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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@DRS008758
|DRA_sample_Accession=CAGE@SAMD00005758
|accession_numbers=CAGE;DRX008868;DRR009740;DRZ001165;DRZ002550
|accession_numbers=CAGE;DRX008868;DRR009740;DRZ001165;DRZ002550
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000013,UBERON:0004121,UBERON:0011216,UBERON:0002410,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0000010,UBERON:0001016
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000013,UBERON:0004121,UBERON:0011216,UBERON:0002410,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0010317,UBERON:0000010,UBERON:0001016

Revision as of 20:37, 31 July 2014


Name:neurospheres - sympathetic neuron derived, biol_rep1
Species:Mouse (Mus musculus)
Library ID:CNhs13081
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companyNA
collaborationHideki Enomoto (RIKEN CDB)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numbersym1
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005758
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13081 CAGE DRX008868 DRR009740
Accession ID Mm9

Library idBAMCTSS
CNhs13081 DRZ001165 DRZ002550
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

CNhs13081

00
10
100
1000
10000
1001-0.0262
1002-0.0708
1003-0.0671
10040
1005-0.0389
1006-0.143
1007-0.00185
10080
10090.2
101-0.0182
10100
1011-0.108
10120
10130.0497
1014-0.0851
10150.248
10160.271
10170
10180
10190
1020
10200.258
10210.0989
1022-0.196
10230
1024-0.14
1025-0.0611
10260
10270.536
10280
10290.0747
103-0.0317
10300
10310.449
10320.074
10330.148
10340
10350
10360.162
10370
10380.0602
1039-0.181
1040
10400.137
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: CNhs13081

Jaspar motifP-value
MA0002.27.62982e-6
MA0003.10.00575
MA0004.10.616
MA0006.10.376
MA0007.10.55
MA0009.10.0988
MA0014.10.916
MA0017.19.75597e-5
MA0018.20.00783
MA0019.10.543
MA0024.14.75145e-4
MA0025.10.328
MA0027.10.346
MA0028.10.617
MA0029.10.199
MA0030.10.664
MA0031.10.199
MA0035.26.07397e-4
MA0038.10.0825
MA0039.20.118
MA0040.10.514
MA0041.10.415
MA0042.10.83
MA0043.10.204
MA0046.11.26522e-12
MA0047.20.00365
MA0048.10.773
MA0050.10.00783
MA0051.10.00694
MA0052.11.76075e-4
MA0055.10.982
MA0057.10.135
MA0058.10.27
MA0059.10.565
MA0060.12.03227e-6
MA0061.10.0757
MA0062.20.842
MA0065.25.04823e-6
MA0066.10.22
MA0067.10.783
MA0068.10.166
MA0069.10.651
MA0070.10.0436
MA0071.10.226
MA0072.10.168
MA0073.10.959
MA0074.10.684
MA0076.10.367
MA0077.10.0335
MA0078.10.202
MA0079.20.582
MA0080.27.48407e-9
MA0081.10.641
MA0083.10.636
MA0084.10.704
MA0087.10.743
MA0088.10.73
MA0090.10.479
MA0091.10.33
MA0092.10.993
MA0093.10.532
MA0099.20.406
MA0100.10.451
MA0101.10.321
MA0102.20.724
MA0103.14.26651e-4
MA0104.20.973
MA0105.13.93693e-4
MA0106.10.0617
MA0107.10.158
MA0108.20.0142
MA0111.10.928
MA0112.21.3078e-5
MA0113.10.19
MA0114.16.60723e-5
MA0115.10.0103
MA0116.10.00121
MA0117.10.805
MA0119.10.13
MA0122.10.539
MA0124.10.616
MA0125.10.152
MA0131.10.599
MA0135.10.0695
MA0136.11.58515e-5
MA0137.20.717
MA0138.20.0491
MA0139.10.058
MA0140.12.43632e-5
MA0141.10.00413
MA0142.10.199
MA0143.10.157
MA0144.10.299
MA0145.10.0281
MA0146.10.461
MA0147.10.642
MA0148.10.0142
MA0149.10.506
MA0150.10.18
MA0152.10.534
MA0153.18.10987e-12
MA0154.10.00556
MA0155.10.437
MA0156.10.00472
MA0157.10.0868
MA0159.10.307
MA0160.10.0834
MA0162.10.298
MA0163.10.0083
MA0164.10.782
MA0258.10.01
MA0259.10.823



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: CNhs13081

Novel motifP-value
10.117
100.114
1000.986
1010.853
1020.956
1030.137
1040.977
1050.0687
1060.0247
1070.0485
1080.973
1090.0515
110.142
1100.212
1110.00828
1120.0362
1130.372
1140.0256
1150.338
1160.537
1170.627
1180.464
1190.046
120.484
1200.951
1210.241
1220.371
1230.451
1240.722
1250.68
1260.373
1270.189
1280.0274
1290.167
130.0525
1300.498
1310.795
1320.351
1330.979
1340.945
1350.773
1360.954
1370.419
1380.703
1390.0786
140.371
1400.0134
1410.108
1420.893
1430.996
1440.999
1450.511
1460.606
1470.82
1480.645
1490.19
150.106
1500.381
1510.297
1520.18
1530.986
1540.922
1550.885
1566.70479e-8
1570.351
1580.522
1590.11
1600.0967
1610.293
1620.627
1630.817
1640.172
1650.254
1660.826
1670.483
1680.812
1690.0187
170.0984
180.972
190.258
20.527
200.795
210.28
220.278
230.234
240.22
250.398
260.0686
270.291
280.355
290.776
30.134
300.529
310.817
320.0804
330.423
340.293
350.968
360.611
370.0927
380.212
390.399
40.667
400.515
410.669
420.33
430.224
440.165
450.299
460.244
470.237
480.138
490.131
50.21
500.629
510.518
520.285
530.309
540.584
550.97
560.66
570.826
580.0794
590.0608
60.68
600.0803
610.438
620.0408
630.112
640.457
650.149
660.538
670.916
680.525
690.998
70.0787
700.00414
710.25
720.284
730.35
740.967
750.227
760.786
770.226
780.108
790.349
80.14
800.546
810.545
820.026
830.241
840.472
850.129
860.424
870.44
880.865
890.013
90.481
900.942
910.354
920.166
930.336
940.519
950.217
960.327
970.465
980.11
990.311



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: CNhs13081


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)
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0000107 (autonomic neuron)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000013 (sympathetic nervous system)
0004121 (ectoderm-derived structure)
0011216 (organ system subdivision)
0002410 (autonomic nervous system)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0000010 (peripheral nervous system)
0001016 (nervous system)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000350 (experimentally modified sample)
0011144 (mouse neurospheres - sympathetic neuron derived 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:0000031 (neuroblast)
CL:0000221 (ectodermal cell)

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