.14526e-4
MA0116.10.101
MA0117.10.854
MA0119.10.183
MA0122.10.785
MA0124.10.633
MA0125.10.033
MA0131.10.512
MA0135.10.0723
MA0136.12.59924e-11
MA0137.20.0779
MA0138.25.07395e-5
MA0139.10.77
MA0140.17.6329e-5
MA0141.10.239
MA0142.10.556
MA0143.10.854
MA0144.10.0351
MA0145.10.17
MA0146.10.0913
MA0147.10.805
MA0148.10.00148
MA0149.10.408
MA0150.10.272
MA0152.10.0313
MA0153.11.78499e-7
MA0154.10.0484
MA0155.10.602
MA0156.14.04048e-9
MA0157.10.229
MA0159.10.0297
MA0160.10.135
MA0162.10.279
MA0163.10.00229
MA0164.10.854
MA0258.10.0499
MA0259.10.786


library id: CNhs12821This sample isn't target for the analysis



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: CNhs12612

Novel motifP-value
10.273
100.0355
1000.316
1010.986
1020.791
1030.088
1040.85
1050.462
1060.0316
1070.0762
1080.312
1090.0332
110.23
1100.0424
1110.478
1120.0121
1130.6
1140.836
1150.88
1160.638
1170.00296
1180.355
1190.186
120.94
1200.808
1210.472
1220.742
1234.28563e-4
1240.0815
1250.188
1260.065
1270.503
1280.016
1290.231
133.41613e-8
1300.0973
1310.528
1320.594
1330.764
1340.21
1350.237
1360.716
1370.564
1380.566
1390.347
140.756
1400.136
1410.764
1420.32
1430.447
1440.642
1457.47928e-5
1460.433
1470.241
1480.761
1490.718
150.175
1500.0629
1510.971
1520.164
1530.417
1540.54
1550.721
1560.0164
1570.241
1580.0887
1590.178
1600.216
1610.652
1620.739
1630.762
1640.0249
1650.319
1660.29
1670.95
1680.554
1690.00247
170.103
180.588
190.106
20.45
200.0156
210.322
220.211
230.651
240.112
250.875
262.269e-10
270.192
280.864
290.0493
30.107
300.708
310.541
320.814
330.136
340.968
350.693
360.163
370.0588
380.483
390.37
40.366
400.16
410.639
420.208
430.104
440.825
450.775
460.0248
470.615
480.433
490.137
50.166
500.298
510.651
520.299
530.488
540.951
550.97
560.659
570.539
580.309
590.289
60.748
600.0359
610.0607
620.23
630.22
640.995
650.578
660.942
670.979
680.974
690.809
70.00931
700.269
710.00139
720.667
730.0919
740.732
750.0618
760.286
770.775
780.00322
790.112
80.0838
800.943
810.737
820.414
830.359
840.642
850.251
860.105
870.47
880.718
890.778
90.355
900.144
910.0842
920.468
930.0597
940.449
950.139
960.415
970.979
980.725
990.527


library id: CNhs12821This sample isn't target for the analysis



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: CNhs12612
library id: CNhs12821


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000117 (CNS neuron (sensu Vertebrata))
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0002614 (neuron of the substantia nigra)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0002038 (substantia nigra)
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)
0001062 (anatomical entity)
0000480 (anatomical group)
0009663 (telencephalic nucleus)
0002420 (basal ganglion)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0009661 (midbrain nucleus)
0000125 (neural nucleus)
0002950 (regional part of midbrain)
0002020 (gray matter)
0007245 (nuclear complex of neuraxis)
0010317 (germ layer / neural crest derived structure)
0002308 (nucleus of brain)
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0001893 (telencephalon)
0001890 (forebrain)
0001891 (midbrain)
0010011 (collection of basal ganglia)
0000454 (cerebral subcortex)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000208 (mouse neuron of the substantia nigra 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
CL:0000133 (neurectodermal cell)
CL:0000337 (neuroblast (sensu Vertebrata))
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)

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