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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005045
|DRA_sample_Accession=CAGE@SAMD00005045
|accession_numbers=CAGE;DRX008845;DRR009717;DRZ001142;DRZ002527
|accession_numbers=CAGE;DRX008845;DRR009717;DRZ001142;DRZ002527;DRZ012492;DRZ013877
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0000369,UBERON:0002435,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002420,UBERON:0002616,UBERON:0002780,UBERON:0002020,UBERON:0007245,UBERON:0010317,UBERON:0010009,UBERON:0001017,UBERON:0001016,UBERON:0001893,UBERON:0001890,UBERON:0010011,UBERON:0000204,UBERON:0000454
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000955,UBERON:0000369,UBERON:0002435,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002420,UBERON:0002616,UBERON:0002780,UBERON:0002020,UBERON:0007245,UBERON:0010317,UBERON:0010009,UBERON:0001017,UBERON:0001016,UBERON:0001893,UBERON:0001890,UBERON:0010011,UBERON:0000204,UBERON:0000454
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000117,CL:0000393,CL:0000211,CL:0000404,CL:0000255,CL:0002613
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000117,CL:0000393,CL:0000211,CL:0000404,CL:0000255,CL:0002613

Revision as of 20:58, 10 August 2017


Name:Mouse Neurons - striatal, donor3
Species:Mouse (Mus musculus)
Library ID:CNhs12111
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  SAMD00005045
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12111 CAGE DRX008845 DRR009717
Accession ID Mm9

Library idBAMCTSS
CNhs12111 DRZ001142 DRZ002527
Accession ID Mm10

Library idBAMCTSS
CNhs12111 DRZ012492 DRZ013877
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

CNhs12111

00
10.398
100
1000.409
1000-0.0355
1001-0.0445
1002-0.00676
1003-0.0711
10040
1005-0.0459
10060.34
1007-0.177
10080
1009-0.19
101-0.155
10100
10110.152
10120
1013-0.0888
10140
10150.421
10160.164
10170
10180
10190
1020
10200.489
10210
1022-0.124
10230
1024-0.152
10250
10260
10270.319
10280
1029-0.115
103-0.0829
10300
1031-0.393
1032-0.0325
10330
10340
10350
1036-0.115
10370
10380.0553
1039-0.323
1040
1040-0.254
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: CNhs12111

Jaspar motifP-value
MA0002.20.0037
MA0003.10.172
MA0004.10.645
MA0006.10.0787
MA0007.10.152
MA0009.10.977
MA0014.10.407
MA0017.13.31809e-5
MA0018.20.0193
MA0019.10.325
MA0024.10.921
MA0025.10.213
MA0027.10.537
MA0028.10.528
MA0029.10.811
MA0030.10.264
MA0031.10.0315
MA0035.20.0801
MA0038.10.293
MA0039.20.00892
MA0040.10.471
MA0041.10.375
MA0042.10.84
MA0043.10.132
MA0046.16.08913e-9
MA0047.25.49351e-4
MA0048.10.469
MA0050.11.83841e-10
MA0051.11.86929e-5
MA0052.10.0149
MA0055.10.34
MA0057.10.102
MA0058.10.578
MA0059.10.458
MA0060.10.00366
MA0061.10.0491
MA0062.20.0977
MA0065.22.65608e-5
MA0066.10.233
MA0067.10.785
MA0068.10.924
MA0069.10.127
MA0070.10.944
MA0071.10.175
MA0072.10.126
MA0073.10.738
MA0074.10.323
MA0076.10.91
MA0077.10.0128
MA0078.10.0511
MA0079.20.925
MA0080.22.44692e-10
MA0081.10.285
MA0083.10.00325
MA0084.10.8
MA0087.10.263
MA0088.10.249
MA0090.10.00837
MA0091.10.171
MA0092.10.185
MA0093.10.643
MA0099.29.15911e-5
MA0100.10.965
MA0101.10.0285
MA0102.20.958
MA0103.10.126
MA0104.20.572
MA0105.10.0698
MA0106.10.126
MA0107.10.0313
MA0108.20.0856
MA0111.10.902
MA0112.21.52331e-4
MA0113.10.245
MA0114.17.73243e-5
MA0115.10.0168
MA0116.10.087
MA0117.10.774
MA0119.10.04
MA0122.10.506
MA0124.10.945
MA0125.10.0821
MA0131.10.889
MA0135.10.219
MA0136.12.3536e-8
MA0137.20.00421
MA0138.20.289
MA0139.10.27
MA0140.10.00353
MA0141.10.00534
MA0142.10.0168
MA0143.10.00625
MA0144.10.0101
MA0145.10.0374
MA0146.10.0399
MA0147.10.63
MA0148.12.10993e-6
MA0149.10.0759
MA0150.10.04
MA0152.10.107
MA0153.11.66945e-8
MA0154.10.0174
MA0155.10.765
MA0156.12.29417e-6
MA0157.10.0354
MA0159.10.00503
MA0160.10.0483
MA0162.10.308
MA0163.10.00814
MA0164.10.94
MA0258.10.0138
MA0259.10.512



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: CNhs12111

Novel motifP-value
10.166
100.132
1000.708
1010.899
1020.728
1030.0713
1040.829
1050.188
1060.00624
1070.0326
1080.476
1090.00171
110.0877
1100.0973
1110.153
1120.0136
1130.952
1140.275
1150.995
1160.436
1170.0554
1180.531
1190.0993
120.604
1200.904
1210.286
1220.885
1230.0999
1240.959
1250.452
1260.133
1270.129
1280.038
1290.224
131.45978e-6
1300.254
1310.695
1320.97
1330.283
1340.478
1350.72
1360.0537
1370.199
1380.74
1390.163
140.63
1400.192
1410.252
1420.0635
1430.528
1440.902
1450.0216
1460.353
1470.708
1480.421
1490.16
150.252
1500.126
1510.412
1520.0381
1530.527
1540.712
1550.51
1560.00393
1570.0673
1580.211
1590.218
1600.281
1610.249
1620.807
1630.251
1640.0224
1650.0445
1660.972
1670.805
1680.763
1690.00462
170.0228
180.586
190.0501
20.842
200.492
210.558
220.0849
230.28
240.0353
250.705
263.20157e-4
270.796
280.317
290.156
30.0806
300.584
310.921
320.373
330.174
340.415
350.386
360.495
370.00882
380.303
390.132
40.529
400.188
410.845
420.238
430.142
440.737
450.427
460.16
470.209
480.114
490.17
50.17
500.219
510.55
520.0882
530.676
540.642
550.915
560.366
570.724
580.266
590.0688
60.527
600.0112
610.164
620.155
630.0821
640.902
650.259
660.843
670.903
680.626
690.517
70.0189
700.0145
710.0179
720.335
730.0208
740.581
750.148
760.699
770.265
780.0148
790.591
80.204
800.817
810.543
820.117
830.0586
840.97
850.0625
860.272
870.072
880.285
890.246
90.35
900.155
910.32
920.345
930.0119
940.944
950.0229
960.32
970.8
980.793
990.237



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: CNhs12111


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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