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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008725
|DRA_sample_Accession=CAGE@SAMD00004921
|accession_numbers=CAGE;DRX008835;DRR009707;DRZ001132;DRZ002517
|accession_numbers=CAGE;DRX008835;DRR009707;DRZ001132;DRZ002517
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002240,UBERON:0004121,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0000489,UBERON:0005174,UBERON:0001948,UBERON:0002020,UBERON:0010317,UBERON:0001017,UBERON:0002256,UBERON:0001016,UBERON:0001137,UBERON:0002315
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002240,UBERON:0004121,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0000489,UBERON:0005174,UBERON:0001948,UBERON:0002020,UBERON:0010317,UBERON:0001017,UBERON:0002256,UBERON:0001016,UBERON:0001137,UBERON:0002315

Revision as of 20:22, 31 July 2014


Name:Mouse Neurons - dorsal spinal cord, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12635
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuespinal cord
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 numberRNADOR2
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004921
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12635 CAGE DRX008835 DRR009707
Accession ID Mm9

Library idBAMCTSS
CNhs12635 DRZ001132 DRZ002517
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

CNhs12635

00
10.554
100
1000.0887
10000
1001-0.0749
10020.0151
10030.0575
10040
10050
10060.667
1007-0.223
10080
1009-0.151
101-0.281
10100
10110.319
10120
10130.136
1014-0.0851
10150.214
10160.216
10170
10180
10190
1020
10200.452
10210.109
1022-0.0554
10230
10240
10250.048
10260
10270.269
10280
1029-0.176
1030
10300
1031-0.222
10320.508
1033-0.0665
10340
10350
1036-0.173
10370
10380.0327
10390.112
1040
1040-0.293
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: CNhs12635

Jaspar motifP-value
MA0002.20.00516
MA0003.10.548
MA0004.10.484
MA0006.10.223
MA0007.10.218
MA0009.10.829
MA0014.10.548
MA0017.15.10269e-6
MA0018.20.0543
MA0019.10.841
MA0024.10.511
MA0025.10.818
MA0027.10.262
MA0028.10.0371
MA0029.10.767
MA0030.10.575
MA0031.10.0823
MA0035.20.0795
MA0038.10.429
MA0039.20.148
MA0040.10.804
MA0041.10.172
MA0042.10.44
MA0043.10.589
MA0046.11.16136e-5
MA0047.28.60336e-4
MA0048.10.0797
MA0050.13.63345e-7
MA0051.13.17976e-5
MA0052.10.543
MA0055.10.0539
MA0057.10.431
MA0058.10.519
MA0059.10.21
MA0060.10.0715
MA0061.10.0526
MA0062.21.60251e-4
MA0065.26.16213e-5
MA0066.10.0465
MA0067.10.898
MA0068.10.882
MA0069.10.0609
MA0070.10.111
MA0071.10.196
MA0072.10.201
MA0073.10.878
MA0074.10.221
MA0076.10.0888
MA0077.10.0815
MA0078.10.866
MA0079.20.138
MA0080.22.23842e-9
MA0081.10.276
MA0083.10.0673
MA0084.10.396
MA0087.10.385
MA0088.10.122
MA0090.10.085
MA0091.10.259
MA0092.10.203
MA0093.10.531
MA0099.20.00684
MA0100.10.14
MA0101.10.0246
MA0102.20.427
MA0103.10.198
MA0104.20.926
MA0105.10.0138
MA0106.10.0615
MA0107.10.0488
MA0108.20.697
MA0111.10.996
MA0112.24.27394e-4
MA0113.10.235
MA0114.11.98411e-5
MA0115.12.03282e-4
MA0116.10.0788
MA0117.10.586
MA0119.10.192
MA0122.10.688
MA0124.10.7
MA0125.10.285
MA0131.10.534
MA0135.10.0794
MA0136.11.40206e-11
MA0137.20.00956
MA0138.20.00888
MA0139.10.519
MA0140.12.44548e-4
MA0141.10.0859
MA0142.10.593
MA0143.10.789
MA0144.10.0155
MA0145.10.101
MA0146.10.0402
MA0147.10.808
MA0148.18.97309e-5
MA0149.10.169
MA0150.10.0288
MA0152.10.024
MA0153.12.87169e-6
MA0154.10.0359
MA0155.10.943
MA0156.14.68132e-9
MA0157.10.065
MA0159.10.00489
MA0160.10.0572
MA0162.10.328
MA0163.10.00177
MA0164.10.904
MA0258.10.0244
MA0259.10.889



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: CNhs12635

Novel motifP-value
10.145
100.0292
1000.451
1010.832
1020.967
1030.0756
1040.649
1050.552
1060.0849
1070.153
1080.366
1090.0162
110.111
1100.0338
1110.0495
1120.00179
1130.771
1140.187
1150.51
1160.886
1170.00257
1180.262
1190.093
120.947
1200.842
1210.339
1220.849
1230.00842
1240.121
1250.514
1260.0732
1270.166
1280.0781
1290.221
131.89587e-6
1300.266
1310.544
1320.485
1330.763
1340.172
1350.268
1360.459
1370.384
1380.857
1390.252
140.977
1400.058
1410.357
1420.0835
1430.555
1440.974
1450.00142
1460.504
1470.517
1480.734
1490.709
150.0826
1500.123
1510.705
1520.148
1530.351
1540.527
1550.999
1560.00829
1570.255
1580.0326
1590.0814
1600.229
1610.172
1620.825
1630.293
1640.0115
1650.122
1660.691
1670.521
1680.5
1690.00177
170.0687
180.914
190.15
20.522
200.0426
210.446
220.184
230.576
240.104
250.661
262.42206e-8
270.43
280.527
290.0238
30.0571
300.688
310.756
320.972
330.0753
340.74
350.987
360.25
370.0286
380.466
390.402
40.671
400.501
410.57
420.138
430.106
440.93
450.876
460.02
470.241
480.198
490.107
50.0879
500.375
510.644
520.552
530.706
540.797
550.969
560.559
570.481
580.21
590.259
60.813
600.0481
610.0649
620.104
630.204
640.845
650.381
660.981
670.777
680.935
690.9
70.0105
700.0797
710.00439
720.535
730.0412
740.542
750.0439
760.374
770.58
780.00967
790.353
80.108
800.599
810.795
820.212
830.454
840.793
850.198
860.114
870.929
880.202
890.457
90.518
900.0405
910.337
920.422
930.0314
940.429
950.0922
960.179
970.918
980.722
990.684



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: CNhs12635


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)
0002611 (neuron of the dorsal spinal cord)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002240 (spinal cord)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0000489 (cavitated compound organ)
0005174 (dorsal region element)
0001948 (regional part of spinal cord)
0002020 (gray matter)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0002256 (dorsal horn of spinal cord)
0001016 (nervous system)
0001137 (dorsum)
0002315 (gray matter of spinal cord)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000206 (mouse neuron of the dorsal spinal cord 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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