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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008731
|DRA_sample_Accession=CAGE@SAMD00004769
|accession_numbers=CAGE;DRX008841;DRR009713;DRZ001138;DRZ002523
|accession_numbers=CAGE;DRX008841;DRR009713;DRZ001138;DRZ002523
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0004121,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0004684,UBERON:0001016,UBERON:0002275
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0004121,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0004684,UBERON:0001016,UBERON:0002275

Revision as of 20:22, 31 July 2014


Name:Mouse Neurons - raphe, donor2
Species:Mouse (Mus musculus)
Library ID:CNhs12636
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueraphe nuclei
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 numberRNARAP3
catalog numbercustom
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004769
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12636 CAGE DRX008841 DRR009713
Accession ID Mm9

Library idBAMCTSS
CNhs12636 DRZ001138 DRZ002523
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

CNhs12636

00
10.777
100
1000
10000
10010.097
10020.00416
1003-0.0108
10040
1005-0.00803
10060.624
1007-0.116
10080
1009-0.0912
101-0.141
10100
10110.443
10120.141
10130.284
1014-0.0408
1015-0.0519
1016-0.016
10170
10180
10190
1020
10200.518
10210.0522
10220.0169
10230
10240
10250
10260
10270.356
10280
1029-0.0488
103-0.0788
10300
1031-0.413
10320.459
1033-0.0665
10340
10350
1036-0.24
10370
1038-0.0615
10390.117
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: CNhs12636

Jaspar motifP-value
MA0002.29.96019e-4
MA0003.10.302
MA0004.10.504
MA0006.10.19
MA0007.10.267
MA0009.10.763
MA0014.10.8
MA0017.14.48578e-6
MA0018.20.0118
MA0019.10.528
MA0024.10.0824
MA0025.10.00112
MA0027.10.109
MA0028.10.0838
MA0029.10.874
MA0030.10.912
MA0031.10.198
MA0035.20.0284
MA0038.10.898
MA0039.20.0286
MA0040.10.568
MA0041.10.177
MA0042.10.32
MA0043.10.0543
MA0046.12.67482e-8
MA0047.20.00107
MA0048.10.0531
MA0050.13.45223e-6
MA0051.13.84505e-4
MA0052.10.967
MA0055.10.0155
MA0057.10.355
MA0058.10.501
MA0059.10.187
MA0060.10.859
MA0061.10.025
MA0062.20.00192
MA0065.25.4068e-6
MA0066.10.101
MA0067.10.355
MA0068.10.212
MA0069.10.0458
MA0070.10.573
MA0071.10.219
MA0072.10.841
MA0073.10.943
MA0074.10.133
MA0076.10.218
MA0077.10.255
MA0078.10.932
MA0079.20.324
MA0080.22.37523e-10
MA0081.10.28
MA0083.10.00516
MA0084.10.658
MA0087.10.112
MA0088.10.28
MA0090.10.0807
MA0091.10.188
MA0092.10.14
MA0093.10.551
MA0099.20.00451
MA0100.10.205
MA0101.10.0115
MA0102.20.581
MA0103.10.236
MA0104.20.886
MA0105.10.00408
MA0106.10.062
MA0107.10.0297
MA0108.27.39012e-4
MA0111.10.926
MA0112.28.18438e-4
MA0113.10.378
MA0114.11.41811e-5
MA0115.18.97439e-5
MA0116.10.0637
MA0117.10.906
MA0119.10.104
MA0122.10.752
MA0124.10.663
MA0125.10.0447
MA0131.10.701
MA0135.10.48
MA0136.15.91469e-12
MA0137.20.115
MA0138.21.87678e-4
MA0139.10.45
MA0140.11.58507e-4
MA0141.10.0195
MA0142.10.447
MA0143.10.814
MA0144.10.0735
MA0145.10.116
MA0146.10.0371
MA0147.10.73
MA0148.13.98357e-4
MA0149.10.185
MA0150.10.166
MA0152.10.0565
MA0153.11.09703e-9
MA0154.10.0422
MA0155.10.417
MA0156.11.17721e-8
MA0157.10.142
MA0159.10.00869
MA0160.10.043
MA0162.10.233
MA0163.17.60967e-4
MA0164.10.848
MA0258.10.0208
MA0259.10.855



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: CNhs12636

Novel motifP-value
10.211
100.0448
1000.278
1010.94
1020.921
1030.0818
1040.927
1050.575
1060.0564
1070.145
1080.493
1090.00718
110.109
1100.0495
1110.275
1120.00911
1130.647
1140.482
1150.974
1160.379
1170.00421
1180.471
1190.169
120.835
1200.762
1210.416
1220.832
1232.68192e-4
1240.181
1250.186
1260.0575
1270.517
1280.0562
1290.197
133.01135e-7
1300.128
1310.297
1320.682
1330.949
1340.0818
1350.296
1360.225
1370.664
1380.657
1390.26
140.874
1400.227
1410.818
1420.813
1430.349
1440.603
1452.74394e-4
1460.253
1470.254
1480.992
1490.774
150.205
1500.0736
1510.777
1520.137
1530.432
1540.754
1550.41
1560.00385
1570.155
1580.147
1590.567
1600.237
1610.223
1620.666
1630.947
1640.0442
1650.198
1660.44
1670.681
1680.523
1690.0028
170.0638
180.807
190.103
20.678
200.0355
210.215
220.148
230.661
240.0579
250.723
266.88064e-8
270.38
280.754
290.0485
30.0709
300.808
310.718
320.572
330.0956
340.752
350.716
360.109
370.036
380.426
390.389
40.235
400.0827
410.568
420.149
430.117
440.944
450.673
460.0532
470.378
480.296
490.14
50.165
500.256
510.715
520.3
530.574
540.958
550.976
560.478
570.526
580.247
590.179
60.9
600.0395
610.041
620.169
630.156
640.711
650.366
660.697
670.668
680.8
690.435
70.0122
700.0828
710.00338
720.508
730.0521
740.969
750.0517
760.392
770.514
780.00337
790.0636
80.0649
800.718
810.795
820.291
830.142
840.843
850.191
860.135
870.462
880.684
890.617
90.382
900.0983
910.126
920.349
930.0471
940.654
950.0623
960.218
970.743
980.637
990.474



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: CNhs12636


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)
0002610 (raphe nuclei neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0004121 (ectoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0004684 (raphe nuclei)
0001016 (nervous system)
0002275 (reticular formation)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000203 (mouse neuron samples)
0000205 (mouse raphe nuclei 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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