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|sample_category=primary cells
|sample_cell_catalog=
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|sample_cell_line=
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Revision as of 16:23, 26 December 2012


Name:neurospheres - sympathetic neuron derived, biol_rep2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
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 numbersym2
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
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

CNhs13082

00
10.111
100
1000.05
10000
1001-0.0356
1002-0.0941
1003-0.0467
10040
10050
10060
1007-0.0275
10080
10090.0833
101-0.00347
10100
10110
10120
10130.0653
1014-0.0851
10150.145
10160.397
10170
10180
10190
1020
10200.391
10210.111
1022-0.124
10230
1024-0.14
1025-0.0611
10260
10270.44
10280
1029-0.0363
1030
10300
10310.514
10320.0262
10330.0743
10340
10350
1036-0.0419
10370
10380.0367
1039-0.162
1040
10400.319
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: CNhs13082

Jaspar motifP-value
MA0002.23.22114e-6
MA0003.10.0103
MA0004.10.971
MA0006.10.446
MA0007.10.361
MA0009.10.0625
MA0014.10.894
MA0017.13.38682e-6
MA0018.20.0341
MA0019.10.359
MA0024.10.0423
MA0025.10.265
MA0027.10.711
MA0028.10.915
MA0029.10.48
MA0030.10.342
MA0031.10.0107
MA0035.22.83557e-4
MA0038.10.263
MA0039.20.101
MA0040.10.51
MA0041.10.487
MA0042.10.42
MA0043.10.326
MA0046.12.8135e-14
MA0047.26.4813e-5
MA0048.10.725
MA0050.10.00896
MA0051.10.00442
MA0052.13.13642e-6
MA0055.10.473
MA0057.10.123
MA0058.10.594
MA0059.10.425
MA0060.10.00459
MA0061.10.0514
MA0062.20.262
MA0065.21.93051e-6
MA0066.10.239
MA0067.10.61
MA0068.10.23
MA0069.10.527
MA0070.10.0173
MA0071.10.281
MA0072.10.269
MA0073.10.887
MA0074.10.642
MA0076.10.843
MA0077.10.0768
MA0078.10.359
MA0079.20.49
MA0080.23.66839e-9
MA0081.10.392
MA0083.10.829
MA0084.10.457
MA0087.10.771
MA0088.10.844
MA0090.10.673
MA0091.10.712
MA0092.10.978
MA0093.10.889
MA0099.20.226
MA0100.10.84
MA0101.10.135
MA0102.20.568
MA0103.17.5403e-4
MA0104.20.758
MA0105.15.24016e-4
MA0106.10.0478
MA0107.10.059
MA0108.20.00835
MA0111.10.871
MA0112.24.14692e-5
MA0113.10.102
MA0114.11.39601e-5
MA0115.10.00505
MA0116.10.0024
MA0117.10.658
MA0119.10.0895
MA0122.10.756
MA0124.10.233
MA0125.10.186
MA0131.10.533
MA0135.10.144
MA0136.11.13197e-7
MA0137.20.718
MA0138.20.179
MA0139.10.0934
MA0140.15.77652e-5
MA0141.10.00195
MA0142.10.0596
MA0143.10.284
MA0144.10.354
MA0145.10.0591
MA0146.10.413
MA0147.10.522
MA0148.15.31719e-4
MA0149.10.683
MA0150.10.0656
MA0152.10.439
MA0153.11.09888e-14
MA0154.10.00326
MA0155.10.477
MA0156.14.22661e-5
MA0157.10.0116
MA0159.10.133
MA0160.10.0229
MA0162.10.316
MA0163.10.00414
MA0164.10.702
MA0258.10.00796
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: CNhs13082

Novel motifP-value
10.153
100.0757
1000.954
1010.869
1020.941
1030.202
1040.657
1050.0739
1060.0382
1070.0614
1080.997
1090.0375
110.132
1100.13
1110.0171
1120.0246
1130.503
1140.0822
1150.629
1160.487
1170.359
1180.697
1190.0371
120.663
1200.607
1210.119
1220.354
1230.469
1240.398
1250.733
1260.205
1270.219
1280.0242
1290.372
130.0134
1300.975
1310.72
1320.315
1330.517
1340.953
1350.726
1360.69
1370.319
1380.938
1390.165
140.444
1400.152
1410.275
1420.663
1430.93
1440.912
1450.333
1460.374
1470.653
1480.424
1490.118
150.0736
1500.461
1510.338
1520.113
1530.85
1540.944
1550.636
1561.2857e-11
1570.253
1580.32
1590.23
1600.106
1610.321
1620.9
1630.683
1640.0939
1650.173
1660.857
1670.395
1680.706
1690.00729
170.0854
180.864
190.194
20.554
200.775
210.363
220.288
230.289
240.0691
250.342
260.0213
270.228
280.417
290.389
30.123
300.641
310.797
320.199
330.268
340.406
350.885
360.643
370.0721
380.225
390.572
40.524
400.414
410.165
420.288
430.25
440.226
450.351
460.251
470.19
480.113
490.158
50.23
500.711
510.558
520.337
530.382
540.692
550.661
560.644
570.784
580.104
590.0313
60.58
600.0743
610.324
620.0373
630.115
640.399
650.108
660.676
670.598
680.67
690.976
70.0404
700.00599
710.111
720.203
730.224
740.97
750.15
760.83
770.185
780.0661
790.167
80.098
800.328
810.67
820.0158
830.0773
840.295
850.149
860.326
870.985
880.568
890.069
90.453
900.465
910.333
920.223
930.317
940.389
950.131
960.544
970.77
980.0988
990.299



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: CNhs13082


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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