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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 16:24, 26 December 2012


Name:neurospheres - enteric 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 numberEN2
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

CNhs13088

00
10.0216
100
1000
10000
1001-0.0749
1002-0.116
1003-0.0693
10040
1005-0.0824
10060
1007-0.144
10080
1009-0.0468
1010.0454
10100
1011-0.132
10120
1013-0.0382
1014-0.0229
10150.101
10160.289
10170
10180
10190
1020
10200.251
10210.202
1022-0.124
10230
1024-0.164
10250
10260
10270.476
10280
1029-0.115
103-0.0532
10300
10310.322
10320.112
10330.143
10340
10350
10360.129
10370
1038-0.0109
1039-0.13
1040
10400.26
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: CNhs13088

Jaspar motifP-value
MA0002.26.33801e-4
MA0003.10.0133
MA0004.10.731
MA0006.10.421
MA0007.10.497
MA0009.10.0337
MA0014.10.699
MA0017.16.96045e-6
MA0018.20.00458
MA0019.10.218
MA0024.10.00185
MA0025.10.508
MA0027.10.207
MA0028.10.315
MA0029.10.0627
MA0030.10.13
MA0031.10.0163
MA0035.29.2183e-4
MA0038.10.00527
MA0039.20.138
MA0040.10.971
MA0041.10.407
MA0042.10.857
MA0043.10.253
MA0046.15.23907e-16
MA0047.21.39905e-4
MA0048.10.801
MA0050.10.00193
MA0051.10.0093
MA0052.10.00581
MA0055.10.878
MA0057.10.0532
MA0058.10.385
MA0059.10.719
MA0060.19.26713e-8
MA0061.10.0525
MA0062.20.82
MA0065.21.68393e-6
MA0066.10.189
MA0067.10.573
MA0068.10.073
MA0069.10.367
MA0070.10.316
MA0071.10.541
MA0072.10.605
MA0073.10.866
MA0074.10.76
MA0076.10.244
MA0077.10.026
MA0078.10.155
MA0079.20.802
MA0080.21.36667e-8
MA0081.10.539
MA0083.10.95
MA0084.10.91
MA0087.10.824
MA0088.10.736
MA0090.10.77
MA0091.10.63
MA0092.10.953
MA0093.10.678
MA0099.20.141
MA0100.10.537
MA0101.10.254
MA0102.20.776
MA0103.17.03716e-4
MA0104.20.7
MA0105.19.87127e-4
MA0106.10.148
MA0107.10.105
MA0108.20.14
MA0111.10.751
MA0112.21.59787e-5
MA0113.10.084
MA0114.13.12686e-5
MA0115.10.013
MA0116.16.74547e-4
MA0117.10.817
MA0119.10.0617
MA0122.10.988
MA0124.10.913
MA0125.10.376
MA0131.10.461
MA0135.10.234
MA0136.12.61218e-5
MA0137.20.564
MA0138.20.178
MA0139.10.106
MA0140.16.79003e-5
MA0141.10.0129
MA0142.10.019
MA0143.10.0565
MA0144.10.352
MA0145.10.0444
MA0146.10.44
MA0147.10.945
MA0148.10.00255
MA0149.10.509
MA0150.10.141
MA0152.10.521
MA0153.11.04044e-13
MA0154.10.00358
MA0155.10.354
MA0156.10.00466
MA0157.10.05
MA0159.10.263
MA0160.10.104
MA0162.10.38
MA0163.10.00939
MA0164.10.932
MA0258.10.00976
MA0259.10.796



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: CNhs13088

Novel motifP-value
10.142
100.109
1000.728
1010.972
1020.794
1030.136
1040.851
1050.0655
1060.0167
1070.114
1080.824
1090.0573
110.131
1100.206
1110.0298
1120.0297
1130.424
1140.0534
1150.642
1160.685
1170.35
1180.353
1190.0223
120.676
1200.643
1210.323
1220.315
1230.53
1240.549
1250.941
1260.247
1270.124
1280.0501
1290.13
130.0371
1300.542
1310.292
1320.289
1330.549
1340.895
1350.824
1360.999
1370.295
1380.747
1390.122
140.37
1403.30797e-4
1410.502
1420.712
1430.573
1440.81
1450.533
1460.692
1470.888
1480.455
1490.169
150.141
1500.495
1510.325
1520.0857
1530.64
1540.886
1550.974
1563.82151e-9
1570.599
1580.251
1590.0451
1600.127
1610.275
1620.981
1630.806
1640.212
1650.363
1660.759
1670.472
1680.688
1690.00654
170.0457
180.718
190.138
20.457
200.796
210.483
220.236
230.161
240.181
250.432
260.0303
270.37
280.318
290.694
30.0996
300.459
310.626
320.0499
330.578
340.337
350.791
360.933
370.0545
380.255
390.253
40.682
400.53
410.79
420.313
430.176
440.248
450.3
460.218
470.208
480.121
490.137
50.249
500.526
510.437
520.364
530.324
540.428
550.781
560.584
570.697
580.0819
590.0234
60.864
600.0942
610.205
620.0408
630.076
640.463
650.112
660.487
670.577
680.304
690.497
70.0993
700.00192
710.181
720.358
730.203
740.989
750.175
760.84
770.172
780.0645
790.147
80.157
800.504
810.607
820.0165
830.369
840.343
850.0783
860.256
870.267
880.607
890.0317
90.373
900.604
910.231
920.194
930.611
940.573
950.19
960.645
970.634
980.133
990.29



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: CNhs13088


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)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0002410 (autonomic nervous system)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0010313 (neural crest-derived structure)
0001062 (anatomical entity)
0000480 (anatomical group)
0010317 (germ layer / neural crest derived structure)
0000010 (peripheral nervous system)
0002005 (enteric 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)
0011142 (mouse neurospheres - enteric 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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