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|microRNAs=
|microRNAs=
|microRNAs_nn=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/mouse#cage;sample;11741
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11741
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/mouse#cage;sample;11741
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11741
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520striatal%252c%2520donor2.CNhs12360.11741-123F4.mm10.nobarcode.bam
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520striatal%252c%2520donor2.CNhs12360.11741-123F4.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520striatal%252c%2520donor2.CNhs12360.11741-123F4.mm10.nobarcode.ctss.bed.gz
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Neurons%2520-%2520striatal%252c%2520donor2.CNhs12360.11741-123F4.mm10.nobarcode.ctss.bed.gz

Revision as of 16:57, 4 August 2017


Name:Mouse Neurons - striatal, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12360
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuecorpus striatum
dev stageNA
sexNA
ageNA
cell typeneuron
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRNAMNS1
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005038
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12360 CAGE DRX008844 DRR009716
Accession ID Mm9

Library idBAMCTSS
CNhs12360 DRZ001141 DRZ002526
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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

CNhs12360

00
10.423
100
1000.423
10000
1001-0.0668
10020.0456
10030.0293
10040.0717
10050
10060.37
1007-0.0312
10080
1009-0.2
101-0.163
10100
10110.198
10120
1013-0.0266
10140.0503
10150.444
10160.236
10170
10180
10190
1020
10200.552
10210.135
1022-0.0704
10230
1024-0.14
10250
10260
10270.375
10280
1029-0.115
103-0.0709
10300
1031-0.568
10320.01
10330.0234
10340
10350
1036-0.225
10370
10380.108
1039-0.213
1040
1040-0.271
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: CNhs12360

Jaspar motifP-value
MA0002.20.00164
MA0003.10.173
MA0004.10.604
MA0006.10.085
MA0007.10.154
MA0009.10.805
MA0014.10.424
MA0017.11.64739e-5
MA0018.20.0154
MA0019.10.429
MA0024.10.953
MA0025.10.533
MA0027.10.533
MA0028.10.679
MA0029.10.62
MA0030.10.339
MA0031.10.0575
MA0035.20.0873
MA0038.10.427
MA0039.20.0173
MA0040.10.688
MA0041.10.253
MA0042.10.539
MA0043.10.0696
MA0046.12.65618e-8
MA0047.20.00146
MA0048.10.396
MA0050.16.31981e-9
MA0051.11.53189e-4
MA0052.10.0453
MA0055.10.485
MA0057.10.115
MA0058.10.566
MA0059.10.372
MA0060.10.00769
MA0061.10.0565
MA0062.20.207
MA0065.21.78908e-5
MA0066.10.201
MA0067.10.767
MA0068.10.887
MA0069.10.124
MA0070.10.453
MA0071.10.208
MA0072.10.143
MA0073.10.891
MA0074.10.355
MA0076.10.63
MA0077.10.0134
MA0078.10.0945
MA0079.20.613
MA0080.23.50162e-10
MA0081.10.363
MA0083.10.0061
MA0084.10.696
MA0087.10.528
MA0088.10.224
MA0090.10.0084
MA0091.10.191
MA0092.10.138
MA0093.10.621
MA0099.21.13922e-4
MA0100.10.821
MA0101.10.0577
MA0102.20.923
MA0103.10.168
MA0104.20.623
MA0105.10.0541
MA0106.10.12
MA0107.10.0518
MA0108.20.0681
MA0111.10.99
MA0112.28.5774e-5
MA0113.10.295
MA0114.11.05204e-4
MA0115.10.0102
MA0116.10.0848
MA0117.10.821
MA0119.10.0418
MA0122.10.677
MA0124.10.813
MA0125.10.208
MA0131.10.842
MA0135.10.128
MA0136.17.65572e-8
MA0137.20.0233
MA0138.20.21
MA0139.10.304
MA0140.10.00174
MA0141.10.00903
MA0142.10.0977
MA0143.10.0119
MA0144.10.0208
MA0145.10.0416
MA0146.10.0458
MA0147.10.712
MA0148.11.06855e-5
MA0149.10.0575
MA0150.10.0195
MA0152.10.0768
MA0153.11.77314e-7
MA0154.10.023
MA0155.10.698
MA0156.12.66772e-5
MA0157.10.0584
MA0159.10.003
MA0160.10.0766
MA0162.10.319
MA0163.10.00311
MA0164.10.996
MA0258.10.00769
MA0259.10.56



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: CNhs12360

Novel motifP-value
10.141
100.104
1000.795
1010.9
1020.978
1030.137
1040.914
1050.173
1060.00488
1070.0329
1080.42
1090.00459
110.112
1100.0966
1110.167
1120.00951
1130.942
1140.341
1150.999
1160.555
1170.0616
1180.499
1190.115
120.603
1200.746
1210.383
1220.821
1230.123
1240.676
1250.371
1260.242
1270.0906
1280.0184
1290.245
136.65885e-6
1300.25
1310.295
1320.957
1330.356
1340.293
1350.941
1360.222
1370.295
1380.709
1390.154
140.618
1400.094
1410.245
1420.027
1430.598
1440.982
1450.0166
1460.384
1470.938
1480.409
1490.178
150.181
1500.127
1510.41
1520.0407
1530.45
1540.609
1550.72
1560.00657
1570.0785
1580.14
1590.103
1600.209
1610.42
1620.873
1630.43
1640.0164
1650.0439
1660.763
1670.911
1680.541
1690.00281
170.0256
180.686
190.0458
20.889
200.577
210.481
220.0762
230.256
240.0402
250.616
267.1553e-4
270.898
280.368
290.111
30.0915
300.713
310.948
320.524
330.147
340.489
350.512
360.321
370.0114
380.319
390.207
40.585
400.271
410.752
420.202
430.136
440.817
450.518
460.139
470.197
480.14
490.155
50.126
500.27
510.515
520.0948
530.658
540.629
550.875
560.329
570.568
580.219
590.0889
60.607
600.0128
610.145
620.108
630.0989
640.944
650.242
660.621
670.769
680.291
690.505
70.0192
700.0248
710.0138
720.364
730.0203
740.358
750.126
760.775
770.281
780.0162
790.59
80.161
800.704
810.515
820.102
830.155
840.844
850.143
860.259
870.256
880.306
890.378
90.288
900.106
910.25
920.322
930.0112
940.752
950.0598
960.292
970.886
980.82
990.36



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: CNhs12360


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)
0002613 (striatum neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000955 (brain)
0000369 (corpus striatum)
0002435 (striatum)
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)
0002420 (basal ganglion)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0007245 (nuclear complex of neuraxis)
0010317 (germ layer / neural crest derived structure)
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0001893 (telencephalon)
0001890 (forebrain)
0010011 (collection of basal ganglia)
0000204 (ventral part of telencephalon)
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)
0000209 (mouse striatal neuron 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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